From yuetian926 at 163.com  Mon Sep  1 02:32:05 2014
From: yuetian926 at 163.com (Yuetian Liu)
Date: Mon, 1 Sep 2014 14:32:05 +0800 (CST)
Subject: [ITK-users] How to fusion the MR volume to the CT volume
Message-ID: <1cad6eb0.8e53.1482fe9d05d.Coremail.yuetian926@163.com>



Hi itkusers,


Recently I want to fuse the MR volume to the CT volume, but I search the itk mailist. 
I haven;t known how to realise it. And there isn't example in the InsightSoftwareGuide-4.5.0.pdf
and InsightSphinxExamplesPDF-4.5.0.pdf. 
So I want to ask how to fuse the MR volume to the CT volume by itk.


Thank you for helping me! 


Best 
Yuetian


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From matt.mccormick at kitware.com  Mon Sep  1 15:09:38 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 1 Sep 2014 15:09:38 -0400
Subject: [ITK-users] How to fusion the MR volume to the CT volume
In-Reply-To: <1cad6eb0.8e53.1482fe9d05d.Coremail.yuetian926@163.com>
References: <1cad6eb0.8e53.1482fe9d05d.Coremail.yuetian926@163.com>
Message-ID: <CALzTN-QUVzNgj7rMKbQ7-HNmHmPiePVBfah5ZX=O7heA4H1yew@mail.gmail.com>

Hi Yeutian,

Try a registration algorithm using a mutual information based metric.
See also the Slicer Registration Case Library [1], which uses ITK
under the hood, for examples.

HTH,
Matt

[1] http://www.na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:UseCaseInventory

On Mon, Sep 1, 2014 at 2:32 AM, Yuetian Liu <yuetian926 at 163.com> wrote:
>
> Hi itkusers,
>
> Recently I want to fuse the MR volume to the CT volume, but I search the itk
> mailist.
> I haven;t known how to realise it. And there isn't example in the
> InsightSoftwareGuide-4.5.0.pdf
> and InsightSphinxExamplesPDF-4.5.0.pdf.
> So I want to ask how to fuse the MR volume to the CT volume by itk.
>
> Thank you for helping me!
>
> Best
> Yuetian
>
>
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>

From matt.mccormick at kitware.com  Tue Sep  2 11:52:03 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 2 Sep 2014 11:52:03 -0400
Subject: [ITK-users] ResampleDICOM example and DCMTK
In-Reply-To: <CALzTN-TBe7P43_vCantDDGXXNT_H9oLhaZ6EXT6Fmfe5qWVuRQ@mail.gmail.com>
References: <95FBA78F-1DFC-4F33-9572-DA0DD9DE1E73@gmail.com>
 <1409515613801-7586158.post@n2.nabble.com>
 <CALzTN-TBe7P43_vCantDDGXXNT_H9oLhaZ6EXT6Fmfe5qWVuRQ@mail.gmail.com>
Message-ID: <CALzTN-RHz0=MnvJDGHoRpDTwnRXR-uGp7qNfm67NLrjLKtpxQQ@mail.gmail.com>

Hi Nick,

The DCMTKImageIO class does not yet populate and extract tag
information to / from the an Image's MetaDataDictionary.  This will
have to be implemented for this to work.

HTH,
Matt

On Sun, Aug 31, 2014 at 5:38 PM, Matt McCormick
<matt.mccormick at kitware.com> wrote:
> Hi Nick,
>
> Nothing stands out from inspecting the code.  Could you please send an
> example dataset?
>
> Thanks,
> Matt
>
> On Sun, Aug 31, 2014 at 4:06 PM, NPatterson <pattersonnp.work at gmail.com> wrote:
>> Hi, I wondered if anyone could test the code attached in the thread header
>> "ResampleDICOM example and DCMTK" regarding the use of DCMTK for DICOM
>> reading writing in ITK. I adapted the ResampleDICOM example to work with
>> DCMTK instead of GDCM, and although I get no errors, I also do not get any
>> output dicom images. If someone has the time to test this code to see if
>> they observe the same behaviour/or can suggest a fix, I would be very
>> appreciative.
>>
>> Regards, Nick.
>>
>>
>>
>> --
>> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/ITK-users-ResampleDICOM-example-and-DCMTK-tp7586131p7586158.html
>> Sent from the ITK Insight Users mailing list archive at Nabble.com.
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users

From pattersonnp.work at gmail.com  Wed Sep  3 11:10:02 2014
From: pattersonnp.work at gmail.com (Nick Patterson)
Date: Wed, 3 Sep 2014 16:10:02 +0100
Subject: [ITK-users] ResampleDICOM and Assertion failed: (slope ==
	(int)slope)
Message-ID: <5D3EF85B-30FA-4432-B735-5D56FEB5CA3F@gmail.com>

Hi,

  This is a problem that I have had before and have reported it as a ticket on the GDCM Git page. I have written some code which is heavily dependent on being able to read in a series of DICOM images, in this case they are of PET/NM modality. 

When a series of images are provided, which have "non-integer" rescale slope, the following error is returned at the final stage when SeriesWriter->Update() is invoked. 

Assertion failed: (slope == (int)slope), function InverseRescaleFunction, file /opt/SOURCE/GDCM/2.5/Source/MediaStorageAndFileFormat/gdcmRescaler.cxx, line 67.
Abort trap: 6


I cannot provide my own code here, as it may make the problem less clear. However, the problem is directly recreated using the ResampleDICOM.cxx example from the ITK examples page. If a series of PT/NM images are run through the code the above problem occurs. This is particularly problematic since NM/PT modality images do often have non-integer rescale slopes and currently I am not able to deal with images of this modality.

There are 2 things to note:-
1) I have reported this error with GDCM developer and this problem appeared to have been resolved. I have previously been resampling NM/PT DICOM images using the ResampleDICOM.cxx example in the past without issue. If I recall correctly, ITK 4.5.2 worked with the latest GDCM release. 

2) CT images (where the slope/intercepts are integer) work fine. 


I shall re-log this on the GDCM pages, but since I am unsure that something didn?t change in latest versions of ITK I wanted to report it here too.

I would be much obliged if anyone would be able to test the ResampleDICOM.cxx example with DICOM images which have a rescale slope which is not-integer - and see if the problem can be recreated.

I am currently using:- ITK 4.7 (from git) and pulled the latest GDCM from Git Repo yesterday.


Regards, Nick.


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From pattersonnp.work at gmail.com  Wed Sep  3 11:51:14 2014
From: pattersonnp.work at gmail.com (Nick Patterson)
Date: Wed, 3 Sep 2014 16:51:14 +0100
Subject: [ITK-users] [ITK] ResampleDICOM and Assertion failed: (slope ==
	(int)slope)
In-Reply-To: <F7A87F9A-6E01-4E06-92E6-19FCF9FD1810@gmail.com>
References: <5D3EF85B-30FA-4432-B735-5D56FEB5CA3F@gmail.com>
 <CALzTN-TaAOP=NPS2ST4Bi6dRhPABNREpLOvXMAokC0nnGXXviQ@mail.gmail.com>
 <F7A87F9A-6E01-4E06-92E6-19FCF9FD1810@gmail.com>
Message-ID: <B6131E1B-A98B-455D-9CF1-5D55853BBB9F@gmail.com>

Confirmed? a roll back to ITK 4.5.2 gets rid of this problem for the time being. It seems to reappear in any version after 4.6.

Nick.


>> Hi Nick,
>> 
>> This issue may be coming up now because a bug was fixed before ITK 4.6
>> which makes sure the rescale slope is applied when using GDCMImageIO
>> for writing [1].
>> 
>> HTH,
>> Matt
>> 
>> 
>> [1] http://itk.org/gitweb?p=ITK.git;a=commit;h=847ec2b79ac2cedaab6714678c0677793aa23a1e
>> 
>> On Wed, Sep 3, 2014 at 11:10 AM, Nick Patterson
>> <pattersonnp.work at gmail.com> wrote:
>>> Hi,
>>> 
>>> This is a problem that I have had before and have reported it as a ticket
>>> on the GDCM Git page. I have written some code which is heavily dependent on
>>> being able to read in a series of DICOM images, in this case they are of
>>> PET/NM modality.
>>> 
>>> When a series of images are provided, which have "non-integer" rescale
>>> slope, the following error is returned at the final stage when
>>> SeriesWriter->Update() is invoked.
>>> 
>>> Assertion failed: (slope == (int)slope), function InverseRescaleFunction,
>>> file /opt/SOURCE/GDCM/2.5/Source/MediaStorageAndFileFormat/gdcmRescaler.cxx,
>>> line 67.
>>> Abort trap: 6
>>> 
>>> 
>>> I cannot provide my own code here, as it may make the problem less clear.
>>> However, the problem is directly recreated using the ResampleDICOM.cxx
>>> example from the ITK examples page. If a series of PT/NM images are run
>>> through the code the above problem occurs. This is particularly problematic
>>> since NM/PT modality images do often have non-integer rescale slopes and
>>> currently I am not able to deal with images of this modality.
>>> 
>>> There are 2 things to note:-
>>> 1) I have reported this error with GDCM developer and this problem appeared
>>> to have been resolved. I have previously been resampling NM/PT DICOM images
>>> using the ResampleDICOM.cxx example in the past without issue. If I recall
>>> correctly, ITK 4.5.2 worked with the latest GDCM release.
>>> 
>>> 2) CT images (where the slope/intercepts are integer) work fine.
>>> 
>>> 
>>> I shall re-log this on the GDCM pages, but since I am unsure that something
>>> didn?t change in latest versions of ITK I wanted to report it here too.
>>> 
>>> I would be much obliged if anyone would be able to test the
>>> ResampleDICOM.cxx example with DICOM images which have a rescale slope which
>>> is not-integer - and see if the problem can be recreated.
>>> 
>>> I am currently using:- ITK 4.7 (from git) and pulled the latest GDCM from
>>> Git Repo yesterday.
>>> 
>>> 
>>> Regards, Nick.
>>> 
>>> 
>>> 
>>> _____________________________________
>>> Powered by www.kitware.com
>>> 
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>> 
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>> 
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>> 
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>> 
>>> _______________________________________________
>>> Community mailing list
>>> Community at itk.org
>>> http://public.kitware.com/mailman/listinfo/community
>>> 
> 


From matt.mccormick at kitware.com  Wed Sep  3 12:30:25 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 3 Sep 2014 12:30:25 -0400
Subject: [ITK-users] [ITK] ResampleDICOM and Assertion failed: (slope ==
	(int)slope)
In-Reply-To: <B6131E1B-A98B-455D-9CF1-5D55853BBB9F@gmail.com>
References: <5D3EF85B-30FA-4432-B735-5D56FEB5CA3F@gmail.com>
 <CALzTN-TaAOP=NPS2ST4Bi6dRhPABNREpLOvXMAokC0nnGXXviQ@mail.gmail.com>
 <F7A87F9A-6E01-4E06-92E6-19FCF9FD1810@gmail.com>
 <B6131E1B-A98B-455D-9CF1-5D55853BBB9F@gmail.com>
Message-ID: <CALzTN-TwZF=D13e0A44MUuH=_pN=3+QbuPzXtd_q9yXphO62WQ@mail.gmail.com>

Hi Nick,

A reasonable way move forward;

1) A patch could be made to ITK's internal GDCM to support non-integer slope's.
2) This patch could then be submitted to upstream GDCM.

Thanks,
Matt

On Wed, Sep 3, 2014 at 11:51 AM, Nick Patterson
<pattersonnp.work at gmail.com> wrote:
> Confirmed? a roll back to ITK 4.5.2 gets rid of this problem for the time being. It seems to reappear in any version after 4.6.
>
> Nick.
>
>
>>> Hi Nick,
>>>
>>> This issue may be coming up now because a bug was fixed before ITK 4.6
>>> which makes sure the rescale slope is applied when using GDCMImageIO
>>> for writing [1].
>>>
>>> HTH,
>>> Matt
>>>
>>>
>>> [1] http://itk.org/gitweb?p=ITK.git;a=commit;h=847ec2b79ac2cedaab6714678c0677793aa23a1e
>>>
>>> On Wed, Sep 3, 2014 at 11:10 AM, Nick Patterson
>>> <pattersonnp.work at gmail.com> wrote:
>>>> Hi,
>>>>
>>>> This is a problem that I have had before and have reported it as a ticket
>>>> on the GDCM Git page. I have written some code which is heavily dependent on
>>>> being able to read in a series of DICOM images, in this case they are of
>>>> PET/NM modality.
>>>>
>>>> When a series of images are provided, which have "non-integer" rescale
>>>> slope, the following error is returned at the final stage when
>>>> SeriesWriter->Update() is invoked.
>>>>
>>>> Assertion failed: (slope == (int)slope), function InverseRescaleFunction,
>>>> file /opt/SOURCE/GDCM/2.5/Source/MediaStorageAndFileFormat/gdcmRescaler.cxx,
>>>> line 67.
>>>> Abort trap: 6
>>>>
>>>>
>>>> I cannot provide my own code here, as it may make the problem less clear.
>>>> However, the problem is directly recreated using the ResampleDICOM.cxx
>>>> example from the ITK examples page. If a series of PT/NM images are run
>>>> through the code the above problem occurs. This is particularly problematic
>>>> since NM/PT modality images do often have non-integer rescale slopes and
>>>> currently I am not able to deal with images of this modality.
>>>>
>>>> There are 2 things to note:-
>>>> 1) I have reported this error with GDCM developer and this problem appeared
>>>> to have been resolved. I have previously been resampling NM/PT DICOM images
>>>> using the ResampleDICOM.cxx example in the past without issue. If I recall
>>>> correctly, ITK 4.5.2 worked with the latest GDCM release.
>>>>
>>>> 2) CT images (where the slope/intercepts are integer) work fine.
>>>>
>>>>
>>>> I shall re-log this on the GDCM pages, but since I am unsure that something
>>>> didn?t change in latest versions of ITK I wanted to report it here too.
>>>>
>>>> I would be much obliged if anyone would be able to test the
>>>> ResampleDICOM.cxx example with DICOM images which have a rescale slope which
>>>> is not-integer - and see if the problem can be recreated.
>>>>
>>>> I am currently using:- ITK 4.7 (from git) and pulled the latest GDCM from
>>>> Git Repo yesterday.
>>>>
>>>>
>>>> Regards, Nick.
>>>>
>>>>
>>>>
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>
>>>> _______________________________________________
>>>> Community mailing list
>>>> Community at itk.org
>>>> http://public.kitware.com/mailman/listinfo/community
>>>>
>>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

From hans-johnson at uiowa.edu  Wed Sep  3 13:58:53 2014
From: hans-johnson at uiowa.edu (Johnson, Hans J)
Date: Wed, 3 Sep 2014 17:58:53 +0000
Subject: [ITK-users] [ITK] ResampleDICOM and Assertion failed: (slope ==
 (int)slope)
In-Reply-To: <CALzTN-TwZF=D13e0A44MUuH=_pN=3+QbuPzXtd_q9yXphO62WQ@mail.gmail.com>
References: <5D3EF85B-30FA-4432-B735-5D56FEB5CA3F@gmail.com>
 <CALzTN-TaAOP=NPS2ST4Bi6dRhPABNREpLOvXMAokC0nnGXXviQ@mail.gmail.com>
 <F7A87F9A-6E01-4E06-92E6-19FCF9FD1810@gmail.com>
 <B6131E1B-A98B-455D-9CF1-5D55853BBB9F@gmail.com>
 <CALzTN-TwZF=D13e0A44MUuH=_pN=3+QbuPzXtd_q9yXphO62WQ@mail.gmail.com>
Message-ID: <D02CC00B.1BEC1%hans-johnson@uiowa.edu>

Matt,

Can you comment on the efforts to update GDCM to a newer version?  The
version of GDCM in ITK is very much out of date.

Hans


-----Original Message-----
From: Matt McCormick <matt.mccormick at kitware.com>
Date: Wednesday, September 3, 2014 at 11:30 AM
To: Nick Patterson <pattersonnp.work at gmail.com>
Cc: "insight-users at itk.org" <insight-users at itk.org>
Subject: Re: [ITK-users] [ITK] ResampleDICOM and Assertion failed: (slope
==      (int)slope)

Hi Nick,

A reasonable way move forward;

1) A patch could be made to ITK's internal GDCM to support non-integer
slope's.
2) This patch could then be submitted to upstream GDCM.

Thanks,
Matt

On Wed, Sep 3, 2014 at 11:51 AM, Nick Patterson
<pattersonnp.work at gmail.com> wrote:
> Confirmed? a roll back to ITK 4.5.2 gets rid of this problem for the
>time being. It seems to reappear in any version after 4.6.
>
> Nick.
>
>
>>> Hi Nick,
>>>
>>> This issue may be coming up now because a bug was fixed before ITK 4.6
>>> which makes sure the rescale slope is applied when using GDCMImageIO
>>> for writing [1].
>>>
>>> HTH,
>>> Matt
>>>
>>>
>>> [1]
>>>http://itk.org/gitweb?p=ITK.git;a=commit;h=847ec2b79ac2cedaab6714678c067
>>>7793aa23a1e
>>>
>>> On Wed, Sep 3, 2014 at 11:10 AM, Nick Patterson
>>> <pattersonnp.work at gmail.com> wrote:
>>>> Hi,
>>>>
>>>> This is a problem that I have had before and have reported it as a
>>>>ticket
>>>> on the GDCM Git page. I have written some code which is heavily
>>>>dependent on
>>>> being able to read in a series of DICOM images, in this case they are
>>>>of
>>>> PET/NM modality.
>>>>
>>>> When a series of images are provided, which have "non-integer" rescale
>>>> slope, the following error is returned at the final stage when
>>>> SeriesWriter->Update() is invoked.
>>>>
>>>> Assertion failed: (slope == (int)slope), function
>>>>InverseRescaleFunction,
>>>> file
>>>>/opt/SOURCE/GDCM/2.5/Source/MediaStorageAndFileFormat/gdcmRescaler.cxx,
>>>> line 67.
>>>> Abort trap: 6
>>>>
>>>>
>>>> I cannot provide my own code here, as it may make the problem less
>>>>clear.
>>>> However, the problem is directly recreated using the ResampleDICOM.cxx
>>>> example from the ITK examples page. If a series of PT/NM images are
>>>>run
>>>> through the code the above problem occurs. This is particularly
>>>>problematic
>>>> since NM/PT modality images do often have non-integer rescale slopes
>>>>and
>>>> currently I am not able to deal with images of this modality.
>>>>
>>>> There are 2 things to note:-
>>>> 1) I have reported this error with GDCM developer and this problem
>>>>appeared
>>>> to have been resolved. I have previously been resampling NM/PT DICOM
>>>>images
>>>> using the ResampleDICOM.cxx example in the past without issue. If I
>>>>recall
>>>> correctly, ITK 4.5.2 worked with the latest GDCM release.
>>>>
>>>> 2) CT images (where the slope/intercepts are integer) work fine.
>>>>
>>>>
>>>> I shall re-log this on the GDCM pages, but since I am unsure that
>>>>something
>>>> didn?t change in latest versions of ITK I wanted to report it here
>>>>too.
>>>>
>>>> I would be much obliged if anyone would be able to test the
>>>> ResampleDICOM.cxx example with DICOM images which have a rescale
>>>>slope which
>>>> is not-integer - and see if the problem can be recreated.
>>>>
>>>> I am currently using:- ITK 4.7 (from git) and pulled the latest GDCM
>>>>from
>>>> Git Repo yesterday.
>>>>
>>>>
>>>> Regards, Nick.
>>>>
>>>>
>>>>
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>
>>>> _______________________________________________
>>>> Community mailing list
>>>> Community at itk.org
>>>> http://public.kitware.com/mailman/listinfo/community
>>>>
>>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
_____________________________________
Powered by www.kitware.com

Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html

Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php

Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/insight-users



________________________________
Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged.  If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited.  Please reply to the sender that you have received the message in error, then delete it.  Thank you.
________________________________

From matt.mccormick at kitware.com  Wed Sep  3 14:28:19 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 3 Sep 2014 14:28:19 -0400
Subject: [ITK-users] [ITK] ResampleDICOM and Assertion failed: (slope ==
	(int)slope)
In-Reply-To: <D02CC00B.1BEC1%hans-johnson@uiowa.edu>
References: <5D3EF85B-30FA-4432-B735-5D56FEB5CA3F@gmail.com>
 <CALzTN-TaAOP=NPS2ST4Bi6dRhPABNREpLOvXMAokC0nnGXXviQ@mail.gmail.com>
 <F7A87F9A-6E01-4E06-92E6-19FCF9FD1810@gmail.com>
 <B6131E1B-A98B-455D-9CF1-5D55853BBB9F@gmail.com>
 <CALzTN-TwZF=D13e0A44MUuH=_pN=3+QbuPzXtd_q9yXphO62WQ@mail.gmail.com>
 <D02CC00B.1BEC1%hans-johnson@uiowa.edu>
Message-ID: <CALzTN-Q3cuBbcndaV7Y72maKgYu6ATcbQmzg6cb_nxMit1KyMQ@mail.gmail.com>

Hi Hans,

Brian did work on it, but those efforts stalled.

I will not have resources to put on it until sometime after the 4.7 release.

Thanks,
Matt

On Wed, Sep 3, 2014 at 1:58 PM, Johnson, Hans J <hans-johnson at uiowa.edu> wrote:
> Matt,
>
> Can you comment on the efforts to update GDCM to a newer version?  The
> version of GDCM in ITK is very much out of date.
>
> Hans
>
>
> -----Original Message-----
> From: Matt McCormick <matt.mccormick at kitware.com>
> Date: Wednesday, September 3, 2014 at 11:30 AM
> To: Nick Patterson <pattersonnp.work at gmail.com>
> Cc: "insight-users at itk.org" <insight-users at itk.org>
> Subject: Re: [ITK-users] [ITK] ResampleDICOM and Assertion failed: (slope
> ==      (int)slope)
>
> Hi Nick,
>
> A reasonable way move forward;
>
> 1) A patch could be made to ITK's internal GDCM to support non-integer
> slope's.
> 2) This patch could then be submitted to upstream GDCM.
>
> Thanks,
> Matt
>
> On Wed, Sep 3, 2014 at 11:51 AM, Nick Patterson
> <pattersonnp.work at gmail.com> wrote:
>> Confirmed? a roll back to ITK 4.5.2 gets rid of this problem for the
>>time being. It seems to reappear in any version after 4.6.
>>
>> Nick.
>>
>>
>>>> Hi Nick,
>>>>
>>>> This issue may be coming up now because a bug was fixed before ITK 4.6
>>>> which makes sure the rescale slope is applied when using GDCMImageIO
>>>> for writing [1].
>>>>
>>>> HTH,
>>>> Matt
>>>>
>>>>
>>>> [1]
>>>>http://itk.org/gitweb?p=ITK.git;a=commit;h=847ec2b79ac2cedaab6714678c067
>>>>7793aa23a1e
>>>>
>>>> On Wed, Sep 3, 2014 at 11:10 AM, Nick Patterson
>>>> <pattersonnp.work at gmail.com> wrote:
>>>>> Hi,
>>>>>
>>>>> This is a problem that I have had before and have reported it as a
>>>>>ticket
>>>>> on the GDCM Git page. I have written some code which is heavily
>>>>>dependent on
>>>>> being able to read in a series of DICOM images, in this case they are
>>>>>of
>>>>> PET/NM modality.
>>>>>
>>>>> When a series of images are provided, which have "non-integer" rescale
>>>>> slope, the following error is returned at the final stage when
>>>>> SeriesWriter->Update() is invoked.
>>>>>
>>>>> Assertion failed: (slope == (int)slope), function
>>>>>InverseRescaleFunction,
>>>>> file
>>>>>/opt/SOURCE/GDCM/2.5/Source/MediaStorageAndFileFormat/gdcmRescaler.cxx,
>>>>> line 67.
>>>>> Abort trap: 6
>>>>>
>>>>>
>>>>> I cannot provide my own code here, as it may make the problem less
>>>>>clear.
>>>>> However, the problem is directly recreated using the ResampleDICOM.cxx
>>>>> example from the ITK examples page. If a series of PT/NM images are
>>>>>run
>>>>> through the code the above problem occurs. This is particularly
>>>>>problematic
>>>>> since NM/PT modality images do often have non-integer rescale slopes
>>>>>and
>>>>> currently I am not able to deal with images of this modality.
>>>>>
>>>>> There are 2 things to note:-
>>>>> 1) I have reported this error with GDCM developer and this problem
>>>>>appeared
>>>>> to have been resolved. I have previously been resampling NM/PT DICOM
>>>>>images
>>>>> using the ResampleDICOM.cxx example in the past without issue. If I
>>>>>recall
>>>>> correctly, ITK 4.5.2 worked with the latest GDCM release.
>>>>>
>>>>> 2) CT images (where the slope/intercepts are integer) work fine.
>>>>>
>>>>>
>>>>> I shall re-log this on the GDCM pages, but since I am unsure that
>>>>>something
>>>>> didn?t change in latest versions of ITK I wanted to report it here
>>>>>too.
>>>>>
>>>>> I would be much obliged if anyone would be able to test the
>>>>> ResampleDICOM.cxx example with DICOM images which have a rescale
>>>>>slope which
>>>>> is not-integer - and see if the problem can be recreated.
>>>>>
>>>>> I am currently using:- ITK 4.7 (from git) and pulled the latest GDCM
>>>>>from
>>>>> Git Repo yesterday.
>>>>>
>>>>>
>>>>> Regards, Nick.
>>>>>
>>>>>
>>>>>
>>>>> _____________________________________
>>>>> Powered by www.kitware.com
>>>>>
>>>>> Visit other Kitware open-source projects at
>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>
>>>>> Kitware offers ITK Training Courses, for more information visit:
>>>>> http://www.kitware.com/products/protraining.php
>>>>>
>>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>>
>>>>> Follow this link to subscribe/unsubscribe:
>>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>>
>>>>> _______________________________________________
>>>>> Community mailing list
>>>>> Community at itk.org
>>>>> http://public.kitware.com/mailman/listinfo/community
>>>>>
>>>
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
>
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> Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged.  If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited.  Please reply to the sender that you have received the message in error, then delete it.  Thank you.
> ________________________________

From arman.eshaghi at gmail.com  Thu Sep  4 03:39:52 2014
From: arman.eshaghi at gmail.com (Arman Eshaghi)
Date: Thu, 4 Sep 2014 12:09:52 +0430
Subject: [ITK-users] Update on integration with R
Message-ID: <CAKy1A=FDA0+tA3ecZ-26hu_YNU-tERJUdZZZRWewENEcvuH4Cw@mail.gmail.com>

Hi,

I'm wondering whether this proposal below from 2009 had any progresses
regarding the integration of R statistics with ITK?

http://www.itk.org/Wiki/Proposals:Integration_with_R_Language#R_Interface_Examples_with_other_languages

Thanks
Arman
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From matt.mccormick at kitware.com  Thu Sep  4 08:44:21 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 4 Sep 2014 08:44:21 -0400
Subject: [ITK-users] Update on integration with R
In-Reply-To: <CAKy1A=FDA0+tA3ecZ-26hu_YNU-tERJUdZZZRWewENEcvuH4Cw@mail.gmail.com>
References: <CAKy1A=FDA0+tA3ecZ-26hu_YNU-tERJUdZZZRWewENEcvuH4Cw@mail.gmail.com>
Message-ID: <CALzTN-R49=S-L2r7f1Fb=Z0--gkV1zcUZRmu_OSHUNGyENzMAg@mail.gmail.com>

Hi Arman,

Since WrapITK uses SWIG, generating an R interface should be possible,
but I do not know anyone who has tried it recently.

SimpleITK uses SWIG and the R interface is enabled [1].

HTH,
Matt

[1] http://www.itk.org/Wiki/SimpleITK/GettingStarted#R_installation

On Thu, Sep 4, 2014 at 3:39 AM, Arman Eshaghi <arman.eshaghi at gmail.com> wrote:
> Hi,
>
> I'm wondering whether this proposal below from 2009 had any progresses
> regarding the integration of R statistics with ITK?
>
> http://www.itk.org/Wiki/Proposals:Integration_with_R_Language#R_Interface_Examples_with_other_languages
>
> Thanks
> Arman
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>

From blowekamp at mail.nih.gov  Thu Sep  4 08:58:40 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Thu, 4 Sep 2014 08:58:40 -0400
Subject: [ITK-users] Update on integration with R
In-Reply-To: <CALzTN-R49=S-L2r7f1Fb=Z0--gkV1zcUZRmu_OSHUNGyENzMAg@mail.gmail.com>
References: <CAKy1A=FDA0+tA3ecZ-26hu_YNU-tERJUdZZZRWewENEcvuH4Cw@mail.gmail.com>
 <CALzTN-R49=S-L2r7f1Fb=Z0--gkV1zcUZRmu_OSHUNGyENzMAg@mail.gmail.com>
Message-ID: <EA21F944-E4D9-45CE-9AAB-F88171E8D580@mail.nih.gov>

Hello,

What are you looking to do with R and ITK?

The SimpleITK 0.8.0 release works well with R and the SWIG 2.0.11 version and is tested on linux and OSX. There are some issue with building R on windows that have not been addressed. Please let us know if you have further questions about getting this built.

Good luck,
Brad

On Sep 4, 2014, at 8:44 AM, Matt McCormick <matt.mccormick at kitware.com> wrote:

> Hi Arman,
> 
> Since WrapITK uses SWIG, generating an R interface should be possible,
> but I do not know anyone who has tried it recently.
> 
> SimpleITK uses SWIG and the R interface is enabled [1].
> 
> HTH,
> Matt
> 
> [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted#R_installation
> 
> On Thu, Sep 4, 2014 at 3:39 AM, Arman Eshaghi <arman.eshaghi at gmail.com> wrote:
>> Hi,
>> 
>> I'm wondering whether this proposal below from 2009 had any progresses
>> regarding the integration of R statistics with ITK?
>> 
>> http://www.itk.org/Wiki/Proposals:Integration_with_R_Language#R_Interface_Examples_with_other_languages
>> 
>> Thanks
>> Arman
>> 
>> _____________________________________
>> Powered by www.kitware.com
>> 
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>> 
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>> 
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>> 
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>> 
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users


From arman.eshaghi at gmail.com  Thu Sep  4 09:09:57 2014
From: arman.eshaghi at gmail.com (Arman Eshaghi)
Date: Thu, 4 Sep 2014 17:39:57 +0430
Subject: [ITK-users] Update on integration with R
In-Reply-To: <EA21F944-E4D9-45CE-9AAB-F88171E8D580@mail.nih.gov>
References: <CAKy1A=FDA0+tA3ecZ-26hu_YNU-tERJUdZZZRWewENEcvuH4Cw@mail.gmail.com>
 <CALzTN-R49=S-L2r7f1Fb=Z0--gkV1zcUZRmu_OSHUNGyENzMAg@mail.gmail.com>
 <EA21F944-E4D9-45CE-9AAB-F88171E8D580@mail.nih.gov>
Message-ID: <CAKy1A=H2GP3fadvGSV0sX1W+N5g5RNfZNLy_E1X82Vjfh2GRfw@mail.gmail.com>

Thanks Brad and Matt, just wanted to read and write files with ITK in R.
SITK works fine on Linux.

All the best,
Arman

ps Just found another package (Rcpp) that may be useful for this as well


On Thu, Sep 4, 2014 at 5:28 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:

> Hello,
>
> What are you looking to do with R and ITK?
>
> The SimpleITK 0.8.0 release works well with R and the SWIG 2.0.11 version
> and is tested on linux and OSX. There are some issue with building R on
> windows that have not been addressed. Please let us know if you have
> further questions about getting this built.
>
> Good luck,
> Brad
>
> On Sep 4, 2014, at 8:44 AM, Matt McCormick <matt.mccormick at kitware.com>
> wrote:
>
> > Hi Arman,
> >
> > Since WrapITK uses SWIG, generating an R interface should be possible,
> > but I do not know anyone who has tried it recently.
> >
> > SimpleITK uses SWIG and the R interface is enabled [1].
> >
> > HTH,
> > Matt
> >
> > [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted#R_installation
> >
> > On Thu, Sep 4, 2014 at 3:39 AM, Arman Eshaghi <arman.eshaghi at gmail.com>
> wrote:
> >> Hi,
> >>
> >> I'm wondering whether this proposal below from 2009 had any progresses
> >> regarding the integration of R statistics with ITK?
> >>
> >>
> http://www.itk.org/Wiki/Proposals:Integration_with_R_Language#R_Interface_Examples_with_other_languages
> >>
> >> Thanks
> >> Arman
> >>
> >> _____________________________________
> >> Powered by www.kitware.com
> >>
> >> Visit other Kitware open-source projects at
> >> http://www.kitware.com/opensource/opensource.html
> >>
> >> Kitware offers ITK Training Courses, for more information visit:
> >> http://www.kitware.com/products/protraining.php
> >>
> >> Please keep messages on-topic and check the ITK FAQ at:
> >> http://www.itk.org/Wiki/ITK_FAQ
> >>
> >> Follow this link to subscribe/unsubscribe:
> >> http://public.kitware.com/mailman/listinfo/insight-users
> >>
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.php
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/insight-users
>
>
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From stnava at gmail.com  Thu Sep  4 09:33:44 2014
From: stnava at gmail.com (brian avants)
Date: Thu, 4 Sep 2014 09:33:44 -0400
Subject: [ITK-users] Update on integration with R
In-Reply-To: <CAKy1A=H2GP3fadvGSV0sX1W+N5g5RNfZNLy_E1X82Vjfh2GRfw@mail.gmail.com>
References: <CAKy1A=FDA0+tA3ecZ-26hu_YNU-tERJUdZZZRWewENEcvuH4Cw@mail.gmail.com>
 <CALzTN-R49=S-L2r7f1Fb=Z0--gkV1zcUZRmu_OSHUNGyENzMAg@mail.gmail.com>
 <EA21F944-E4D9-45CE-9AAB-F88171E8D580@mail.nih.gov>
 <CAKy1A=H2GP3fadvGSV0sX1W+N5g5RNfZNLy_E1X82Vjfh2GRfw@mail.gmail.com>
Message-ID: <CABWzF4WWTvSK=F9wN29jKffeTYW-H2SOzkfDzykSQhf-JpygAg@mail.gmail.com>

you can also do ( in R )

install.packages("devtools")
library(devtools)
install_github("stnava/ANTsR")
library(ANTsR)
img<-antsImageRead("image.nii.gz",3)
antsImageWrite(img,'temp.nii.gz')

it's itk underneath


brian




On Thu, Sep 4, 2014 at 9:09 AM, Arman Eshaghi <arman.eshaghi at gmail.com>
wrote:

> Thanks Brad and Matt, just wanted to read and write files with ITK in R.
> SITK works fine on Linux.
>
> All the best,
> Arman
>
> ps Just found another package (Rcpp) that may be useful for this as well
>
>
> On Thu, Sep 4, 2014 at 5:28 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
> wrote:
>
>> Hello,
>>
>> What are you looking to do with R and ITK?
>>
>> The SimpleITK 0.8.0 release works well with R and the SWIG 2.0.11 version
>> and is tested on linux and OSX. There are some issue with building R on
>> windows that have not been addressed. Please let us know if you have
>> further questions about getting this built.
>>
>> Good luck,
>> Brad
>>
>> On Sep 4, 2014, at 8:44 AM, Matt McCormick <matt.mccormick at kitware.com>
>> wrote:
>>
>> > Hi Arman,
>> >
>> > Since WrapITK uses SWIG, generating an R interface should be possible,
>> > but I do not know anyone who has tried it recently.
>> >
>> > SimpleITK uses SWIG and the R interface is enabled [1].
>> >
>> > HTH,
>> > Matt
>> >
>> > [1] http://www.itk.org/Wiki/SimpleITK/GettingStarted#R_installation
>> >
>> > On Thu, Sep 4, 2014 at 3:39 AM, Arman Eshaghi <arman.eshaghi at gmail.com>
>> wrote:
>> >> Hi,
>> >>
>> >> I'm wondering whether this proposal below from 2009 had any progresses
>> >> regarding the integration of R statistics with ITK?
>> >>
>> >>
>> http://www.itk.org/Wiki/Proposals:Integration_with_R_Language#R_Interface_Examples_with_other_languages
>> >>
>> >> Thanks
>> >> Arman
>> >>
>> >> _____________________________________
>> >> Powered by www.kitware.com
>> >>
>> >> Visit other Kitware open-source projects at
>> >> http://www.kitware.com/opensource/opensource.html
>> >>
>> >> Kitware offers ITK Training Courses, for more information visit:
>> >> http://www.kitware.com/products/protraining.php
>> >>
>> >> Please keep messages on-topic and check the ITK FAQ at:
>> >> http://www.itk.org/Wiki/ITK_FAQ
>> >>
>> >> Follow this link to subscribe/unsubscribe:
>> >> http://public.kitware.com/mailman/listinfo/insight-users
>> >>
>> > _____________________________________
>> > Powered by www.kitware.com
>> >
>> > Visit other Kitware open-source projects at
>> > http://www.kitware.com/opensource/opensource.html
>> >
>> > Kitware offers ITK Training Courses, for more information visit:
>> > http://www.kitware.com/products/protraining.php
>> >
>> > Please keep messages on-topic and check the ITK FAQ at:
>> > http://www.itk.org/Wiki/ITK_FAQ
>> >
>> > Follow this link to subscribe/unsubscribe:
>> > http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
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From matt.mccormick at kitware.com  Thu Sep  4 11:50:13 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 4 Sep 2014 11:50:13 -0400
Subject: [ITK-users] Opportunity to share, discuss, design,
 and learn with other ITK community members
Message-ID: <CALzTN-QZdjwJeQ=tsxxjTo9+45AEHdR3kVDW-326JkwHEq8gTQ@mail.gmail.com>

There is an opportunity to share, discuss, design, and learn with your
fellow ITK community members.


On Friday, 11 AM Eastern USA time, join us as we discuss ITK
development.  We will use the Hangout link for the Event.

  https://plus.google.com/events/c4np6cgd8oosd5je818d9r1n3j8


For those that cannot join via Hangout, telephone call-in is also
possible.  Dial:

  +1-585-632-6296

Enter pin:

  31423?


All are welcome.  Hope to talk to you then!

From zeinsalah at gmail.com  Mon Sep  8 04:18:10 2014
From: zeinsalah at gmail.com (Zein Salah)
Date: Mon, 8 Sep 2014 10:18:10 +0200
Subject: [ITK-users] Background / Foreground separation
Message-ID: <CADiSopNNxH88sPbU9krFk2ci9UK4NvFERf_h9KNr2poWdi743w@mail.gmail.com>

Hello,

I want to reliably define the main object in CT/MRI image from the
background. I.e. I want to do some kind of defining the boundary (skin) of
the patient. Are there filters in ITK dedicated for this? or should I adapt
filters like the Otsu?

Thanks,
Zein

Sorry! I have not been using ITK since Release 3.20 :).
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From matt.mccormick at kitware.com  Mon Sep  8 10:52:54 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 8 Sep 2014 10:52:54 -0400
Subject: [ITK-users] Background / Foreground separation
In-Reply-To: <CADiSopNNxH88sPbU9krFk2ci9UK4NvFERf_h9KNr2poWdi743w@mail.gmail.com>
References: <CADiSopNNxH88sPbU9krFk2ci9UK4NvFERf_h9KNr2poWdi743w@mail.gmail.com>
Message-ID: <CALzTN-T+A93HgF55TuGMrzCMWmjqx3OxapaKm6zzjPMOcTcmrg@mail.gmail.com>

Hi Zein,

Welcome back! :-)

One possible sequence of filters to obtain the "skin":

OtsuThresholdImageFilter [1]
BinaryShapeKeepNObjectImageFilter (keep only the largest object) [2]
BinaryClosingByReconstructionImageFilter or BinaryFillholeImageFilter [3][4]
BinaryContourImageFilter [5]

HTH,
Matt

[1] http://www.itk.org/Doxygen/html/classitk_1_1OtsuThresholdImageFilter.html

[2] http://www.itk.org/Doxygen/html/classitk_1_1BinaryShapeKeepNObjectsImageFilter.html

[3] http://www.itk.org/Doxygen/html/classitk_1_1BinaryClosingByReconstructionImageFilter.html

[4] http://www.itk.org/Doxygen/html/classitk_1_1BinaryFillholeImageFilter.html

[5] http://www.itk.org/Doxygen/html/classitk_1_1BinaryContourImageFilter.html

On Mon, Sep 8, 2014 at 4:18 AM, Zein Salah <zeinsalah at gmail.com> wrote:
> Hello,
>
> I want to reliably define the main object in CT/MRI image from the
> background. I.e. I want to do some kind of defining the boundary (skin) of
> the patient. Are there filters in ITK dedicated for this? or should I adapt
> filters like the Otsu?
>
> Thanks,
> Zein
>
> Sorry! I have not been using ITK since Release 3.20 :).
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>

From elena.bresciani87 at gmail.com  Tue Sep  9 11:50:31 2014
From: elena.bresciani87 at gmail.com (elena bresciani)
Date: Tue, 9 Sep 2014 17:50:31 +0200
Subject: [ITK-users] Pipeline update problem (I suppose)
Message-ID: <CACxk=WzVPcO7Pb84No92toW98oYaoEjtbkCXALtKYCA-NS6-9Q@mail.gmail.com>

Hello guys,

I'm writing an ITK script using C++ functions in order to reduce the number
of operations repetition. What I need to do is: given a scan with 4 objects
I need to separate them in 4 images and, if vertically oriented, rotate
them 90 degrees in order to have them horizontal.
I already have successfully compiled the code necessary to crop ROIs and
the rotation step separately, everything works well, but when I try to
unify all in a single script I don't get the desired output. I suppose that
the problem could be in a missing Update() or something but I can't
identify it.

Attached you can find a concise version of the code; whilst
SegmentedImage1..4 are as attended OutputImage1..4 have right size but are
all filled with gray level 100. As I said before, I can't understand the
problem because the same code used alone (attachment rotation.cxx), works
well.


Any guess?
Thanks
Elena
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From dagarshali at gmail.com  Tue Sep  9 22:33:46 2014
From: dagarshali at gmail.com (dagarshali)
Date: Tue, 9 Sep 2014 19:33:46 -0700 (PDT)
Subject: [ITK-users] using simpleITK with anaconda python distribution
Message-ID: <1410316426142-7586179.post@n2.nabble.com>

I downloaded the source code for simple itk and complied it as instructed. In
the cmake configuration, I changed the python paths according to using the
python distribution of anaconda. I was able to compile it. I have attached a
snapshot of the cmake configuration
<http://itk-insight-users.2283740.n2.nabble.com/file/n7586179/Screen_Shot_2014-09-09_at_3.png>
I am not sure what to do after the compiling.. If I enter import SimpleITK
as sitk, I get a fatal python error. Can anybody please suggest how to
overcome this problem?Thanks in advance.dagarshali



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/using-simpleITK-with-anaconda-python-distribution-tp7586179.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From matt.mccormick at kitware.com  Tue Sep  9 22:41:57 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 9 Sep 2014 22:41:57 -0400
Subject: [ITK-users] using simpleITK with anaconda python distribution
In-Reply-To: <1410316426142-7586179.post@n2.nabble.com>
References: <1410316426142-7586179.post@n2.nabble.com>
Message-ID: <CALzTN-SXqLjCJjNTbMy-Z25NZ098Z+y2TSd3c5HSbE3ngODYTg@mail.gmail.com>

Hi dagarshall,

There is a SimpleITK recipe for conda [1].  To install it from a
manual build, use the same commands at the end of build.sh:

cd ${BUILD_DIR}/SimpleITK-build/Wrapping
${PYTHON} PythonPackage/setup.py install

HTH,
Matt

[1] https://github.com/conda/conda-recipes/tree/master/simpleitk

On Tue, Sep 9, 2014 at 10:33 PM, dagarshali <dagarshali at gmail.com> wrote:
> I downloaded the source code for simple itk and complied it as instructed. In
> the cmake configuration, I changed the python paths according to using the
> python distribution of anaconda. I was able to compile it. I have attached a
> snapshot of the cmake configuration
> <http://itk-insight-users.2283740.n2.nabble.com/file/n7586179/Screen_Shot_2014-09-09_at_3.png>
> I am not sure what to do after the compiling.. If I enter import SimpleITK
> as sitk, I get a fatal python error. Can anybody please suggest how to
> overcome this problem?Thanks in advance.dagarshali
>
>
>
> --
> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/using-simpleITK-with-anaconda-python-distribution-tp7586179.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

From vishwanath.somashekar at gmail.com  Tue Sep  9 22:55:20 2014
From: vishwanath.somashekar at gmail.com (Vishwa)
Date: Tue, 9 Sep 2014 21:55:20 -0500
Subject: [ITK-users] using simpleITK with anaconda python distribution
In-Reply-To: <CALzTN-SXqLjCJjNTbMy-Z25NZ098Z+y2TSd3c5HSbE3ngODYTg@mail.gmail.com>
References: <1410316426142-7586179.post@n2.nabble.com>
 <CALzTN-SXqLjCJjNTbMy-Z25NZ098Z+y2TSd3c5HSbE3ngODYTg@mail.gmail.com>
Message-ID: <CAN9DaKbrYx9+UzYdJVJnDtNv1ABSXg5OieXCNO14QsKY_TY8Yw@mail.gmail.com>

Thanks for getting back to me.. I am not sure how to use the build.sh. Am i
to create those variables mentioned in that file?

In the previous mail, I forgot to mention after I compiled, I tried what
you suggest here

cd ${BUILD_DIR}/SimpleITK-build/Wrapping
${PYTHON} PythonPackage/setup.py install

The last few lines of the output is shown below

Installed
/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.9.0.dev584-py2.7-macosx-10.5-x86_64.egg

Processing dependencies for SimpleITK==0.9.0.dev584

Finished processing dependencies for SimpleITK==0.9.0.dev584

However, when i import simple itk in python,

import SimpleITK as sitk

Fatal Python error: PyThreadState_Get: no current thread

Abort trap: 6

On Tue, Sep 9, 2014 at 9:41 PM, Matt McCormick <matt.mccormick at kitware.com>
wrote:

> Hi dagarshall,
>
> There is a SimpleITK recipe for conda [1].  To install it from a
> manual build, use the same commands at the end of build.sh:
>
> cd ${BUILD_DIR}/SimpleITK-build/Wrapping
> ${PYTHON} PythonPackage/setup.py install
>
> HTH,
> Matt
>
> [1] https://github.com/conda/conda-recipes/tree/master/simpleitk
>
> On Tue, Sep 9, 2014 at 10:33 PM, dagarshali <dagarshali at gmail.com> wrote:
> > I downloaded the source code for simple itk and complied it as
> instructed. In
> > the cmake configuration, I changed the python paths according to using
> the
> > python distribution of anaconda. I was able to compile it. I have
> attached a
> > snapshot of the cmake configuration
> > <
> http://itk-insight-users.2283740.n2.nabble.com/file/n7586179/Screen_Shot_2014-09-09_at_3.png
> >
> > I am not sure what to do after the compiling.. If I enter import
> SimpleITK
> > as sitk, I get a fatal python error. Can anybody please suggest how to
> > overcome this problem?Thanks in advance.dagarshali
> >
> >
> >
> > --
> > View this message in context:
> http://itk-insight-users.2283740.n2.nabble.com/using-simpleITK-with-anaconda-python-distribution-tp7586179.html
> > Sent from the ITK Insight Users mailing list archive at Nabble.com.
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.php
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/insight-users
>
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From 88172828 at qq.com  Wed Sep 10 07:42:59 2014
From: 88172828 at qq.com (Eping Wang)
Date: Wed, 10 Sep 2014 04:42:59 -0700 (MST)
Subject: [ITK-users]
 =?utf-8?q?itk=3A_=3AImageFileReader_to_igstk=3A_=3AIm?=
 =?utf-8?q?ageSpatialObject=E2=80=8F?=
In-Reply-To: <1403279378508-34126.post@n7.nabble.com>
References: <1403279378508-34126.post@n7.nabble.com>
Message-ID: <1410349379582-34523.post@n7.nabble.com>

Hi SeanLee,

Try this:

igstk::Friends::ImageReaderToImageSpatialObject::ConnectImage(&m_MhdImageReader,&m_ImageSpatialObject.GetPointer());

It worked in my project.



--
View this message in context: http://itk-users.7.n7.nabble.com/itk-ImageFileReader-to-igstk-ImageSpatialObject-tp34126p34523.html
Sent from the ITK - Users mailing list archive at Nabble.com.

From matt.mccormick at kitware.com  Wed Sep 10 08:22:44 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 10 Sep 2014 08:22:44 -0400
Subject: [ITK-users] using simpleITK with anaconda python distribution
In-Reply-To: <CAN9DaKbLiz0t0JzHZ7WcZXpns41ReAo5=CgA4hZBBfSSUMvp4Q@mail.gmail.com>
References: <1410316426142-7586179.post@n2.nabble.com>
 <CALzTN-SXqLjCJjNTbMy-Z25NZ098Z+y2TSd3c5HSbE3ngODYTg@mail.gmail.com>
 <CAN9DaKbrYx9+UzYdJVJnDtNv1ABSXg5OieXCNO14QsKY_TY8Yw@mail.gmail.com>
 <CALzTN-QKGkfKm-rDD4fJyOxEGbbDmVsK3+ePOVB5=csw1_strA@mail.gmail.com>
 <CAN9DaKbLiz0t0JzHZ7WcZXpns41ReAo5=CgA4hZBBfSSUMvp4Q@mail.gmail.com>
Message-ID: <CALzTN-QCF7eq3Lm4Ewo+1pyfMJc+C6vPJwrT11waNvTtudko-A@mail.gmail.com>

Hi,

I think the best route is to use their package build system so the
build environment is set up correctly.  However, the SimpleITK package
may need some tweaks.

HTH,
Matt

On Wed, Sep 10, 2014 at 2:27 AM, Vishwa <vishwanath.somashekar at gmail.com> wrote:
> I tried installing again. Get the same error. Any ideas as to why this might
> be happening? or how to even debug the issue?
>
> Vishwa
>
> On Tue, Sep 9, 2014 at 10:44 PM, Matt McCormick <matt.mccormick at kitware.com>
> wrote:
>>
>> Instructions to build the recipe are here [1], although there is
>> currently a bug in the clone url [2].
>>
>> The error you get is usually from using incompatible versions of
>> Python in the CMake configuration. Your screenshot in the first
>> message look good, but conda may be doing some  funny business.
>>
>> HTH,
>> Matt
>>
>> [1] http://conda.pydata.org/docs/build_tutorials/pkgs.html
>>
>> [2] https://github.com/conda/conda-recipes/pull/176
>>
>> On Tue, Sep 9, 2014 at 10:55 PM, Vishwa <vishwanath.somashekar at gmail.com>
>> wrote:
>> > Thanks for getting back to me.. I am not sure how to use the build.sh.
>> > Am i
>> > to create those variables mentioned in that file?
>> >
>> > In the previous mail, I forgot to mention after I compiled, I tried what
>> > you
>> > suggest here
>> >
>> > cd ${BUILD_DIR}/SimpleITK-build/Wrapping
>> > ${PYTHON} PythonPackage/setup.py install
>> >
>> > The last few lines of the output is shown below
>> >
>> > Installed
>> >
>> > /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.9.0.dev584-py2.7-macosx-10.5-x86_64.egg
>> >
>> > Processing dependencies for SimpleITK==0.9.0.dev584
>> >
>> > Finished processing dependencies for SimpleITK==0.9.0.dev584
>> >
>> > However, when i import simple itk in python,
>> >
>> > import SimpleITK as sitk
>> >
>> > Fatal Python error: PyThreadState_Get: no current thread
>> >
>> > Abort trap: 6
>> >
>> >
>> > On Tue, Sep 9, 2014 at 9:41 PM, Matt McCormick
>> > <matt.mccormick at kitware.com>
>> > wrote:
>> >>
>> >> Hi dagarshall,
>> >>
>> >> There is a SimpleITK recipe for conda [1].  To install it from a
>> >> manual build, use the same commands at the end of build.sh:
>> >>
>> >> cd ${BUILD_DIR}/SimpleITK-build/Wrapping
>> >> ${PYTHON} PythonPackage/setup.py install
>> >>
>> >> HTH,
>> >> Matt
>> >>
>> >> [1] https://github.com/conda/conda-recipes/tree/master/simpleitk
>> >>
>> >> On Tue, Sep 9, 2014 at 10:33 PM, dagarshali <dagarshali at gmail.com>
>> >> wrote:
>> >> > I downloaded the source code for simple itk and complied it as
>> >> > instructed. In
>> >> > the cmake configuration, I changed the python paths according to
>> >> > using
>> >> > the
>> >> > python distribution of anaconda. I was able to compile it. I have
>> >> > attached a
>> >> > snapshot of the cmake configuration
>> >> >
>> >> >
>> >> > <http://itk-insight-users.2283740.n2.nabble.com/file/n7586179/Screen_Shot_2014-09-09_at_3.png>
>> >> > I am not sure what to do after the compiling.. If I enter import
>> >> > SimpleITK
>> >> > as sitk, I get a fatal python error. Can anybody please suggest how
>> >> > to
>> >> > overcome this problem?Thanks in advance.dagarshali
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > View this message in context:
>> >> >
>> >> > http://itk-insight-users.2283740.n2.nabble.com/using-simpleITK-with-anaconda-python-distribution-tp7586179.html
>> >> > Sent from the ITK Insight Users mailing list archive at Nabble.com.
>> >> > _____________________________________
>> >> > Powered by www.kitware.com
>> >> >
>> >> > Visit other Kitware open-source projects at
>> >> > http://www.kitware.com/opensource/opensource.html
>> >> >
>> >> > Kitware offers ITK Training Courses, for more information visit:
>> >> > http://www.kitware.com/products/protraining.php
>> >> >
>> >> > Please keep messages on-topic and check the ITK FAQ at:
>> >> > http://www.itk.org/Wiki/ITK_FAQ
>> >> >
>> >> > Follow this link to subscribe/unsubscribe:
>> >> > http://public.kitware.com/mailman/listinfo/insight-users
>> >
>> >
>> >
>> > _____________________________________
>> > Powered by www.kitware.com
>> >
>> > Visit other Kitware open-source projects at
>> > http://www.kitware.com/opensource/opensource.html
>> >
>> > Kitware offers ITK Training Courses, for more information visit:
>> > http://www.kitware.com/products/protraining.php
>> >
>> > Please keep messages on-topic and check the ITK FAQ at:
>> > http://www.itk.org/Wiki/ITK_FAQ
>> >
>> > Follow this link to subscribe/unsubscribe:
>> > http://public.kitware.com/mailman/listinfo/insight-users
>> >
>
>

From blowekamp at mail.nih.gov  Wed Sep 10 10:13:10 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 10 Sep 2014 10:13:10 -0400
Subject: [ITK-users] using simpleITK with anaconda python distribution
In-Reply-To: <CAN9DaKbrYx9+UzYdJVJnDtNv1ABSXg5OieXCNO14QsKY_TY8Yw@mail.gmail.com>
References: <1410316426142-7586179.post@n2.nabble.com>
 <CALzTN-SXqLjCJjNTbMy-Z25NZ098Z+y2TSd3c5HSbE3ngODYTg@mail.gmail.com>
 <CAN9DaKbrYx9+UzYdJVJnDtNv1ABSXg5OieXCNO14QsKY_TY8Yw@mail.gmail.com>
Message-ID: <9F0DD3DF-F5AD-4A68-8CA0-BD1F76D548DA@mail.nih.gov>

Hello,

This error message frequently happens when SimpleITK is compiled against a different version of  Python than the runtime. This generally indicate there is something conflicting funny in your runtime environment.

I was easily able to use the build script from the conda-recipes repository. I would strongly recommend this approach when building for the anaconda enviroment as it does simplify some of there issue. Your CMake configuration does look correct.

You should look at you environment variables, such as PATH, DYLD_LIBRARY_PATH, and PYTHONPATH. Additionally look in you user install path [1]. You are looking for multiple copies of the SimpleITK module or library and or python runtime libraries which could confuse the linker.

Also you can inspect the runtime libraries:

 otool -L /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so
/Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so:
	@loader_path/../../../libpython2.7.dylib (compatibility version 2.7.0, current version 2.7.0)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 855.17.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)
	/usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 60.0.0)
	/usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 2577.0.0)

[1] https://docs.python.org/2/install/#alternate-installation-the-user-scheme

Hope this helps,
Brad

On Sep 9, 2014, at 10:55 PM, Vishwa <vishwanath.somashekar at gmail.com> wrote:

> import SimpleITK as sitk
> 
> Fatal Python error: PyThreadState_Get: no current thread
> 
> 
> Abort trap: 6
> 

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From vishwanath.somashekar at gmail.com  Wed Sep 10 11:01:23 2014
From: vishwanath.somashekar at gmail.com (Vishwa)
Date: Wed, 10 Sep 2014 10:01:23 -0500
Subject: [ITK-users] using simpleITK with anaconda python distribution
In-Reply-To: <9F0DD3DF-F5AD-4A68-8CA0-BD1F76D548DA@mail.nih.gov>
References: <1410316426142-7586179.post@n2.nabble.com>
 <CALzTN-SXqLjCJjNTbMy-Z25NZ098Z+y2TSd3c5HSbE3ngODYTg@mail.gmail.com>
 <CAN9DaKbrYx9+UzYdJVJnDtNv1ABSXg5OieXCNO14QsKY_TY8Yw@mail.gmail.com>
 <9F0DD3DF-F5AD-4A68-8CA0-BD1F76D548DA@mail.nih.gov>
Message-ID: <CAN9DaKZaXy2E=W-ATiEG8XQHBNp+U6rsQg4bZncbQOkOQMA3ww@mail.gmail.com>

Thanks very much for the information. I looked at the conda recipe. There
are three files.
One is .sh file, the second is yaml file, and the third is just a test
code. How am i to use that recipe to compile..

There are variables like Source_Dir in the .sh file. How do i get those. I
am not familiar using it.

Am I to just copy the file build.sh into the SimpleITK source code directly
and run sh ./build.sh? I tried that, and it ran for a while and gave an
error.

Best regards,
Vishwa



On Wed, Sep 10, 2014 at 9:13 AM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:

> Hello,
>
> This error message frequently happens when SimpleITK is compiled against a
> different version of  Python than the runtime. This generally indicate
> there is something conflicting funny in your runtime environment.
>
> I was easily able to use the build script from the conda-recipes
> repository. I would strongly recommend this approach when building for the
> anaconda enviroment as it does simplify some of there issue. Your CMake
> configuration does look correct.
>
> You should look at you environment variables, such as PATH,
> DYLD_LIBRARY_PATH, and PYTHONPATH. Additionally look in you user install
> path [1]. You are looking for multiple copies of the SimpleITK module or
> library and or python runtime libraries which could confuse the linker.
>
> Also you can inspect the runtime libraries:
>
>  otool -L
> /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so
>
> /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so:
> @loader_path/../../../libpython2.7.dylib (compatibility version 2.7.0,
> current version 2.7.0)
> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
> (compatibility version 150.0.0, current version 855.17.0)
> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
> 1197.1.1)
> /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version
> 60.0.0)
> /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version
> 2577.0.0)
>
> [1]
> https://docs.python.org/2/install/#alternate-installation-the-user-scheme
>
> Hope this helps,
> Brad
>
> On Sep 9, 2014, at 10:55 PM, Vishwa <vishwanath.somashekar at gmail.com>
> wrote:
>
> import SimpleITK as sitk
>
> Fatal Python error: PyThreadState_Get: no current thread
>
> Abort trap: 6
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
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From blowekamp at mail.nih.gov  Wed Sep 10 11:10:37 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 10 Sep 2014 11:10:37 -0400
Subject: [ITK-users] using simpleITK with anaconda python distribution
In-Reply-To: <CAN9DaKZaXy2E=W-ATiEG8XQHBNp+U6rsQg4bZncbQOkOQMA3ww@mail.gmail.com>
References: <1410316426142-7586179.post@n2.nabble.com>
 <CALzTN-SXqLjCJjNTbMy-Z25NZ098Z+y2TSd3c5HSbE3ngODYTg@mail.gmail.com>
 <CAN9DaKbrYx9+UzYdJVJnDtNv1ABSXg5OieXCNO14QsKY_TY8Yw@mail.gmail.com>
 <9F0DD3DF-F5AD-4A68-8CA0-BD1F76D548DA@mail.nih.gov>
 <CAN9DaKZaXy2E=W-ATiEG8XQHBNp+U6rsQg4bZncbQOkOQMA3ww@mail.gmail.com>
Message-ID: <953347C0-D04D-4620-9C9A-E8533C3C48CC@mail.nih.gov>

Hello,

You need to use the conda build environment. Look at the readme in this repo[1].

Basically you'll need to do the following:

$ conda install conda-build
$ cd src
$ git clone https://github.com/thewtex/conda-recipes.git
$ git checkout simpleitk-clone-url
$ conda build simpleitk



[1] https://github.com/conda/conda-recipes

On Sep 10, 2014, at 11:01 AM, Vishwa <vishwanath.somashekar at gmail.com> wrote:

> Thanks very much for the information. I looked at the conda recipe. There are three files. 
> One is .sh file, the second is yaml file, and the third is just a test code. How am i to use that recipe to compile..
> 
> There are variables like Source_Dir in the .sh file. How do i get those. I am not familiar using it. 
> 
> Am I to just copy the file build.sh into the SimpleITK source code directly and run sh ./build.sh? I tried that, and it ran for a while and gave an error. 
> 
> Best regards,
> Vishwa
> 
> 
> 
> On Wed, Sep 10, 2014 at 9:13 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
> Hello,
> 
> This error message frequently happens when SimpleITK is compiled against a different version of  Python than the runtime. This generally indicate there is something conflicting funny in your runtime environment.
> 
> I was easily able to use the build script from the conda-recipes repository. I would strongly recommend this approach when building for the anaconda enviroment as it does simplify some of there issue. Your CMake configuration does look correct.
> 
> You should look at you environment variables, such as PATH, DYLD_LIBRARY_PATH, and PYTHONPATH. Additionally look in you user install path [1]. You are looking for multiple copies of the SimpleITK module or library and or python runtime libraries which could confuse the linker.
> 
> Also you can inspect the runtime libraries:
> 
>  otool -L /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so
> /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so:
> 	@loader_path/../../../libpython2.7.dylib (compatibility version 2.7.0, current version 2.7.0)
> 	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 855.17.0)
> 	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)
> 	/usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 60.0.0)
> 	/usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 2577.0.0)
> 
> [1] https://docs.python.org/2/install/#alternate-installation-the-user-scheme
> 
> Hope this helps,
> Brad
> 
> On Sep 9, 2014, at 10:55 PM, Vishwa <vishwanath.somashekar at gmail.com> wrote:
> 
>> import SimpleITK as sitk
>> 
>> Fatal Python error: PyThreadState_Get: no current thread
>> 
>> 
>> Abort trap: 6
>> 
> 
> 
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
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From biradarsumangala at gmail.com  Wed Sep 10 18:06:29 2014
From: biradarsumangala at gmail.com (biradarsumangala at gmail.com)
Date: Wed, 10 Sep 2014 17:06:29 -0500
Subject: [ITK-users] biradarsumangala@gmail.com has indicated you're a
	friend. Accept?
Message-ID: <0.0.40B.1D8.1CFCD42FD330A84.277B@mail2.info-emailer.com>

Hi,

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If Yes please follow the link below:
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From gabrielgimenez85 at gmail.com  Wed Sep 10 21:55:56 2014
From: gabrielgimenez85 at gmail.com (=?UTF-8?Q?Gabriel_A=2E_Gim=C3=A9nez?=)
Date: Wed, 10 Sep 2014 18:55:56 -0700 (PDT)
Subject: [ITK-users] itkParticleSwarmOptimizer - Example
Message-ID: <1410400556611-7586188.post@n2.nabble.com>

Hello everyone, 

is there an example of using the ParticleSwarmOptimizer in ITK? 

I tried using it but it throws the following error:
*itkParticleSwarmOptimizerBase.cxx
Line: 360
Description: itk::ERROR: ParticleSwarmOptimizer(0xa2a19d8): cost function
and parameter bounds dimensions mismatch*

I found no information about the error nor the optimizer.


Thank you very much.




--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/itkParticleSwarmOptimizer-Example-tp7586188.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From vishwanath.somashekar at gmail.com  Thu Sep 11 00:43:17 2014
From: vishwanath.somashekar at gmail.com (Vishwa)
Date: Wed, 10 Sep 2014 23:43:17 -0500
Subject: [ITK-users] Fwd: using simpleITK with anaconda python distribution
In-Reply-To: <CAN9DaKbScEu4X5mo83cWo=8M5GsisqHkCVBfoZk7R5WDF=NUjw@mail.gmail.com>
References: <1410316426142-7586179.post@n2.nabble.com>
 <CALzTN-SXqLjCJjNTbMy-Z25NZ098Z+y2TSd3c5HSbE3ngODYTg@mail.gmail.com>
 <CAN9DaKbrYx9+UzYdJVJnDtNv1ABSXg5OieXCNO14QsKY_TY8Yw@mail.gmail.com>
 <9F0DD3DF-F5AD-4A68-8CA0-BD1F76D548DA@mail.nih.gov>
 <CAN9DaKZaXy2E=W-ATiEG8XQHBNp+U6rsQg4bZncbQOkOQMA3ww@mail.gmail.com>
 <953347C0-D04D-4620-9C9A-E8533C3C48CC@mail.nih.gov>
 <CAN9DaKbScEu4X5mo83cWo=8M5GsisqHkCVBfoZk7R5WDF=NUjw@mail.gmail.com>
Message-ID: <CAN9DaKa4gD4YExm18YyodopgoP2_O4HzBsyxq57HSQrQbRoz4w@mail.gmail.com>

I did install anaconda again and ran the conda build like you suggest. It
ran without and problem. However, when I import simpleitk, it gives a error
saying no module found.

Any ideas?

Vishwa

On Wed, Sep 10, 2014 at 10:10 AM, Bradley Lowekamp [via ITK Insight Users] <
ml-node+s2283740n7586186h92 at n2.nabble.com> wrote:

> Hello,
>
> You need to use the conda build environment. Look at the readme in this
> repo[1].
>
> Basically you'll need to do the following:
>
> $ conda install conda-build
> $ cd src
> $ git clone https://github.com/thewtex/conda-recipes.git
> $ git checkout simpleitk-clone-url
> $ conda build simpleitk
>
>
>
> [1] https://github.com/conda/conda-recipes
>
> On Sep 10, 2014, at 11:01 AM, Vishwa <[hidden email]
> <http://user/SendEmail.jtp?type=node&node=7586186&i=0>> wrote:
>
> Thanks very much for the information. I looked at the conda recipe. There
> are three files.
> One is .sh file, the second is yaml file, and the third is just a test
> code. How am i to use that recipe to compile..
>
> There are variables like Source_Dir in the .sh file. How do i get those. I
> am not familiar using it.
>
> Am I to just copy the file build.sh into the SimpleITK source code
> directly and run sh ./build.sh? I tried that, and it ran for a while and
> gave an error.
>
> Best regards,
> Vishwa
>
>
>
> On Wed, Sep 10, 2014 at 9:13 AM, Bradley Lowekamp <[hidden email]
> <http://user/SendEmail.jtp?type=node&node=7586186&i=1>> wrote:
>
>> Hello,
>>
>> This error message frequently happens when SimpleITK is compiled against
>> a different version of  Python than the runtime. This generally indicate
>> there is something conflicting funny in your runtime environment.
>>
>> I was easily able to use the build script from the conda-recipes
>> repository. I would strongly recommend this approach when building for the
>> anaconda enviroment as it does simplify some of there issue. Your CMake
>> configuration does look correct.
>>
>> You should look at you environment variables, such as PATH,
>> DYLD_LIBRARY_PATH, and PYTHONPATH. Additionally look in you user install
>> path [1]. You are looking for multiple copies of the SimpleITK module or
>> library and or python runtime libraries which could confuse the linker.
>>
>> Also you can inspect the runtime libraries:
>>
>>  otool -L
>> /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so
>>
>> /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so:
>> @loader_path/../../../libpython2.7.dylib (compatibility version 2.7.0,
>> current version 2.7.0)
>> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
>> (compatibility version 150.0.0, current version 855.17.0)
>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
>> 1197.1.1)
>> /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version
>> 60.0.0)
>> /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version
>> 2577.0.0)
>>
>> [1]
>> https://docs.python.org/2/install/#alternate-installation-the-user-scheme
>>
>> Hope this helps,
>> Brad
>>
>> On Sep 9, 2014, at 10:55 PM, Vishwa <[hidden email]
>> <http://user/SendEmail.jtp?type=node&node=7586186&i=2>> wrote:
>>
>> import SimpleITK as sitk
>>
>> Fatal Python error: PyThreadState_Get: no current thread
>>
>> Abort trap: 6
>>
>>
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
> ------------------------------
>  If you reply to this email, your message will be added to the discussion
> below:
>
> http://itk-insight-users.2283740.n2.nabble.com/using-simpleITK-with-anaconda-python-distribution-tp7586179p7586186.html
>  To unsubscribe from using simpleITK with anaconda python distribution, click
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From blowekamp at mail.nih.gov  Thu Sep 11 09:05:28 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Thu, 11 Sep 2014 09:05:28 -0400
Subject: [ITK-users] Fwd: using simpleITK with anaconda python
	distribution
In-Reply-To: <CAN9DaKa4gD4YExm18YyodopgoP2_O4HzBsyxq57HSQrQbRoz4w@mail.gmail.com>
References: <1410316426142-7586179.post@n2.nabble.com>
 <CALzTN-SXqLjCJjNTbMy-Z25NZ098Z+y2TSd3c5HSbE3ngODYTg@mail.gmail.com>
 <CAN9DaKbrYx9+UzYdJVJnDtNv1ABSXg5OieXCNO14QsKY_TY8Yw@mail.gmail.com>
 <9F0DD3DF-F5AD-4A68-8CA0-BD1F76D548DA@mail.nih.gov>
 <CAN9DaKZaXy2E=W-ATiEG8XQHBNp+U6rsQg4bZncbQOkOQMA3ww@mail.gmail.com>
 <953347C0-D04D-4620-9C9A-E8533C3C48CC@mail.nih.gov>
 <CAN9DaKbScEu4X5mo83cWo=8M5GsisqHkCVBfoZk7R5WDF=NUjw@mail.gmail.com>
 <CAN9DaKa4gD4YExm18YyodopgoP2_O4HzBsyxq57HSQrQbRoz4w@mail.gmail.com>
Message-ID: <25D4D5FA-E985-486A-BF23-F32A5EF52E13@mail.nih.gov>

Hello,

First I would look at the output of the conda build. What that OK? Did it give a successful output? Next I would look into the site packages directory in your anaconda installation ( e.g. ~/anaconda//lib/python2.7/site-packages) for the SimpleITK directory.

Brad
On Sep 11, 2014, at 12:43 AM, Vishwa <vishwanath.somashekar at gmail.com> wrote:

> 
> 
> I did install anaconda again and ran the conda build like you suggest. It ran without and problem. However, when I import simpleitk, it gives a error saying no module found. 
> 
> Any ideas?
> 
> Vishwa
> 
> On Wed, Sep 10, 2014 at 10:10 AM, Bradley Lowekamp [via ITK Insight Users] <ml-node+s2283740n7586186h92 at n2.nabble.com> wrote:
> Hello,
> 
> You need to use the conda build environment. Look at the readme in this repo[1].
> 
> Basically you'll need to do the following:
> 
> $ conda install conda-build
> $ cd src
> $ git clone https://github.com/thewtex/conda-recipes.git
> $ git checkout simpleitk-clone-url
> $ conda build simpleitk
> 
> 
> 
> [1] https://github.com/conda/conda-recipes
> 
> On Sep 10, 2014, at 11:01 AM, Vishwa <[hidden email]> wrote:
> 
>> Thanks very much for the information. I looked at the conda recipe. There are three files. 
>> One is .sh file, the second is yaml file, and the third is just a test code. How am i to use that recipe to compile..
>> 
>> There are variables like Source_Dir in the .sh file. How do i get those. I am not familiar using it. 
>> 
>> Am I to just copy the file build.sh into the SimpleITK source code directly and run sh ./build.sh? I tried that, and it ran for a while and gave an error. 
>> 
>> Best regards,
>> Vishwa
>> 
>> 
>> 
>> On Wed, Sep 10, 2014 at 9:13 AM, Bradley Lowekamp <[hidden email]> wrote:
>> Hello,
>> 
>> This error message frequently happens when SimpleITK is compiled against a different version of  Python than the runtime. This generally indicate there is something conflicting funny in your runtime environment.
>> 
>> I was easily able to use the build script from the conda-recipes repository. I would strongly recommend this approach when building for the anaconda enviroment as it does simplify some of there issue. Your CMake configuration does look correct.
>> 
>> You should look at you environment variables, such as PATH, DYLD_LIBRARY_PATH, and PYTHONPATH. Additionally look in you user install path [1]. You are looking for multiple copies of the SimpleITK module or library and or python runtime libraries which could confuse the linker.
>> 
>> Also you can inspect the runtime libraries:
>> 
>>  otool -L /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so
>> /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so:
>> 	@loader_path/../../../libpython2.7.dylib (compatibility version 2.7.0, current version 2.7.0)
>> 	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 855.17.0)
>> 	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)
>> 	/usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 60.0.0)
>> 	/usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 2577.0.0)
>> 
>> [1] https://docs.python.org/2/install/#alternate-installation-the-user-scheme
>> 
>> Hope this helps,
>> Brad
>> 
>> On Sep 9, 2014, at 10:55 PM, Vishwa <[hidden email]> wrote:
>> 
>>> import SimpleITK as sitk
>>> 
>>> Fatal Python error: PyThreadState_Get: no current thread
>>> 
>>> 
>>> Abort trap: 6
>>> 
>> 
>> 
>> _____________________________________
>> Powered by www.kitware.com
>> 
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>> 
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>> 
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>> 
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>> 
>> 
> 
> 
> _____________________________________ 
> Powered by www.kitware.com 
> 
> Visit other Kitware open-source projects at 
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit: 
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at: 
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe: 
> http://public.kitware.com/mailman/listinfo/insight-users
> 
> 
> If you reply to this email, your message will be added to the discussion below:
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> To unsubscribe from using simpleITK with anaconda python distribution, click here.
> NAML
> 
> 
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
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> 
> Kitware offers ITK Training Courses, for more information visit:
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> 
> Please keep messages on-topic and check the ITK FAQ at:
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From vishwanath.somashekar at gmail.com  Thu Sep 11 13:06:10 2014
From: vishwanath.somashekar at gmail.com (Vishwa)
Date: Thu, 11 Sep 2014 12:06:10 -0500
Subject: [ITK-users] Fwd: using simpleITK with anaconda python
	distribution
In-Reply-To: <CAN9DaKYOoE7yJ1e7VctJyWOQg82ux7OvCBYaNXn4oEQ3HnKXDw@mail.gmail.com>
References: <1410316426142-7586179.post@n2.nabble.com>
 <CALzTN-SXqLjCJjNTbMy-Z25NZ098Z+y2TSd3c5HSbE3ngODYTg@mail.gmail.com>
 <CAN9DaKbrYx9+UzYdJVJnDtNv1ABSXg5OieXCNO14QsKY_TY8Yw@mail.gmail.com>
 <9F0DD3DF-F5AD-4A68-8CA0-BD1F76D548DA@mail.nih.gov>
 <CAN9DaKZaXy2E=W-ATiEG8XQHBNp+U6rsQg4bZncbQOkOQMA3ww@mail.gmail.com>
 <953347C0-D04D-4620-9C9A-E8533C3C48CC@mail.nih.gov>
 <CAN9DaKbScEu4X5mo83cWo=8M5GsisqHkCVBfoZk7R5WDF=NUjw@mail.gmail.com>
 <CAN9DaKa4gD4YExm18YyodopgoP2_O4HzBsyxq57HSQrQbRoz4w@mail.gmail.com>
 <25D4D5FA-E985-486A-BF23-F32A5EF52E13@mail.nih.gov>
 <CAN9DaKYOoE7yJ1e7VctJyWOQg82ux7OvCBYaNXn4oEQ3HnKXDw@mail.gmail.com>
Message-ID: <CAN9DaKaAt2Ni65pUWF1Ey2tL1yC4KsgfRgaSSYfQGYoP6vZnYg@mail.gmail.com>

Hi All,
I think python PythonPackage/setup.py installed wasn't in the location that
the recipe calls for. I manually went to the location and ran the command.
It was in the following folder

/Users/dagarshali/anaconda/conda-bld/work/build/SimpleITK-build/Wrapping

After that when I checked for simpleITK in
/Users/dagarshali/anaconda/lib/python2.7/site-packages, I found

/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK

Now, when I try to import simpleitk, i get an error which is shown below.

>>> import SimpleITK as sitk

Traceback (most recent call last):

  File "<stdin>", line 1, in <module>

  File
"/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/__init__.py",
line 1, in <module>

    from .SimpleITK import *

  File
"/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py",
line 28, in <module>

    _SimpleITK = swig_import_helper()

  File
"/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py",
line 24, in swig_import_helper

    _mod = imp.load_module('_SimpleITK', fp, pathname, description)

ImportError:
dlopen(/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so,
2): Library not loaded: libjpeg.8.dylib

  Referenced from:
/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so

  Reason: image not found


I am guessing that's a progress from where I was. Any ideas to fix this one?


Vishwa

On Thu, Sep 11, 2014 at 11:18 AM, Vishwa <vishwanath.somashekar at gmail.com>
wrote:

> Hi,
> I looked in ~/anaconda//lib/python2.7/site-packages and couldn't find the
> simpleitk directory. I ran the conda build again and saved the log file. I
> am attaching here for your reference. Hopefully, that should tell us
> something.
>
> Vishwa
>
> On Thu, Sep 11, 2014 at 8:05 AM, Bradley Lowekamp <blowekamp at mail.nih.gov>
> wrote:
>
>> Hello,
>>
>> First I would look at the output of the conda build. What that OK? Did it
>> give a successful output? Next I would look into the site packages
>> directory in your anaconda installation ( e.g. ~/anaconda//lib/python2.7/site-packages)
>> for the SimpleITK directory.
>>
>> Brad
>> On Sep 11, 2014, at 12:43 AM, Vishwa <vishwanath.somashekar at gmail.com>
>> wrote:
>>
>>
>>
>> I did install anaconda again and ran the conda build like you suggest. It
>> ran without and problem. However, when I import simpleitk, it gives a error
>> saying no module found.
>>
>> Any ideas?
>>
>> Vishwa
>>
>> On Wed, Sep 10, 2014 at 10:10 AM, Bradley Lowekamp [via ITK Insight
>> Users] <ml-node+s2283740n7586186h92 at n2.nabble.com> wrote:
>>
>>> Hello,
>>>
>>> You need to use the conda build environment. Look at the readme in this
>>> repo[1].
>>>
>>> Basically you'll need to do the following:
>>>
>>> $ conda install conda-build
>>> $ cd src
>>> $ git clone https://github.com/thewtex/conda-recipes.git
>>> $ git checkout simpleitk-clone-url
>>> $ conda build simpleitk
>>>
>>>
>>>
>>> [1] https://github.com/conda/conda-recipes
>>>
>>> On Sep 10, 2014, at 11:01 AM, Vishwa <[hidden email]
>>> <http://user/SendEmail.jtp?type=node&node=7586186&i=0>> wrote:
>>>
>>> Thanks very much for the information. I looked at the conda recipe.
>>> There are three files.
>>> One is .sh file, the second is yaml file, and the third is just a test
>>> code. How am i to use that recipe to compile..
>>>
>>> There are variables like Source_Dir in the .sh file. How do i get those.
>>> I am not familiar using it.
>>>
>>> Am I to just copy the file build.sh into the SimpleITK source code
>>> directly and run sh ./build.sh? I tried that, and it ran for a while and
>>> gave an error.
>>>
>>> Best regards,
>>> Vishwa
>>>
>>>
>>>
>>> On Wed, Sep 10, 2014 at 9:13 AM, Bradley Lowekamp <[hidden email]
>>> <http://user/SendEmail.jtp?type=node&node=7586186&i=1>> wrote:
>>>
>>>> Hello,
>>>>
>>>> This error message frequently happens when SimpleITK is compiled
>>>> against a different version of  Python than the runtime. This generally
>>>> indicate there is something conflicting funny in your runtime environment.
>>>>
>>>> I was easily able to use the build script from the conda-recipes
>>>> repository. I would strongly recommend this approach when building for the
>>>> anaconda enviroment as it does simplify some of there issue. Your CMake
>>>> configuration does look correct.
>>>>
>>>> You should look at you environment variables, such as PATH,
>>>> DYLD_LIBRARY_PATH, and PYTHONPATH. Additionally look in you user install
>>>> path [1]. You are looking for multiple copies of the SimpleITK module or
>>>> library and or python runtime libraries which could confuse the linker.
>>>>
>>>> Also you can inspect the runtime libraries:
>>>>
>>>>  otool -L
>>>> /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so
>>>>
>>>> /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so:
>>>> @loader_path/../../../libpython2.7.dylib (compatibility version 2.7.0,
>>>> current version 2.7.0)
>>>> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
>>>> (compatibility version 150.0.0, current version 855.17.0)
>>>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
>>>> version 1197.1.1)
>>>> /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current
>>>> version 60.0.0)
>>>> /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version
>>>> 2577.0.0)
>>>>
>>>> [1]
>>>> https://docs.python.org/2/install/#alternate-installation-the-user-scheme
>>>>
>>>> Hope this helps,
>>>> Brad
>>>>
>>>> On Sep 9, 2014, at 10:55 PM, Vishwa <[hidden email]
>>>> <http://user/SendEmail.jtp?type=node&node=7586186&i=2>> wrote:
>>>>
>>>> import SimpleITK as sitk
>>>>
>>>> Fatal Python error: PyThreadState_Get: no current thread
>>>>
>>>> Abort trap: 6
>>>>
>>>>
>>>>
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>
>>>>
>>>
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>>
>>> ------------------------------
>>>  If you reply to this email, your message will be added to the
>>> discussion below:
>>>
>>> http://itk-insight-users.2283740.n2.nabble.com/using-simpleITK-with-anaconda-python-distribution-tp7586179p7586186.html
>>>  To unsubscribe from using simpleITK with anaconda python distribution, click
>>> here
>>> <http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=7586179&code=ZGFnYXJzaGFsaUBnbWFpbC5jb218NzU4NjE3OXwtMTU3ODY3ODY5MQ==>
>>> .
>>> NAML
>>> <http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
>>>
>>
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
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From blowekamp at mail.nih.gov  Thu Sep 11 20:36:50 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Thu, 11 Sep 2014 20:36:50 -0400
Subject: [ITK-users] Fwd: using simpleITK with anaconda python
	distribution
In-Reply-To: <CAN9DaKaAt2Ni65pUWF1Ey2tL1yC4KsgfRgaSSYfQGYoP6vZnYg@mail.gmail.com>
References: <1410316426142-7586179.post@n2.nabble.com>
 <CALzTN-SXqLjCJjNTbMy-Z25NZ098Z+y2TSd3c5HSbE3ngODYTg@mail.gmail.com>
 <CAN9DaKbrYx9+UzYdJVJnDtNv1ABSXg5OieXCNO14QsKY_TY8Yw@mail.gmail.com>
 <9F0DD3DF-F5AD-4A68-8CA0-BD1F76D548DA@mail.nih.gov>
 <CAN9DaKZaXy2E=W-ATiEG8XQHBNp+U6rsQg4bZncbQOkOQMA3ww@mail.gmail.com>
 <953347C0-D04D-4620-9C9A-E8533C3C48CC@mail.nih.gov>
 <CAN9DaKbScEu4X5mo83cWo=8M5GsisqHkCVBfoZk7R5WDF=NUjw@mail.gmail.com>
 <CAN9DaKa4gD4YExm18YyodopgoP2_O4HzBsyxq57HSQrQbRoz4w@mail.gmail.com>
 <25D4D5FA-E985-486A-BF23-F32A5EF52E13@mail.nih.gov>
 <CAN9DaKYOoE7yJ1e7VctJyWOQg82ux7OvCBYaNXn4oEQ3HnKXDw@mail.gmail.com>
 <CAN9DaKaAt2Ni65pUWF1Ey2tL1yC4KsgfRgaSSYfQGYoP6vZnYg@mail.gmail.com>
Message-ID: <883BDA89-296C-463D-83EF-D39299E91783@mail.nih.gov>

From [1] did you try:

conda install --use-local simpleitk
Brad

[1] http://conda.pydata.org/docs/build_tutorials/pkgs.html

On Sep 11, 2014, at 1:06 PM, Vishwa <vishwanath.somashekar at gmail.com> wrote:

> Hi All,
> I think python PythonPackage/setup.py installed wasn't in the location that the recipe calls for. I manually went to the location and ran the command. It was in the following folder
> 
> /Users/dagarshali/anaconda/conda-bld/work/build/SimpleITK-build/Wrapping
> 
> After that when I checked for simpleITK in /Users/dagarshali/anaconda/lib/python2.7/site-packages, I found
> 
> 
> /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK
> 
> Now, when I try to import simpleitk, i get an error which is shown below. 
> 
> >>> import SimpleITK as sitk
> 
> Traceback (most recent call last):
> 
>   File "<stdin>", line 1, in <module>
> 
>   File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/__init__.py", line 1, in <module>
> 
>     from .SimpleITK import *
> 
>   File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 28, in <module>
> 
>     _SimpleITK = swig_import_helper()
> 
>   File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 24, in swig_import_helper
> 
>     _mod = imp.load_module('_SimpleITK', fp, pathname, description)
> 
> ImportError: dlopen(/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so, 2): Library not loaded: libjpeg.8.dylib
> 
>   Referenced from: /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so
> 
>   Reason: image not found
> 
> 
> 
> I am guessing that's a progress from where I was. Any ideas to fix this one?
> 
> 
> 
> Vishwa
> 
> 
> On Thu, Sep 11, 2014 at 11:18 AM, Vishwa <vishwanath.somashekar at gmail.com> wrote:
> Hi, 
> I looked in ~/anaconda//lib/python2.7/site-packages and couldn't find the simpleitk directory. I ran the conda build again and saved the log file. I am attaching here for your reference. Hopefully, that should tell us something.
> 
> Vishwa
> 
> On Thu, Sep 11, 2014 at 8:05 AM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
> Hello,
> 
> First I would look at the output of the conda build. What that OK? Did it give a successful output? Next I would look into the site packages directory in your anaconda installation ( e.g. ~/anaconda//lib/python2.7/site-packages) for the SimpleITK directory.
> 
> Brad
> On Sep 11, 2014, at 12:43 AM, Vishwa <vishwanath.somashekar at gmail.com> wrote:
> 
>> 
>> 
>> I did install anaconda again and ran the conda build like you suggest. It ran without and problem. However, when I import simpleitk, it gives a error saying no module found. 
>> 
>> Any ideas?
>> 
>> Vishwa
>> 
>> On Wed, Sep 10, 2014 at 10:10 AM, Bradley Lowekamp [via ITK Insight Users] <ml-node+s2283740n7586186h92 at n2.nabble.com> wrote:
>> Hello,
>> 
>> You need to use the conda build environment. Look at the readme in this repo[1].
>> 
>> Basically you'll need to do the following:
>> 
>> $ conda install conda-build
>> $ cd src
>> $ git clone https://github.com/thewtex/conda-recipes.git
>> $ git checkout simpleitk-clone-url
>> $ conda build simpleitk
>> 
>> 
>> 
>> [1] https://github.com/conda/conda-recipes
>> 
>> On Sep 10, 2014, at 11:01 AM, Vishwa <[hidden email]> wrote:
>> 
>>> Thanks very much for the information. I looked at the conda recipe. There are three files. 
>>> One is .sh file, the second is yaml file, and the third is just a test code. How am i to use that recipe to compile..
>>> 
>>> There are variables like Source_Dir in the .sh file. How do i get those. I am not familiar using it. 
>>> 
>>> Am I to just copy the file build.sh into the SimpleITK source code directly and run sh ./build.sh? I tried that, and it ran for a while and gave an error. 
>>> 
>>> Best regards,
>>> Vishwa
>>> 
>>> 
>>> 
>>> On Wed, Sep 10, 2014 at 9:13 AM, Bradley Lowekamp <[hidden email]> wrote:
>>> Hello,
>>> 
>>> This error message frequently happens when SimpleITK is compiled against a different version of  Python than the runtime. This generally indicate there is something conflicting funny in your runtime environment.
>>> 
>>> I was easily able to use the build script from the conda-recipes repository. I would strongly recommend this approach when building for the anaconda enviroment as it does simplify some of there issue. Your CMake configuration does look correct.
>>> 
>>> You should look at you environment variables, such as PATH, DYLD_LIBRARY_PATH, and PYTHONPATH. Additionally look in you user install path [1]. You are looking for multiple copies of the SimpleITK module or library and or python runtime libraries which could confuse the linker.
>>> 
>>> Also you can inspect the runtime libraries:
>>> 
>>>  otool -L /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so
>>> /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so:
>>> 	@loader_path/../../../libpython2.7.dylib (compatibility version 2.7.0, current version 2.7.0)
>>> 	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 855.17.0)
>>> 	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)
>>> 	/usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 60.0.0)
>>> 	/usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 2577.0.0)
>>> 
>>> [1] https://docs.python.org/2/install/#alternate-installation-the-user-scheme
>>> 
>>> Hope this helps,
>>> Brad
>>> 
>>> On Sep 9, 2014, at 10:55 PM, Vishwa <[hidden email]> wrote:
>>> 
>>>> import SimpleITK as sitk
>>>> 
>>>> Fatal Python error: PyThreadState_Get: no current thread
>>>> 
>>>> 
>>>> Abort trap: 6
>>>> 
>>> 
>>> 
>>> _____________________________________
>>> Powered by www.kitware.com
>>> 
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>> 
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>> 
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>> 
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>> 
>>> 
>> 
>> 
>> _____________________________________ 
>> Powered by www.kitware.com 
>> 
>> Visit other Kitware open-source projects at 
>> http://www.kitware.com/opensource/opensource.html
>> 
>> Kitware offers ITK Training Courses, for more information visit: 
>> http://www.kitware.com/products/protraining.php
>> 
>> Please keep messages on-topic and check the ITK FAQ at: 
>> http://www.itk.org/Wiki/ITK_FAQ
>> 
>> Follow this link to subscribe/unsubscribe: 
>> http://public.kitware.com/mailman/listinfo/insight-users
>> 
>> 
>> If you reply to this email, your message will be added to the discussion below:
>> http://itk-insight-users.2283740.n2.nabble.com/using-simpleITK-with-anaconda-python-distribution-tp7586179p7586186.html
>> To unsubscribe from using simpleITK with anaconda python distribution, click here.
>> NAML
>> 
>> 
>> _____________________________________
>> Powered by www.kitware.com
>> 
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>> 
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>> 
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>> 
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
> 
> 
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
> 
> 
> 

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From noreply at insightsoftwareconsortium.org  Fri Sep 12 02:02:22 2014
From: noreply at insightsoftwareconsortium.org (Insight Journal)
Date: Fri, 12 Sep 2014 02:02:22 -0400 (EDT)
Subject: [ITK-users] New Submission: DICOM Spatial Transform IO in the
	Insight Toolkit
Message-ID: <20140912060222.BDC953D6C18C@insightsoftwareconsortium.org>

Hello,

A new submission has been added to the Insight Journal.

Title: DICOM Spatial Transform IO in the Insight Toolkit
Authors: McCormick M., Wang K., Lasso A., Sharp G., Pieper S.
Abstract: This document describes a module that extends the Insight Toolkit, ITK, which reads DICOM Spatial Rogistration Object files in itk::Transform's. Currently, DICOM files are read by applying the DCMTK library as a backend. An itk::DCMTKTransformIO class can be registration with the IO factory mechanism so itk::TransformFileReadertemplate will recognize and read these files.

This paper is accompanied with the source code, input data, parameters and output data that the authors used for validating the algorithm described in this paper. This adhere to the fundamental principle that scientific publications must facilitate reproducibility of the reported results.

Download and review this publication at: http://hdl.handle.net/10380/3468

Generated by the Insight Journal

You are receiving this email because you asked to be informed by the Insight Journal for new submissions. To change your email preference visit http://insight-journal.org/ .

From maximilian_oliver.mordig at roche.com  Fri Sep 12 07:10:51 2014
From: maximilian_oliver.mordig at roche.com (maximilian)
Date: Fri, 12 Sep 2014 04:10:51 -0700 (PDT)
Subject: [ITK-users] Integrate SCIFIO into ITK
Message-ID: <1410520251887-7586194.post@n2.nabble.com>

Dear All,

I have problems including the image IO that comes with SCIFIO.
I rebuilt ITK with the MODULE_SCIFIO flag activated. Then, I created a new
project with the same content as "itkSCIFIOImageIOTest.cxx" that comes with
the SCIFIO plugin.

ITK can't find the itkSCIFIOImageIO.h header.
The error is: fatal error C1083: Cannot open include file:
'itkSCIFIOImageIO.h': No such file or directory

What do I have to add in my CMake file? My current CMakeLists.txt is:

cmake_minimum_required(VERSION 2.8)

project( ReadFlex )

find_package(ITK REQUIRED)
include(${ITK_USE_FILE})

add_executable(ReadFlex ReadFlex.cxx)

target_link_libraries(
	ReadFlex ${ITK_LIBRARIES}
)

Thanks in advance




--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Integrate-SCIFIO-into-ITK-tp7586194.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From vishwanath.somashekar at gmail.com  Fri Sep 12 19:59:56 2014
From: vishwanath.somashekar at gmail.com (Vishwa)
Date: Fri, 12 Sep 2014 18:59:56 -0500
Subject: [ITK-users] Fwd: using simpleITK with anaconda python
	distribution
In-Reply-To: <883BDA89-296C-463D-83EF-D39299E91783@mail.nih.gov>
References: <1410316426142-7586179.post@n2.nabble.com>
 <CALzTN-SXqLjCJjNTbMy-Z25NZ098Z+y2TSd3c5HSbE3ngODYTg@mail.gmail.com>
 <CAN9DaKbrYx9+UzYdJVJnDtNv1ABSXg5OieXCNO14QsKY_TY8Yw@mail.gmail.com>
 <9F0DD3DF-F5AD-4A68-8CA0-BD1F76D548DA@mail.nih.gov>
 <CAN9DaKZaXy2E=W-ATiEG8XQHBNp+U6rsQg4bZncbQOkOQMA3ww@mail.gmail.com>
 <953347C0-D04D-4620-9C9A-E8533C3C48CC@mail.nih.gov>
 <CAN9DaKbScEu4X5mo83cWo=8M5GsisqHkCVBfoZk7R5WDF=NUjw@mail.gmail.com>
 <CAN9DaKa4gD4YExm18YyodopgoP2_O4HzBsyxq57HSQrQbRoz4w@mail.gmail.com>
 <25D4D5FA-E985-486A-BF23-F32A5EF52E13@mail.nih.gov>
 <CAN9DaKYOoE7yJ1e7VctJyWOQg82ux7OvCBYaNXn4oEQ3HnKXDw@mail.gmail.com>
 <CAN9DaKaAt2Ni65pUWF1Ey2tL1yC4KsgfRgaSSYfQGYoP6vZnYg@mail.gmail.com>
 <883BDA89-296C-463D-83EF-D39299E91783@mail.nih.gov>
Message-ID: <CAN9DaKbNsZb0DxqFOwx=s-9W58cen91ysOfBs9yJKiapSF35hQ@mail.gmail.com>

Hi Brad,
Thanks for all the help. I tried the conda install --use-local simpleitk
from the conda-recipes folder. It didn't seem to matter..

Here is the thing that I noticed..

If I add the path of the lib (~/anaconda/lib) to DYLD_LIBRARY_PATH, then i
can get it to work from the python that's invoked from the terminal.
However, when I try the same thing from the notebook or from spyder, I get
the following error.

>>import SimpleITK as sitk
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File
"/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/__init__.py",
line 1, in <module>
    from .SimpleITK import *
  File
"/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py",
line 28, in <module>
    _SimpleITK = swig_import_helper()
  File
"/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py",
line 24, in swig_import_helper
    _mod = imp.load_module('_SimpleITK', fp, pathname, description)
ImportError:
dlopen(/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so,
2): Library not loaded: libpng15.15.dylib
  Referenced from:
/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so
  Reason: image not found

Any suggestions?

On Thu, Sep 11, 2014 at 7:36 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:

> From [1] did you try:
>
> conda install --use-local simpleitk
>
> Brad
>
> [1] http://conda.pydata.org/docs/build_tutorials/pkgs.html
>
> On Sep 11, 2014, at 1:06 PM, Vishwa <vishwanath.somashekar at gmail.com>
> wrote:
>
> Hi All,
> I think python PythonPackage/setup.py installed wasn't in the location
> that the recipe calls for. I manually went to the location and ran the
> command. It was in the following folder
>
> /Users/dagarshali/anaconda/conda-bld/work/build/SimpleITK-build/Wrapping
>
> After that when I checked for simpleITK in
> /Users/dagarshali/anaconda/lib/python2.7/site-packages, I found
>
>
> /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK
>
> Now, when I try to import simpleitk, i get an error which is shown below.
>
> >>> import SimpleITK as sitk
>
> Traceback (most recent call last):
>
>   File "<stdin>", line 1, in <module>
>
>   File
> "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/__init__.py",
> line 1, in <module>
>
>     from .SimpleITK import *
>
>   File
> "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py",
> line 28, in <module>
>
>     _SimpleITK = swig_import_helper()
>
>   File
> "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py",
> line 24, in swig_import_helper
>
>     _mod = imp.load_module('_SimpleITK', fp, pathname, description)
>
> ImportError:
> dlopen(/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so,
> 2): Library not loaded: libjpeg.8.dylib
>
>   Referenced from:
> /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so
>
>   Reason: image not found
>
>
> I am guessing that's a progress from where I was. Any ideas to fix this
> one?
>
>
> Vishwa
>
> On Thu, Sep 11, 2014 at 11:18 AM, Vishwa <vishwanath.somashekar at gmail.com>
> wrote:
>
>> Hi,
>> I looked in ~/anaconda//lib/python2.7/site-packages and couldn't find
>> the simpleitk directory. I ran the conda build again and saved the log
>> file. I am attaching here for your reference. Hopefully, that should tell
>> us something.
>>
>> Vishwa
>>
>> On Thu, Sep 11, 2014 at 8:05 AM, Bradley Lowekamp <blowekamp at mail.nih.gov
>> > wrote:
>>
>>> Hello,
>>>
>>> First I would look at the output of the conda build. What that OK? Did
>>> it give a successful output? Next I would look into the site packages
>>> directory in your anaconda installation ( e.g. ~/anaconda//lib/python2.7/site-packages)
>>> for the SimpleITK directory.
>>>
>>> Brad
>>> On Sep 11, 2014, at 12:43 AM, Vishwa <vishwanath.somashekar at gmail.com>
>>> wrote:
>>>
>>>
>>>
>>> I did install anaconda again and ran the conda build like you suggest.
>>> It ran without and problem. However, when I import simpleitk, it gives a
>>> error saying no module found.
>>>
>>> Any ideas?
>>>
>>> Vishwa
>>>
>>> On Wed, Sep 10, 2014 at 10:10 AM, Bradley Lowekamp [via ITK Insight
>>> Users] <ml-node+s2283740n7586186h92 at n2.nabble.com> wrote:
>>>
>>>> Hello,
>>>>
>>>> You need to use the conda build environment. Look at the readme in this
>>>> repo[1].
>>>>
>>>> Basically you'll need to do the following:
>>>>
>>>> $ conda install conda-build
>>>> $ cd src
>>>> $ git clone https://github.com/thewtex/conda-recipes.git
>>>> $ git checkout simpleitk-clone-url
>>>> $ conda build simpleitk
>>>>
>>>>
>>>>
>>>> [1] https://github.com/conda/conda-recipes
>>>>
>>>> On Sep 10, 2014, at 11:01 AM, Vishwa <[hidden email]
>>>> <http://user/SendEmail.jtp?type=node&node=7586186&i=0>> wrote:
>>>>
>>>> Thanks very much for the information. I looked at the conda recipe.
>>>> There are three files.
>>>> One is .sh file, the second is yaml file, and the third is just a test
>>>> code. How am i to use that recipe to compile..
>>>>
>>>> There are variables like Source_Dir in the .sh file. How do i get
>>>> those. I am not familiar using it.
>>>>
>>>> Am I to just copy the file build.sh into the SimpleITK source code
>>>> directly and run sh ./build.sh? I tried that, and it ran for a while and
>>>> gave an error.
>>>>
>>>> Best regards,
>>>> Vishwa
>>>>
>>>>
>>>>
>>>> On Wed, Sep 10, 2014 at 9:13 AM, Bradley Lowekamp <[hidden email]
>>>> <http://user/SendEmail.jtp?type=node&node=7586186&i=1>> wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> This error message frequently happens when SimpleITK is compiled
>>>>> against a different version of  Python than the runtime. This generally
>>>>> indicate there is something conflicting funny in your runtime environment.
>>>>>
>>>>> I was easily able to use the build script from the conda-recipes
>>>>> repository. I would strongly recommend this approach when building for the
>>>>> anaconda enviroment as it does simplify some of there issue. Your CMake
>>>>> configuration does look correct.
>>>>>
>>>>> You should look at you environment variables, such as PATH,
>>>>> DYLD_LIBRARY_PATH, and PYTHONPATH. Additionally look in you user install
>>>>> path [1]. You are looking for multiple copies of the SimpleITK module or
>>>>> library and or python runtime libraries which could confuse the linker.
>>>>>
>>>>> Also you can inspect the runtime libraries:
>>>>>
>>>>>  otool -L
>>>>> /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so
>>>>>
>>>>> /Users/blowekamp/anaconda//lib/python2.7/site-packages/SimpleITK/_SimpleITK.so:
>>>>> @loader_path/../../../libpython2.7.dylib (compatibility version 2.7.0,
>>>>> current version 2.7.0)
>>>>> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
>>>>> (compatibility version 150.0.0, current version 855.17.0)
>>>>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
>>>>> version 1197.1.1)
>>>>> /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current
>>>>> version 60.0.0)
>>>>> /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current
>>>>> version 2577.0.0)
>>>>>
>>>>> [1]
>>>>> https://docs.python.org/2/install/#alternate-installation-the-user-scheme
>>>>>
>>>>> Hope this helps,
>>>>> Brad
>>>>>
>>>>> On Sep 9, 2014, at 10:55 PM, Vishwa <[hidden email]
>>>>> <http://user/SendEmail.jtp?type=node&node=7586186&i=2>> wrote:
>>>>>
>>>>> import SimpleITK as sitk
>>>>>
>>>>> Fatal Python error: PyThreadState_Get: no current thread
>>>>>
>>>>> Abort trap: 6
>>>>>
>>>>>
>>>>>
>>>>> _____________________________________
>>>>> Powered by www.kitware.com
>>>>>
>>>>> Visit other Kitware open-source projects at
>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>
>>>>> Kitware offers ITK Training Courses, for more information visit:
>>>>> http://www.kitware.com/products/protraining.php
>>>>>
>>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>>
>>>>> Follow this link to subscribe/unsubscribe:
>>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>>
>>>>>
>>>>
>>>>
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>
>>>>
>>>> ------------------------------
>>>>  If you reply to this email, your message will be added to the
>>>> discussion below:
>>>>
>>>> http://itk-insight-users.2283740.n2.nabble.com/using-simpleITK-with-anaconda-python-distribution-tp7586179p7586186.html
>>>>  To unsubscribe from using simpleITK with anaconda python distribution, click
>>>> here
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>>>> .
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>>>> <http://itk-insight-users.2283740.n2.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
>>>>
>>>
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
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>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
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>>> Kitware offers ITK Training Courses, for more information visit:
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>>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
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>
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From vishwanath.somashekar at gmail.com  Fri Sep 12 22:52:04 2014
From: vishwanath.somashekar at gmail.com (Vishwa)
Date: Fri, 12 Sep 2014 21:52:04 -0500
Subject: [ITK-users] Fwd: using simpleITK with anaconda python
	distribution
In-Reply-To: <CAN9DaKbNsZb0DxqFOwx=s-9W58cen91ysOfBs9yJKiapSF35hQ@mail.gmail.com>
References: <1410316426142-7586179.post@n2.nabble.com>
 <CALzTN-SXqLjCJjNTbMy-Z25NZ098Z+y2TSd3c5HSbE3ngODYTg@mail.gmail.com>
 <CAN9DaKbrYx9+UzYdJVJnDtNv1ABSXg5OieXCNO14QsKY_TY8Yw@mail.gmail.com>
 <9F0DD3DF-F5AD-4A68-8CA0-BD1F76D548DA@mail.nih.gov>
 <CAN9DaKZaXy2E=W-ATiEG8XQHBNp+U6rsQg4bZncbQOkOQMA3ww@mail.gmail.com>
 <953347C0-D04D-4620-9C9A-E8533C3C48CC@mail.nih.gov>
 <CAN9DaKbScEu4X5mo83cWo=8M5GsisqHkCVBfoZk7R5WDF=NUjw@mail.gmail.com>
 <CAN9DaKa4gD4YExm18YyodopgoP2_O4HzBsyxq57HSQrQbRoz4w@mail.gmail.com>
 <25D4D5FA-E985-486A-BF23-F32A5EF52E13@mail.nih.gov>
 <CAN9DaKYOoE7yJ1e7VctJyWOQg82ux7OvCBYaNXn4oEQ3HnKXDw@mail.gmail.com>
 <CAN9DaKaAt2Ni65pUWF1Ey2tL1yC4KsgfRgaSSYfQGYoP6vZnYg@mail.gmail.com>
 <883BDA89-296C-463D-83EF-D39299E91783@mail.nih.gov>
 <CAN9DaKbNsZb0DxqFOwx=s-9W58cen91ysOfBs9yJKiapSF35hQ@mail.gmail.com>
Message-ID: <CAN9DaKaVh+unszbQ0oFtJZd7KHrUjg6W2FtK=d=0u614yT9c4g@mail.gmail.com>

Hi Brad,
Thanks for all the help. I tried the conda install --use-local simpleitk
from the conda-recipes folder. It didn't seem to matter..

Here is the thing that I noticed..

If I add the path of the lib (~/anaconda/lib) to DYLD_LIBRARY_PATH, then i
can get it to work from the python that's invoked from the terminal.
However, when I try the same thing from the notebook or from spyder, I get
the following error.

>>import SimpleITK as sitk
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File
"/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/__init__.py",
line 1, in <module>
    from .SimpleITK import *
  File
"/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py",
line 28, in <module>
    _SimpleITK = swig_import_helper()
  File
"/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py",
line 24, in swig_import_helper
    _mod = imp.load_module('_SimpleITK', fp, pathname, description)
ImportError:
dlopen(/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so,
2): Library not loaded: libpng15.15.dylib
  Referenced from:
/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so
  Reason: image not found

Any suggestions?


On Fri, Sep 12, 2014 at 6:59 PM, Vishwa <vishwanath.somashekar at gmail.com>
wrote:

> Hi Brad,
> Thanks for all the help. I tried the conda install --use-local simpleitk
> from the conda-recipes folder. It didn't seem to matter..
>
> Here is the thing that I noticed..
>
> If I add the path of the lib (~/anaconda/lib) to DYLD_LIBRARY_PATH, then i
> can get it to work from the python that's invoked from the terminal.
> However, when I try the same thing from the notebook or from spyder, I get
> the following error.
>
> >>import SimpleITK as sitk
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File
> "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/__init__.py",
> line 1, in <module>
>     from .SimpleITK import *
>   File
> "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py",
> line 28, in <module>
>     _SimpleITK = swig_import_helper()
>   File
> "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py",
> line 24, in swig_import_helper
>     _mod = imp.load_module('_SimpleITK', fp, pathname, description)
> ImportError:
> dlopen(/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so,
> 2): Library not loaded: libpng15.15.dylib
>   Referenced from:
> /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so
>   Reason: image not found
>
> Any suggestions?
>
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From vijayarani.shanmugavadivu at appasamy.com  Sat Sep 13 08:34:42 2014
From: vijayarani.shanmugavadivu at appasamy.com (vijayarani)
Date: Sat, 13 Sep 2014 05:34:42 -0700 (PDT)
Subject: [ITK-users] Resampling a mha image and finding histogram
Message-ID: <1410611682783-7586198.post@n2.nabble.com>

Hi
I have a mha image which is very large.How to subsample it and find
histogram of the image?

Thanks
Vijaya Rani S 



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Resampling-a-mha-image-and-finding-histogram-tp7586198.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From vijayarani.shanmugavadivu at appasamy.com  Sat Sep 13 08:39:28 2014
From: vijayarani.shanmugavadivu at appasamy.com (vijayarani)
Date: Sat, 13 Sep 2014 18:09:28 +0530
Subject: [ITK-users] Subsampling a mha image and finding histogram
Message-ID: <54143B00.1070906@appasamy.com>

Hi
I have a mha image which is very large in size.How to subsample it and 
find histogram?

Thanks
Vijaya Rani S

From blowekamp at mail.nih.gov  Sat Sep 13 13:00:50 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Sat, 13 Sep 2014 13:00:50 -0400
Subject: [ITK-users] Fwd: using simpleITK with anaconda python
	distribution
In-Reply-To: <CAN9DaKaVh+unszbQ0oFtJZd7KHrUjg6W2FtK=d=0u614yT9c4g@mail.gmail.com>
References: <1410316426142-7586179.post@n2.nabble.com>
 <CALzTN-SXqLjCJjNTbMy-Z25NZ098Z+y2TSd3c5HSbE3ngODYTg@mail.gmail.com>
 <CAN9DaKbrYx9+UzYdJVJnDtNv1ABSXg5OieXCNO14QsKY_TY8Yw@mail.gmail.com>
 <9F0DD3DF-F5AD-4A68-8CA0-BD1F76D548DA@mail.nih.gov>
 <CAN9DaKZaXy2E=W-ATiEG8XQHBNp+U6rsQg4bZncbQOkOQMA3ww@mail.gmail.com>
 <953347C0-D04D-4620-9C9A-E8533C3C48CC@mail.nih.gov>
 <CAN9DaKbScEu4X5mo83cWo=8M5GsisqHkCVBfoZk7R5WDF=NUjw@mail.gmail.com>
 <CAN9DaKa4gD4YExm18YyodopgoP2_O4HzBsyxq57HSQrQbRoz4w@mail.gmail.com>
 <25D4D5FA-E985-486A-BF23-F32A5EF52E13@mail.nih.gov>
 <CAN9DaKYOoE7yJ1e7VctJyWOQg82ux7OvCBYaNXn4oEQ3HnKXDw@mail.gmail.com>
 <CAN9DaKaAt2Ni65pUWF1Ey2tL1yC4KsgfRgaSSYfQGYoP6vZnYg@mail.gmail.com>
 <883BDA89-296C-463D-83EF-D39299E91783@mail.nih.gov>
 <CAN9DaKbNsZb0DxqFOwx=s-9W58cen91ysOfBs9yJKiapSF35hQ@mail.gmail.com>
 <CAN9DaKaVh+unszbQ0oFtJZd7KHrUjg6W2FtK=d=0u614yT9c4g@mail.gmail.com>
Message-ID: <35D99DFD-469B-4151-B856-74974B7247EB@mail.nih.gov>

Did you remove the installed SimpleITK from the setup.py script before running "const install --use-local simpleitk". I am guessing conda didn't install simpleitk correctly because of the old version manually installed. 

Brad
On Sep 12, 2014, at 10:52 PM, Vishwa <vishwanath.somashekar at gmail.com> wrote:

> Hi Brad,
> Thanks for all the help. I tried the conda install --use-local simpleitk from the conda-recipes folder. It didn't seem to matter..
> 
> Here is the thing that I noticed..
> 
> If I add the path of the lib (~/anaconda/lib) to DYLD_LIBRARY_PATH, then i can get it to work from the python that's invoked from the terminal. However, when I try the same thing from the notebook or from spyder, I get the following error.
> 
> >>import SimpleITK as sitk
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/__init__.py", line 1, in <module>
>     from .SimpleITK import *
>   File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 28, in <module>
>     _SimpleITK = swig_import_helper()
>   File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 24, in swig_import_helper
>     _mod = imp.load_module('_SimpleITK', fp, pathname, description)
> ImportError: dlopen(/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so, 2): Library not loaded: libpng15.15.dylib
>   Referenced from: /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so
>   Reason: image not found
> 
> Any suggestions?
> 
> 
> On Fri, Sep 12, 2014 at 6:59 PM, Vishwa <vishwanath.somashekar at gmail.com> wrote:
> Hi Brad,
> Thanks for all the help. I tried the conda install --use-local simpleitk from the conda-recipes folder. It didn't seem to matter..
> 
> Here is the thing that I noticed..
> 
> If I add the path of the lib (~/anaconda/lib) to DYLD_LIBRARY_PATH, then i can get it to work from the python that's invoked from the terminal. However, when I try the same thing from the notebook or from spyder, I get the following error.
> 
> >>import SimpleITK as sitk
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/__init__.py", line 1, in <module>
>     from .SimpleITK import *
>   File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 28, in <module>
>     _SimpleITK = swig_import_helper()
>   File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 24, in swig_import_helper
>     _mod = imp.load_module('_SimpleITK', fp, pathname, description)
> ImportError: dlopen(/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so, 2): Library not loaded: libpng15.15.dylib
>   Referenced from: /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so
>   Reason: image not found
> 
> Any suggestions?
> 
> 

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From vishwanath.somashekar at gmail.com  Sat Sep 13 15:36:45 2014
From: vishwanath.somashekar at gmail.com (Vishwa)
Date: Sat, 13 Sep 2014 14:36:45 -0500
Subject: [ITK-users] Fwd: using simpleITK with anaconda python
	distribution
In-Reply-To: <35D99DFD-469B-4151-B856-74974B7247EB@mail.nih.gov>
References: <1410316426142-7586179.post@n2.nabble.com>
 <CALzTN-SXqLjCJjNTbMy-Z25NZ098Z+y2TSd3c5HSbE3ngODYTg@mail.gmail.com>
 <CAN9DaKbrYx9+UzYdJVJnDtNv1ABSXg5OieXCNO14QsKY_TY8Yw@mail.gmail.com>
 <9F0DD3DF-F5AD-4A68-8CA0-BD1F76D548DA@mail.nih.gov>
 <CAN9DaKZaXy2E=W-ATiEG8XQHBNp+U6rsQg4bZncbQOkOQMA3ww@mail.gmail.com>
 <953347C0-D04D-4620-9C9A-E8533C3C48CC@mail.nih.gov>
 <CAN9DaKbScEu4X5mo83cWo=8M5GsisqHkCVBfoZk7R5WDF=NUjw@mail.gmail.com>
 <CAN9DaKa4gD4YExm18YyodopgoP2_O4HzBsyxq57HSQrQbRoz4w@mail.gmail.com>
 <25D4D5FA-E985-486A-BF23-F32A5EF52E13@mail.nih.gov>
 <CAN9DaKYOoE7yJ1e7VctJyWOQg82ux7OvCBYaNXn4oEQ3HnKXDw@mail.gmail.com>
 <CAN9DaKaAt2Ni65pUWF1Ey2tL1yC4KsgfRgaSSYfQGYoP6vZnYg@mail.gmail.com>
 <883BDA89-296C-463D-83EF-D39299E91783@mail.nih.gov>
 <CAN9DaKbNsZb0DxqFOwx=s-9W58cen91ysOfBs9yJKiapSF35hQ@mail.gmail.com>
 <CAN9DaKaVh+unszbQ0oFtJZd7KHrUjg6W2FtK=d=0u614yT9c4g@mail.gmail.com>
 <35D99DFD-469B-4151-B856-74974B7247EB@mail.nih.gov>
Message-ID: <CAN9DaKZJERA-uo3-W3VCkg+hVtEnmV=sjHduw74q8p3yryDqJQ@mail.gmail.com>

I didn't remove it. How exactly do I do that? Also, from which folder
should i run the conda install --use-local simpleitk command.

I changed to conda recipes folder and issued the command. I got an error

 conda install --use-local simpleitk

Fetching package metadata: ...Error: Could not find URL:
file:///Users/dagarshali/anaconda/conda-bld/osx-64/

On Sat, Sep 13, 2014 at 12:00 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:

> Did you remove the installed SimpleITK from the setup.py script before
> running "const install --use-local simpleitk". I am guessing conda didn't
> install simpleitk correctly because of the old version manually installed.
>
> Brad
>
> On Sep 12, 2014, at 10:52 PM, Vishwa <vishwanath.somashekar at gmail.com>
> wrote:
>
> Hi Brad,
> Thanks for all the help. I tried the conda install --use-local simpleitk
> from the conda-recipes folder. It didn't seem to matter..
>
> Here is the thing that I noticed..
>
> If I add the path of the lib (~/anaconda/lib) to DYLD_LIBRARY_PATH, then i
> can get it to work from the python that's invoked from the terminal.
> However, when I try the same thing from the notebook or from spyder, I get
> the following error.
>
> >>import SimpleITK as sitk
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File
> "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/__init__.py",
> line 1, in <module>
>     from .SimpleITK import *
>   File
> "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py",
> line 28, in <module>
>     _SimpleITK = swig_import_helper()
>   File
> "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py",
> line 24, in swig_import_helper
>     _mod = imp.load_module('_SimpleITK', fp, pathname, description)
> ImportError:
> dlopen(/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so,
> 2): Library not loaded: libpng15.15.dylib
>   Referenced from:
> /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so
>   Reason: image not found
>
> Any suggestions?
>
>
> On Fri, Sep 12, 2014 at 6:59 PM, Vishwa <vishwanath.somashekar at gmail.com>
> wrote:
>
>> Hi Brad,
>> Thanks for all the help. I tried the conda install --use-local simpleitk
>> from the conda-recipes folder. It didn't seem to matter..
>>
>> Here is the thing that I noticed..
>>
>> If I add the path of the lib (~/anaconda/lib) to DYLD_LIBRARY_PATH, then
>> i can get it to work from the python that's invoked from the terminal.
>> However, when I try the same thing from the notebook or from spyder, I get
>> the following error.
>>
>> >>import SimpleITK as sitk
>> Traceback (most recent call last):
>>   File "<stdin>", line 1, in <module>
>>   File
>> "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/__init__.py",
>> line 1, in <module>
>>     from .SimpleITK import *
>>   File
>> "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py",
>> line 28, in <module>
>>     _SimpleITK = swig_import_helper()
>>   File
>> "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py",
>> line 24, in swig_import_helper
>>     _mod = imp.load_module('_SimpleITK', fp, pathname, description)
>> ImportError:
>> dlopen(/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so,
>> 2): Library not loaded: libpng15.15.dylib
>>   Referenced from:
>> /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so
>>   Reason: image not found
>>
>> Any suggestions?
>>
>
>
>
>
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From vishwanath.somashekar at gmail.com  Sat Sep 13 20:20:08 2014
From: vishwanath.somashekar at gmail.com (Vishwa)
Date: Sat, 13 Sep 2014 19:20:08 -0500
Subject: [ITK-users] Fwd: using simpleITK with anaconda python
	distribution
In-Reply-To: <CAN9DaKZJERA-uo3-W3VCkg+hVtEnmV=sjHduw74q8p3yryDqJQ@mail.gmail.com>
References: <1410316426142-7586179.post@n2.nabble.com>
 <CALzTN-SXqLjCJjNTbMy-Z25NZ098Z+y2TSd3c5HSbE3ngODYTg@mail.gmail.com>
 <CAN9DaKbrYx9+UzYdJVJnDtNv1ABSXg5OieXCNO14QsKY_TY8Yw@mail.gmail.com>
 <9F0DD3DF-F5AD-4A68-8CA0-BD1F76D548DA@mail.nih.gov>
 <CAN9DaKZaXy2E=W-ATiEG8XQHBNp+U6rsQg4bZncbQOkOQMA3ww@mail.gmail.com>
 <953347C0-D04D-4620-9C9A-E8533C3C48CC@mail.nih.gov>
 <CAN9DaKbScEu4X5mo83cWo=8M5GsisqHkCVBfoZk7R5WDF=NUjw@mail.gmail.com>
 <CAN9DaKa4gD4YExm18YyodopgoP2_O4HzBsyxq57HSQrQbRoz4w@mail.gmail.com>
 <25D4D5FA-E985-486A-BF23-F32A5EF52E13@mail.nih.gov>
 <CAN9DaKYOoE7yJ1e7VctJyWOQg82ux7OvCBYaNXn4oEQ3HnKXDw@mail.gmail.com>
 <CAN9DaKaAt2Ni65pUWF1Ey2tL1yC4KsgfRgaSSYfQGYoP6vZnYg@mail.gmail.com>
 <883BDA89-296C-463D-83EF-D39299E91783@mail.nih.gov>
 <CAN9DaKbNsZb0DxqFOwx=s-9W58cen91ysOfBs9yJKiapSF35hQ@mail.gmail.com>
 <CAN9DaKaVh+unszbQ0oFtJZd7KHrUjg6W2FtK=d=0u614yT9c4g@mail.gmail.com>
 <35D99DFD-469B-4151-B856-74974B7247EB@mail.nih.gov>
 <CAN9DaKZJERA-uo3-W3VCkg+hVtEnmV=sjHduw74q8p3yryDqJQ@mail.gmail.com>
Message-ID: <CAN9DaKZZfWra5qLwzG7jV12faBdvMRs4wkbhsuZk6uoGJzL2BQ@mail.gmail.com>

It finally worked with the conda install --use-local simpleitk command.

Thanks everyone

Regards,
vishwa

On Sat, Sep 13, 2014 at 2:36 PM, Vishwa <vishwanath.somashekar at gmail.com>
wrote:

> I didn't remove it. How exactly do I do that? Also, from which folder
> should i run the conda install --use-local simpleitk command.
>
> I changed to conda recipes folder and issued the command. I got an error
>
>  conda install --use-local simpleitk
>
> Fetching package metadata: ...Error: Could not find URL:
> file:///Users/dagarshali/anaconda/conda-bld/osx-64/
>
> On Sat, Sep 13, 2014 at 12:00 PM, Bradley Lowekamp <blowekamp at mail.nih.gov
> > wrote:
>
>> Did you remove the installed SimpleITK from the setup.py script before
>> running "const install --use-local simpleitk". I am guessing conda didn't
>> install simpleitk correctly because of the old version manually installed.
>>
>> Brad
>>
>> On Sep 12, 2014, at 10:52 PM, Vishwa <vishwanath.somashekar at gmail.com>
>> wrote:
>>
>> Hi Brad,
>> Thanks for all the help. I tried the conda install --use-local simpleitk
>> from the conda-recipes folder. It didn't seem to matter..
>>
>> Here is the thing that I noticed..
>>
>> If I add the path of the lib (~/anaconda/lib) to DYLD_LIBRARY_PATH, then
>> i can get it to work from the python that's invoked from the terminal.
>> However, when I try the same thing from the notebook or from spyder, I get
>> the following error.
>>
>> >>import SimpleITK as sitk
>> Traceback (most recent call last):
>>   File "<stdin>", line 1, in <module>
>>   File
>> "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/__init__.py",
>> line 1, in <module>
>>     from .SimpleITK import *
>>   File
>> "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py",
>> line 28, in <module>
>>     _SimpleITK = swig_import_helper()
>>   File
>> "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py",
>> line 24, in swig_import_helper
>>     _mod = imp.load_module('_SimpleITK', fp, pathname, description)
>> ImportError:
>> dlopen(/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so,
>> 2): Library not loaded: libpng15.15.dylib
>>   Referenced from:
>> /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so
>>   Reason: image not found
>>
>> Any suggestions?
>>
>>
>> On Fri, Sep 12, 2014 at 6:59 PM, Vishwa <vishwanath.somashekar at gmail.com>
>> wrote:
>>
>>> Hi Brad,
>>> Thanks for all the help. I tried the conda install --use-local simpleitk
>>> from the conda-recipes folder. It didn't seem to matter..
>>>
>>> Here is the thing that I noticed..
>>>
>>> If I add the path of the lib (~/anaconda/lib) to DYLD_LIBRARY_PATH, then
>>> i can get it to work from the python that's invoked from the terminal.
>>> However, when I try the same thing from the notebook or from spyder, I get
>>> the following error.
>>>
>>> >>import SimpleITK as sitk
>>> Traceback (most recent call last):
>>>   File "<stdin>", line 1, in <module>
>>>   File
>>> "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/__init__.py",
>>> line 1, in <module>
>>>     from .SimpleITK import *
>>>   File
>>> "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py",
>>> line 28, in <module>
>>>     _SimpleITK = swig_import_helper()
>>>   File
>>> "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py",
>>> line 24, in swig_import_helper
>>>     _mod = imp.load_module('_SimpleITK', fp, pathname, description)
>>> ImportError:
>>> dlopen(/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so,
>>> 2): Library not loaded: libpng15.15.dylib
>>>   Referenced from:
>>> /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so
>>>   Reason: image not found
>>>
>>> Any suggestions?
>>>
>>
>>
>>
>>
>
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From brad at lowekamp.net  Sat Sep 13 21:51:48 2014
From: brad at lowekamp.net (Bradley Lowekamp)
Date: Sat, 13 Sep 2014 21:51:48 -0400
Subject: [ITK-users] Fwd: using simpleITK with anaconda python
	distribution
In-Reply-To: <CAN9DaKZZfWra5qLwzG7jV12faBdvMRs4wkbhsuZk6uoGJzL2BQ@mail.gmail.com>
References: <1410316426142-7586179.post@n2.nabble.com>
 <CALzTN-SXqLjCJjNTbMy-Z25NZ098Z+y2TSd3c5HSbE3ngODYTg@mail.gmail.com>
 <CAN9DaKbrYx9+UzYdJVJnDtNv1ABSXg5OieXCNO14QsKY_TY8Yw@mail.gmail.com>
 <9F0DD3DF-F5AD-4A68-8CA0-BD1F76D548DA@mail.nih.gov>
 <CAN9DaKZaXy2E=W-ATiEG8XQHBNp+U6rsQg4bZncbQOkOQMA3ww@mail.gmail.com>
 <953347C0-D04D-4620-9C9A-E8533C3C48CC@mail.nih.gov>
 <CAN9DaKbScEu4X5mo83cWo=8M5GsisqHkCVBfoZk7R5WDF=NUjw@mail.gmail.com>
 <CAN9DaKa4gD4YExm18YyodopgoP2_O4HzBsyxq57HSQrQbRoz4w@mail.gmail.com>
 <25D4D5FA-E985-486A-BF23-F32A5EF52E13@mail.nih.gov>
 <CAN9DaKYOoE7yJ1e7VctJyWOQg82ux7OvCBYaNXn4oEQ3HnKXDw@mail.gmail.com>
 <CAN9DaKaAt2Ni65pUWF1Ey2tL1yC4KsgfRgaSSYfQGYoP6vZnYg@mail.gmail.com>
 <883BDA89-296C-463D-83EF-D39299E91783@mail.nih.gov>
 <CAN9DaKbNsZb0DxqFOwx=s-9W58cen91ysOfBs9yJKiapSF35hQ@mail.gmail.com>
 <CAN9DaKaVh+unszbQ0oFtJZd7KHrUjg6W2FtK=d=0u614yT9c4g@mail.gmail.com>
 <35D99DFD-469B-4151-B856-74974B7247EB@mail.nih.gov>
 <CAN9DaKZJERA-uo3-W3VCkg+hVtEnmV=sjHduw74q8p3yryDqJQ@mail.gmail.com>
 <CAN9DaKZZfWra5qLwzG7jV12faBdvMRs4wkbhsuZk6uoGJzL2BQ@mail.gmail.com>
Message-ID: <358E123A-966E-4C49-B2ED-9EC69B663C37@mail.nih.gov>

Great to hear you got it working!!!

I'll add a FAQ with specific instruction and some of the lessons learned here. 

Brad

> On Sep 13, 2014, at 8:20 PM, Vishwa <vishwanath.somashekar at gmail.com> wrote:
> 
> It finally worked with the conda install --use-local simpleitk command.
> 
> Thanks everyone
> 
> Regards,
> vishwa
> 
>> On Sat, Sep 13, 2014 at 2:36 PM, Vishwa <vishwanath.somashekar at gmail.com> wrote:
>> I didn't remove it. How exactly do I do that? Also, from which folder should i run the conda install --use-local simpleitk command. 
>> 
>> I changed to conda recipes folder and issued the command. I got an error
>> 
>>  conda install --use-local simpleitk
>> Fetching package metadata: ...Error: Could not find URL: file:///Users/dagarshali/anaconda/conda-bld/osx-64/
>> 
>> 
>>> On Sat, Sep 13, 2014 at 12:00 PM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
>>> Did you remove the installed SimpleITK from the setup.py script before running "const install --use-local simpleitk". I am guessing conda didn't install simpleitk correctly because of the old version manually installed. 
>>> 
>>> Brad
>>> 
>>>> On Sep 12, 2014, at 10:52 PM, Vishwa <vishwanath.somashekar at gmail.com> wrote:
>>>> 
>>>> Hi Brad,
>>>> Thanks for all the help. I tried the conda install --use-local simpleitk from the conda-recipes folder. It didn't seem to matter..
>>>> 
>>>> Here is the thing that I noticed..
>>>> 
>>>> If I add the path of the lib (~/anaconda/lib) to DYLD_LIBRARY_PATH, then i can get it to work from the python that's invoked from the terminal. However, when I try the same thing from the notebook or from spyder, I get the following error.
>>>> 
>>>> >>import SimpleITK as sitk
>>>> Traceback (most recent call last):
>>>>   File "<stdin>", line 1, in <module>
>>>>   File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/__init__.py", line 1, in <module>
>>>>     from .SimpleITK import *
>>>>   File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 28, in <module>
>>>>     _SimpleITK = swig_import_helper()
>>>>   File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 24, in swig_import_helper
>>>>     _mod = imp.load_module('_SimpleITK', fp, pathname, description)
>>>> ImportError: dlopen(/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so, 2): Library not loaded: libpng15.15.dylib
>>>>   Referenced from: /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so
>>>>   Reason: image not found
>>>> 
>>>> Any suggestions?
>>>> 
>>>> 
>>>>> On Fri, Sep 12, 2014 at 6:59 PM, Vishwa <vishwanath.somashekar at gmail.com> wrote:
>>>>> Hi Brad,
>>>>> Thanks for all the help. I tried the conda install --use-local simpleitk from the conda-recipes folder. It didn't seem to matter..
>>>>> 
>>>>> Here is the thing that I noticed..
>>>>> 
>>>>> If I add the path of the lib (~/anaconda/lib) to DYLD_LIBRARY_PATH, then i can get it to work from the python that's invoked from the terminal. However, when I try the same thing from the notebook or from spyder, I get the following error.
>>>>> 
>>>>> >>import SimpleITK as sitk
>>>>> Traceback (most recent call last):
>>>>>   File "<stdin>", line 1, in <module>
>>>>>   File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/__init__.py", line 1, in <module>
>>>>>     from .SimpleITK import *
>>>>>   File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 28, in <module>
>>>>>     _SimpleITK = swig_import_helper()
>>>>>   File "/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 24, in swig_import_helper
>>>>>     _mod = imp.load_module('_SimpleITK', fp, pathname, description)
>>>>> ImportError: dlopen(/Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so, 2): Library not loaded: libpng15.15.dylib
>>>>>   Referenced from: /Users/dagarshali/anaconda/lib/python2.7/site-packages/SimpleITK-0.8.0.post29-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so
>>>>>   Reason: image not found
>>>>> 
>>>>> Any suggestions?
> 
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From llliu at umich.edu  Sun Sep 14 13:26:09 2014
From: llliu at umich.edu (Lianli Liu)
Date: Sun, 14 Sep 2014 13:26:09 -0400
Subject: [ITK-users] how to modify existing algorithm in ITK
Message-ID: <CAGKqDmcRiU0wuJZESH0v_3vcMMK-KO1AUZRUcV6xxVZELFNBdQ@mail.gmail.com>

Hi all,

I am brand new to ITK and I want to modify some ITK registration functions
for specific use. But I am not clear about how to do this. After
installation, it seems that I cannot find source code in the ITK-build
folder. I just wonder if I want to redefine some functions, do I need to
download the source code again? Or is there a tutorial giving example on
how to modify existing algorithms in ITK? Thanks a lot!

Regards,
Lianli
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From matt.mccormick at kitware.com  Sun Sep 14 20:12:48 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sun, 14 Sep 2014 20:12:48 -0400
Subject: [ITK-users] how to modify existing algorithm in ITK
In-Reply-To: <CAGKqDmcRiU0wuJZESH0v_3vcMMK-KO1AUZRUcV6xxVZELFNBdQ@mail.gmail.com>
References: <CAGKqDmcRiU0wuJZESH0v_3vcMMK-KO1AUZRUcV6xxVZELFNBdQ@mail.gmail.com>
Message-ID: <CALzTN-SJxKg5Jc+otLu6rh1wYAg9GCqidE3U37e=A5vC1P=hYg@mail.gmail.com>

Hi Lianli,

Welcome to ITK!

ITK separates source from build artifacts.  Usually, all source code
is kept in the source tree, and all build artifacts are kept in the
build tree.  An install tree will install header files from the source
tree and libraries from the build tree, and it will leave out the .cxx
sources and .o object files.

You can extend ITK by writing your own classes in a module as
described here [1].  For investigating registration, some tools built
on ITK like elastix [2] can be useful.  As always, The ITK Software
Guide is a great resource [3].

Hope this helps,
Matt

[1] http://www.kitware.com/blog/home/post/557

[2] http://elastix.isi.uu.nl/

[3] http://itk.org/ITK/resources/software.html

On Sun, Sep 14, 2014 at 1:26 PM, Lianli Liu <llliu at umich.edu> wrote:
> Hi all,
>
> I am brand new to ITK and I want to modify some ITK registration functions
> for specific use. But I am not clear about how to do this. After
> installation, it seems that I cannot find source code in the ITK-build
> folder. I just wonder if I want to redefine some functions, do I need to
> download the source code again? Or is there a tutorial giving example on how
> to modify existing algorithms in ITK? Thanks a lot!
>
> Regards,
> Lianli
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>

From bilgincc at gmail.com  Mon Sep 15 11:50:51 2014
From: bilgincc at gmail.com (Cagatay Bilgin)
Date: Mon, 15 Sep 2014 08:50:51 -0700
Subject: [ITK-users] Motion under Mean Curvature with LevelSetv4
	Framework
In-Reply-To: <CAK3qF+_-3wsSVPNmutDzg6Dy=ME=APJZm_t7yPVHo4tpc_Ce7A@mail.gmail.com>
References: <CAHoiV3ZGmbX7XT6ymjaeL0VLgQRtUR1=vcmdVcm6-7VEWh+LEQ@mail.gmail.com>
 <CAK3qF+_-3wsSVPNmutDzg6Dy=ME=APJZm_t7yPVHo4tpc_Ce7A@mail.gmail.com>
Message-ID: <CAHoiV3ZvYUwNJGaJaYwAAXxnX80ZXydEdGm78Fpb3HFz3vdvcA@mail.gmail.com>

Hi Arnaud,

Sorry for the late response, I somehow missed this email. I have not done
the same experiment in the old framework to compare against. I can giving
it a shot but the old framework is more mysterious to me.

Best,
Cagatay Bilgin

On Fri, Aug 8, 2014 at 1:44 AM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:

> Hi Cagatay,
>
> I just came back from vacation... Have you solved this problem?
> It would be great if we could make the equivalent code in the old
> framework to compare and fix what could be wrong. Have you done something
> like this?
>
> I'll start looking at it...
>
> Best,
> Arnaud
>
>
> On Tue, Jul 22, 2014 at 9:58 AM, Cagatay Bilgin <bilgincc at gmail.com>
> wrote:
>
>> Dear ITK Community,
>>
>> I am trying to familiarize myself with the new level set classes. My goal
>> is to simulate motion under mean curvature using the new design.
>>
>> I have put together the following, looking at the examples and tests.
>> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3872740/ is a great source
>> to understand the design and tests in source directory are very helpful,
>> thank you for the resources!
>>
>> The test scenario I have is a L shaped object. I would expect the object
>> to become somewhat ellipse and then disappear at the end of the evolution.
>> However I get the following results attached to the email. I don't quite
>> follow these results. Am I missing something obvious?
>>
>> Here is the code and CMakeLists.txt. I ran the program with ./Motion 100
>> 0 0 0.05
>>
>> #include "itkBinaryImageToLevelSetImageAdaptor.h"
>> #include "itkImageFileReader.h"
>> #include "itkLevelSetContainer.h"
>> #include "itkLevelSetEquationPropagationTerm.h"
>> #include "itkLevelSetEquationAdvectionTerm2.h"
>> #include "itkLevelSetEquationContainer.h"
>> #include "itkLevelSetEquationTermContainer.h"
>> #include "itkLevelSetEvolution.h"
>> #include "itkLevelSetEvolutionNumberOfIterationsStoppingCriterion.h"
>> #include "itkLevelSetDenseImage.h"
>> #include "itkVTKVisualizeImageLevelSetIsoValues.h"
>> #include "itkSinRegularizedHeavisideStepFunction.h"
>> #include "itkLevelSetIterationUpdateCommand.h"
>> #include "itkLevelSetEquationCurvatureTerm.h"
>> #include "itkCastImageFilter.h"
>> #include "itkWhitakerSparseLevelSetImage.h"
>> #include "itkSpatialObjectToImageFilter.h"
>> #include "itkEllipseSpatialObject.h"
>>
>> typedef itk::Image< float, 2 >  FIT;
>>
>> /*
>>  * L Shape
>>  */
>> void CreateSquareImage(FIT::Pointer image)
>> {
>>     FIT::RegionType region;
>>     FIT::IndexType start;
>>     start[0] = 0;
>>     start[1] = 0;
>>
>>     FIT::SizeType size;
>>     size[0] = 200;
>>     size[1] = 300;
>>
>>     region.SetSize(size);
>>     region.SetIndex(start);
>>
>>     image->SetRegions(region);
>>     image->Allocate();
>>
>>     // Set pixels in a square to one value
>>     for(unsigned int r = 20; r < 160; r++)
>>     {
>>         for(unsigned int c = 30; c < 100; c++)
>>         {
>>             FIT::IndexType pixelIndex;
>>             pixelIndex[0] = r;
>>             pixelIndex[1] = c;
>>
>>             image->SetPixel(pixelIndex, 255);
>>         }
>>     }
>>
>>     for(unsigned int r = 20; r < 80; r++)
>>     {
>>         for(unsigned int c = 100; c < 200; c++)
>>         {
>>             FIT::IndexType pixelIndex;
>>             pixelIndex[0] = r;
>>             pixelIndex[1] = c;
>>
>>             image->SetPixel(pixelIndex, 255);
>>         }
>>     }
>> }
>>
>>
>> /*
>>  */
>> int main( int argc, char* argv[] )
>> {
>>     if( argc != 5)
>>     {
>>         std::cerr << "Missing Arguments" << std::endl;
>>         std::cerr << argv[0] << std::endl;
>>         std::cerr << "1- Number of Iterations" << std::endl;
>>         std::cerr << "2- Propagation Term" << std::endl;
>>         std::cerr << "3- Advection Term" << std::endl;
>>         std::cerr << "4- Curvature Term" << std::endl;
>>         return EXIT_FAILURE;
>>     }
>>
>>     // Image Dimension
>>     const unsigned int Dimension = 2;
>>
>>     typedef unsigned char                            InputPixelType;
>>     typedef itk::Image< InputPixelType, Dimension >  IIT;
>>     typedef itk::Image< float, 2 >  FIT;
>>
>>     FIT::Pointer input = FIT::New();
>>     CreateSquareImage(input);
>>
>>     int numberOfIterations = atoi( argv[1]);
>>
>>     typedef float
>> LevelSetPixelType;
>>     typedef itk::Image< LevelSetPixelType, Dimension >    LSIT;
>>     typedef itk::LevelSetDenseImage< LSIT >  LST;
>>     //typedef itk::WhitakerSparseLevelSetImage< LevelSetPixelType, 2 >
>> LST;
>>
>>     typedef LST::OutputType                      LevelSetOutputType;
>>     typedef LST::OutputRealType                  LevelSetRealType;
>>
>>     // convert a binary mask to a level-set function
>>     typedef itk::BinaryImageToLevelSetImageAdaptor<FIT, LST >  BI2LST;
>>     BI2LST::Pointer adaptor = BI2LST::New();
>>      adaptor->SetInputImage( input );
>>     adaptor->Initialize();
>>     LST::Pointer levelSet = adaptor->GetLevelSet();
>>
>>     // The Heaviside function
>>     typedef itk::SinRegularizedHeavisideStepFunction< LevelSetRealType,
>> LevelSetRealType > HeavisideFunctionType;
>>     HeavisideFunctionType::Pointer heaviside =
>> HeavisideFunctionType::New();
>>     heaviside->SetEpsilon( 1 );
>>
>>     // Create the level set container
>>     typedef itk::LevelSetContainer< itk::IdentifierType, LST >
>> LSContainerT;
>>     LSContainerT::Pointer levelSetContainer = LSContainerT::New();
>>     levelSetContainer->SetHeaviside( heaviside );
>>     levelSetContainer->AddLevelSet( 0, levelSet );
>>
>>     // Create the terms.
>>     typedef itk::LevelSetEquationPropagationTerm<FIT, LSContainerT>
>>  PropagationTermType;
>>     PropagationTermType::Pointer propagationTerm =
>> PropagationTermType::New();
>>     propagationTerm->SetInput(input);
>>     propagationTerm->SetCoefficient(atof(argv[2]));
>>
>>     typedef itk::LevelSetEquationAdvectionTerm2<FIT, LSContainerT>
>>  AdvectionTermType;
>>     AdvectionTermType::Pointer advectionTerm = AdvectionTermType::New();
>>     advectionTerm->SetInput(input);
>>     advectionTerm->SetCoefficient(atof(argv[3]));
>>
>>     typedef itk::LevelSetEquationCurvatureTerm<FIT, LSContainerT>
>>  CurvatureTermType;
>>     CurvatureTermType::Pointer curvatureTerm = CurvatureTermType::New();
>>     //curvatureTerm->SetInput(input);
>>     curvatureTerm->SetCoefficient(atof(argv[4]));
>>
>>
>>     // Create term container (equation rhs)
>>     typedef itk::LevelSetEquationTermContainer< FIT, LSContainerT >
>> TermContainerType;
>>     TermContainerType::Pointer termContainer = TermContainerType::New();
>>     termContainer->SetLevelSetContainer( levelSetContainer );
>>     termContainer->SetInput( input );
>>     //termContainer->AddTerm( 0, propagationTerm );
>>     //termContainer->AddTerm( 1, advectionTerm );
>>     termContainer->AddTerm( 0, curvatureTerm );
>>
>>     // Create equation container
>>     typedef itk::LevelSetEquationContainer< TermContainerType >
>> EquationContainerType;
>>      EquationContainerType::Pointer equationContainer =
>> EquationContainerType::New();
>>     equationContainer->SetLevelSetContainer( levelSetContainer );
>>     equationContainer->AddEquation( 0, termContainer );
>>
>>     // Create stopping criteria
>>     typedef itk::LevelSetEvolutionNumberOfIterationsStoppingCriterion<
>> LSContainerT > StoppingCriterionType;
>>     StoppingCriterionType::Pointer criterion =
>> StoppingCriterionType::New();
>>     criterion->SetNumberOfIterations( numberOfIterations );
>>
>>     // Create the visualizer
>>     typedef itk::VTKVisualizeImageLevelSetIsoValues< FIT, LST >
>> VisualizationType;
>>     VisualizationType::Pointer visualizer = VisualizationType::New();
>>     visualizer->SetInputImage( input );
>>     visualizer->SetLevelSet( levelSet );
>>     visualizer->SetScreenCapture( true );
>>
>>     // Create evolution class
>>     typedef itk::LevelSetEvolution< EquationContainerType, LST >
>> LevelSetEvolutionType;
>>     LevelSetEvolutionType::Pointer evolution =
>> LevelSetEvolutionType::New();
>>     evolution->SetEquationContainer( equationContainer );
>>     evolution->SetStoppingCriterion( criterion );
>>     evolution->SetLevelSetContainer( levelSetContainer );
>>
>>      typedef itk::LevelSetIterationUpdateCommand< LevelSetEvolutionType,
>> VisualizationType > IterationUpdateCommandType;
>>     IterationUpdateCommandType::Pointer iterationUpdateCommand =
>> IterationUpdateCommandType::New();
>>     iterationUpdateCommand->SetFilterToUpdate( visualizer );
>>     iterationUpdateCommand->SetUpdatePeriod( 1 );
>>
>>     evolution->AddObserver( itk::IterationEvent(), iterationUpdateCommand
>> );
>>
>>     evolution->Update();
>>
>>     return EXIT_SUCCESS;
>> }
>>
>>
>>
>> cmake_minimum_required(VERSION 2.8)
>>
>>  project(CurvatureMotion)
>>
>> find_package(ITK REQUIRED)
>> include(${ITK_USE_FILE})
>>
>> find_package(VTK REQUIRED)
>> include(${VTK_USE_FILE})
>>
>> add_executable(Motion main.cpp)
>> target_link_libraries(Motion ${ITK_LIBRARIES}  ${VTK_LIBRARIES})
>>
>> [image: Inline image 4][image: Inline image 3]
>>  --
>> Cemal Cagatay Bilgin, PhD
>> Life Sciences Division
>> Lawrence Berkeley National Lab
>> MS977, One Cyclotron Road
>> Berkeley, CA 94720, USA
>> Email: ccbilgin at lbl.gov
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>


-- 
Cemal Cagatay Bilgin, PhD
Life Sciences Division
Lawrence Berkeley National Lab
MS977, One Cyclotron Road
Berkeley, CA 94720, USA
Email: ccbilgin at lbl.gov
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From bilgincc at gmail.com  Mon Sep 15 11:53:06 2014
From: bilgincc at gmail.com (Cagatay Bilgin)
Date: Mon, 15 Sep 2014 08:53:06 -0700
Subject: [ITK-users] Different output with dense and sparse level set
	representations
In-Reply-To: <CAHoiV3aK+kG_EM=6XPBOH2jOCo+dvHvCHovKNH7i0U7cNtBKTQ@mail.gmail.com>
References: <CAHoiV3aK+kG_EM=6XPBOH2jOCo+dvHvCHovKNH7i0U7cNtBKTQ@mail.gmail.com>
Message-ID: <CAHoiV3bjbhudehnwKwqTzyNCQ70nhHZxo0ANCkibVUgyVuQrTA@mail.gmail.com>

Arnaud, should I also try this with the old framework? This really looks
like a bug to me regardless of the framework used.

Best,
Cagatay Bilgin

On Thu, Aug 21, 2014 at 10:33 AM, Cagatay Bilgin <bilgincc at gmail.com> wrote:

> Hello everybody,
>
> I continue with my exploration of the new level set framework. I have
> modified one of the examples and have an advection field in the positive x
> direction. I would expect the initial contour to move in that direction and
> that's the case with the sparse representation. Using the dense
> representation however, only half of the contour moves to my surprise. Is
> this a bug or I am missing something here. Here is the code and the cmake
> file and snapshots of the movements.
>
> [image: Inline image 2][image: Inline image 1]
>
>
> #include "itkBinaryImageToLevelSetImageAdaptor.h"
> #include "itkLevelSetContainer.h"
> #include "itkLevelSetEquationPropagationTerm.h"
> #include "itkLevelSetEquationAdvectionTerm.h"
> #include "itkLevelSetEquationContainer.h"
> #include "itkLevelSetEquationTermContainer.h"
> #include "itkLevelSetEvolution.h"
> #include "itkLevelSetEvolutionNumberOfIterationsStoppingCriterion.h"
> #include "itkLevelSetDenseImage.h"
> #include "itkVTKVisualizeImageLevelSetIsoValues.h"
> #include "itkSinRegularizedHeavisideStepFunction.h"
> #include "itkLevelSetIterationUpdateCommand.h"
> #include "itkLevelSetEquationCurvatureTerm.h"
> #include "itkWhitakerSparseLevelSetImage.h"
> #include "itkLevelSetSparseImage.h"
>
> typedef itk::Image< float, 2 >  FIT;
>
> void CreateSquareImage(FIT::Pointer image, FIT::Pointer prop, FIT::Pointer
> advec)
> {
>     FIT::RegionType region;
>     FIT::IndexType start;
>     start[0] = 0;
>     start[1] = 0;
>
>     FIT::SizeType size;
>     size[0] = 100;
>     size[1] = 100;
>
>     region.SetSize(size);
>     region.SetIndex(start);
>
>     image->SetRegions(region);
>     image->Allocate();
>     image->FillBuffer(0);
>
>     //constant grow in all directions
>     prop->SetRegions(image->GetLargestPossibleRegion());
>     prop->Allocate();
>     prop->FillBuffer(1);
>
>     //advec will increase in positive x direction
>     advec->SetRegions(image->GetLargestPossibleRegion());
>     advec->Allocate();
>     advec->FillBuffer(0);
>
>     // Set pixels in a square to one value
>     for(unsigned int x = 35; x < 65; x++){
>         for(unsigned int y = 35; y < 65; y++){
>             FIT::IndexType pixelIndex;
>             pixelIndex[0] = x;
>             pixelIndex[1] = y;
>
>             image->SetPixel(pixelIndex, 255);
>         }
>     }
>
>     //advection in positive x direction
>     for(unsigned int x = 0; x < 100; x++){
>         for(unsigned int y = 0; y < 100; y++){
>             FIT::IndexType pixelIndex;
>             pixelIndex[0] = x;
>             pixelIndex[1] = y;
>
>             advec->SetPixel(pixelIndex, x);
>         }
>     }
> }
>
>
> /*
>  */
> int main(int argc, char* argv[] )
> {
>     using namespace itk;
>     if(argc != 5)
>     {
>         std::cerr << "Missing Arguments" << std::endl;
>         std::cerr << argv[0] << std::endl;
>         std::cerr << "1- Number of Iterations" << std::endl;
>         std::cerr << "2- Propagation Term" << std::endl;
>         std::cerr << "3- Advection Term" << std::endl;
>         std::cerr << "4- Curvature Term" << std::endl;
>         return EXIT_FAILURE;
>     }
>
>     FIT::Pointer input = FIT::New();
>     FIT::Pointer prop  = FIT::New();
>     FIT::Pointer advec  = FIT::New();
>
>     CreateSquareImage(input, prop, advec);
>
>     int numberOfIterations = atoi(argv[1]);
>
>     typedef float LSPT;
>     typedef Image< LSPT, 2 >    LSIT;
>     typedef LevelSetDenseImage< LSIT >  LST;
>     //typedef WhitakerSparseLevelSetImage< LSPT, 2 > LST;
>
>     typedef LST::OutputRealType  LSOutputT;
>
>     // convert a binary mask to a level-set function
>     typedef BinaryImageToLevelSetImageAdaptor<FIT, LST >  BI2LST;
>     BI2LST::Pointer adaptor = BI2LST::New();
>     adaptor->SetInputImage(input );
>     adaptor->Initialize();
>     LST::Pointer levelSet = adaptor->GetLevelSet();
>
>     // The Heaviside function
>     typedef SinRegularizedHeavisideStepFunction<LSOutputT, LSOutputT>
> HeavisideFunctionType;
>     HeavisideFunctionType::Pointer heaviside =
> HeavisideFunctionType::New();
>     heaviside->SetEpsilon(1 );
>
>     // Create the level set container
>     typedef LevelSetContainer< IdentifierType, LST > LSContainerT;
>     LSContainerT::Pointer levelSetContainer = LSContainerT::New();
>     levelSetContainer->SetHeaviside(heaviside );
>     levelSetContainer->AddLevelSet(0, levelSet );
>
>     // Create the terms.
>     typedef LevelSetEquationPropagationTerm<FIT, LSContainerT>  PropT;
>     PropT::Pointer propagationTerm = PropT::New();
>     propagationTerm->SetInput(prop);
>     propagationTerm->SetCoefficient(atof(argv[2]));
>
>     typedef LevelSetEquationAdvectionTerm<FIT, LSContainerT>  AdvecT;
>     AdvecT::Pointer advectionTerm = AdvecT::New();
>     advectionTerm->SetInput(advec);
>     advectionTerm->SetCoefficient(atof(argv[3]));
>
>     typedef LevelSetEquationCurvatureTerm<FIT, LSContainerT>  CurvT;
>     CurvT::Pointer curvatureTerm = CurvT::New();
>     curvatureTerm->SetCoefficient(atof(argv[4]));
>
>     // Create term container (equation rhs)
>     typedef LevelSetEquationTermContainer< FIT, LSContainerT >
> TermContainerT;
>     TermContainerT::Pointer termContainer = TermContainerT::New();
>     termContainer->SetLevelSetContainer(levelSetContainer );
>     termContainer->SetInput(input );
>     termContainer->AddTerm(0, curvatureTerm );
>     termContainer->AddTerm(1, advectionTerm );
>     termContainer->AddTerm(2, propagationTerm );
>
>     // Create equation container
>     typedef LevelSetEquationContainer< TermContainerT >
> EquationContainerType;
>     EquationContainerType::Pointer equationContainer =
> EquationContainerType::New();
>     equationContainer->SetLevelSetContainer(levelSetContainer );
>     equationContainer->AddEquation(0, termContainer );
>
>     // Create stopping criteria
>     typedef LevelSetEvolutionNumberOfIterationsStoppingCriterion<
> LSContainerT > StoppingCriterionType;
>     StoppingCriterionType::Pointer criterion =
> StoppingCriterionType::New();
>     criterion->SetNumberOfIterations(numberOfIterations );
>
>     // Create the visualizer
>     typedef VTKVisualizeImageLevelSetIsoValues< FIT, LST > VisT;
>     VisT::Pointer visualizer = VisT::New();
>     visualizer->SetInputImage(input );
>     visualizer->SetLevelSet(levelSet );
>     visualizer->SetScreenCapture(true );
>
>     // Create evolution class
>     typedef LevelSetEvolution< EquationContainerType, LST > LSEvolT;
>     LSEvolT::Pointer evolution = LSEvolT::New();
>     evolution->SetEquationContainer(equationContainer );
>     evolution->SetStoppingCriterion(criterion );
>     evolution->SetLevelSetContainer(levelSetContainer );
>
>     typedef LevelSetIterationUpdateCommand< LSEvolT, VisT >
> IterationUpdateCommandType;
>     IterationUpdateCommandType::Pointer iterationUpdateCommand =
> IterationUpdateCommandType::New();
>     iterationUpdateCommand->SetFilterToUpdate(visualizer );
>     iterationUpdateCommand->SetUpdatePeriod(1 );
>
>     evolution->AddObserver(IterationEvent(), iterationUpdateCommand );
>     evolution->Update();
>
>     return EXIT_SUCCESS;
> }
>
>
> cmake_minimum_required(VERSION 2.8)
> project(Motion)
>
> find_package(ITK REQUIRED)
> include(${ITK_USE_FILE})
>
> find_package(VTK REQUIRED)
> include(${VTK_USE_FILE})
>
> add_executable(Motion main.cpp)
> target_link_libraries(Motion ${ITK_LIBRARIES}  ${VTK_LIBRARIES})
>
> Params used for the experiment:
> Ran sparse representation with
> ./Motion 15 0 1 1
>
> Ran dense representation with
> ./Motion 15 0 1 0
>
>
> Cemal Cagatay Bilgin, PhD
> Life Sciences Division
> Lawrence Berkeley National Lab
> MS977, One Cyclotron Road
> Berkeley, CA 94720, USA
> Email: ccbilgin at lbl.gov
>



-- 
Cemal Cagatay Bilgin, PhD
Life Sciences Division
Lawrence Berkeley National Lab
MS977, One Cyclotron Road
Berkeley, CA 94720, USA
Email: ccbilgin at lbl.gov
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From joel.schaerer at laposte.net  Tue Sep 16 10:27:01 2014
From: joel.schaerer at laposte.net (=?UTF-8?B?Sm/Dq2wgU2NoYWVyZXI=?=)
Date: Tue, 16 Sep 2014 16:27:01 +0200
Subject: [ITK-users] Insight Journal template ITKv4 compatibilty
Message-ID: <541848B5.9060901@laposte.net>

Hi all,

The template for Insight Journal submissions that is available on GitHub 
and recommended on the Insight Journal website 
(https://github.com/InsightSoftwareConsortium/InsightJournalTemplate) 
does not build with ITK4.

I can try to fix it, but before I do I would like to make sure it is 
still the current version?

Thanks!

Jo?l

From yxp233 at postech.ac.kr  Tue Sep 16 10:37:18 2014
From: yxp233 at postech.ac.kr (Xiaopeng Yang)
Date: Tue, 16 Sep 2014 23:37:18 +0900
Subject: [ITK-users] Compiling ITK 4.6.0 error
In-Reply-To: <1410796270474129.115529.ptmail04@ptmail04>
References: <CAHoiV3ZGmbX7XT6ymjaeL0VLgQRtUR1=vcmdVcm6-7VEWh+LEQ@mail.gmail.com>
 <CAK3qF+_-3wsSVPNmutDzg6Dy=ME=APJZm_t7yPVHo4tpc_Ce7A@mail.gmail.com>
 <1410796270474129.115529.ptmail04@ptmail04>
Message-ID: <024f01cfd1bb$b7c4a0c0$274de240$@ac.kr>

Dear Users,

 

I was trying to compile ITK 4.6.0 with MSVS 2010 with GPU enabled, but I got the following error:

 

Found OpenCL: C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v6.5\lib 

CMake Error at C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:304 (set):
Syntax error in cmake code at

C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:304

when parsing string

D:\Toolbox\ITK-4.6.0

Invalid escape sequence \T
Call Stack (most recent call first):
C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:516 (cpack_set_if_not_set)
CMake/ITKModuleEnablement.cmake:171 (include)
CMakeLists.txt:322 (include)

Configuring incomplete, errors occurred!

See also "D:/Toolbox/ITK-4.6.0/bin/CMakeFiles/CMakeOutput.log".

See also "D:/Toolbox/ITK-4.6.0/bin/CMakeFiles/CMakeError.log".

 

Could anyone tell me what caused this error? Thank you.

 

Best regards,

Xiaopeng

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From matt.mccormick at kitware.com  Tue Sep 16 13:26:17 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 16 Sep 2014 13:26:17 -0400
Subject: [ITK-users] Insight Journal template ITKv4 compatibilty
In-Reply-To: <541848B5.9060901@laposte.net>
References: <541848B5.9060901@laposte.net>
Message-ID: <CALzTN-R5pbYay1MQ8nQ6OBGMDow02FRe37m-bGdwXd-CmHc+mA@mail.gmail.com>

Hi Jo?l,

Yes, that the current best repository, and fixes are welcome!  Please
add a pull request on the repository and ping the mailing list if it
is not merged after a few days.

Thanks,
Matt

On Tue, Sep 16, 2014 at 10:27 AM, Jo?l Schaerer
<joel.schaerer at laposte.net> wrote:
> Hi all,
>
> The template for Insight Journal submissions that is available on GitHub and
> recommended on the Insight Journal website
> (https://github.com/InsightSoftwareConsortium/InsightJournalTemplate) does
> not build with ITK4.
>
> I can try to fix it, but before I do I would like to make sure it is still
> the current version?
>
> Thanks!
>
> Jo?l
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

From daviddoria at gmail.com  Tue Sep 16 14:01:46 2014
From: daviddoria at gmail.com (David Doria)
Date: Tue, 16 Sep 2014 14:01:46 -0400
Subject: [ITK-users] Insight Journal template ITKv4 compatibilty
In-Reply-To: <CALzTN-R5pbYay1MQ8nQ6OBGMDow02FRe37m-bGdwXd-CmHc+mA@mail.gmail.com>
References: <541848B5.9060901@laposte.net>
 <CALzTN-R5pbYay1MQ8nQ6OBGMDow02FRe37m-bGdwXd-CmHc+mA@mail.gmail.com>
Message-ID: <CABDpjTn7HyiW23KdEjr3byXVjXK1_7e4f7TU1o_TNYLPEYhCPw@mail.gmail.com>

On Tue, Sep 16, 2014 at 1:26 PM, Matt McCormick <matt.mccormick at kitware.com>
wrote:

> Hi Jo?l,
>
> Yes, that the current best repository, and fixes are welcome!  Please
> add a pull request on the repository and ping the mailing list if it
> is not merged after a few days.
>
> Thanks,
> Matt
>

I found an email from Hans from almost 2 years ago where it looks like he
fixed the compatibility problems here:
https://github.com/BRAINSia/LogSymmetricDemons

I had fixed a few things in the same thread as well:
http://public.kitware.com/pipermail/insight-developers/2012-December/022304.html

Both might be worth a look.

David
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From yxp233 at postech.ac.kr  Tue Sep 16 20:19:21 2014
From: yxp233 at postech.ac.kr (Xiaopeng Yang)
Date: Wed, 17 Sep 2014 09:19:21 +0900
Subject: [ITK-users] Any instruction of compiling ITK with GPU support
In-Reply-To: <1410878838500935.032749.ptmail04@ptmail04>
References: <CAHoiV3ZGmbX7XT6ymjaeL0VLgQRtUR1=vcmdVcm6-7VEWh+LEQ@mail.gmail.com>
 <CAK3qF+_-3wsSVPNmutDzg6Dy=ME=APJZm_t7yPVHo4tpc_Ce7A@mail.gmail.com>
 <1410796270474129.115529.ptmail04@ptmail04>
 <1410878838500935.032749.ptmail04@ptmail04>
Message-ID: <02a501cfd20d$079448c0$16bcda40$@ac.kr>

Hello,

 

Is there any detailed instructions of how to compile ITK with GPU module on? I had a hard time to get it work properly. Any information or help is appreciated. 

 

Thanks,

Xiaopeng

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From arnaudgelas at gmail.com  Wed Sep 17 09:02:21 2014
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Wed, 17 Sep 2014 15:02:21 +0200
Subject: [ITK-users] question about wiki example ResampleDICOM
Message-ID: <C83078BB-3646-40C7-ABFA-DBB4BA55435F@gmail.com>

Hi all,

I have been looking at the following wiki example:

	http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM

It seems to me that the section to rescale the image is not valid anymore with latest ITK version (?)

	https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333

Can anyone confirm?

Is this code validated? are output images compared to input ones in the corresponding test?

Thanks
Arnaud
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From arnaudgelas at gmail.com  Wed Sep 17 09:04:17 2014
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Wed, 17 Sep 2014 15:04:17 +0200
Subject: [ITK-users] question about wiki example ResampleDICOM
In-Reply-To: <75058210-3021-4372-A59C-8880B69CABED@gmail.com>
References: <C83078BB-3646-40C7-ABFA-DBB4BA55435F@gmail.com>
 <582F5FDC-3091-4EB9-B8A3-E11B80DCFF4B@gmail.com>
 <75058210-3021-4372-A59C-8880B69CABED@gmail.com>
Message-ID: <CAK3qF+_B5PEYVJsn2QAJUBqz8vg0cBkRVjDs4E73sVSM87y7fw@mail.gmail.com>

Hi Nick,

I work with CT images, Rescale Intercept / Slope: ( -1024, 1 )

I use system gdcm (release branch from official git repository)

Thanks
Arnaud

On Wed, Sep 17, 2014 at 3:01 PM, Nick Patterson <pattersonnp.work at gmail.com>
wrote:

> Arnauld,
>
>  Can you also say if you are using the version of GDCM bundled with ITK
> release or have you compiled a system version of GDCM from the
> git-repository?
>
> Nick.
>
>
> On 17 Sep 2014, at 13:59, Nick Patterson <pattersonnp.work at gmail.com>
> wrote:
>
> Arnauld,
>
> Which modality image are you working with, and what are the rescale slope
> and intercept of the original image?
>
> Nick.
>
>
>
>
> On 17 Sep 2014, at 14:02, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>
> Hi all,
>
> I have been looking at the following wiki example:
>
> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM
>
> It seems to me that the section to rescale the image is not valid anymore
> with latest ITK version (?)
>
>
> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333
>
> Can anyone confirm?
>
> Is this code validated? are output images compared to input ones in the
> corresponding test?
>
> Thanks
> Arnaud
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
>
>
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From arnaudgelas at gmail.com  Wed Sep 17 09:10:43 2014
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Wed, 17 Sep 2014 15:10:43 +0200
Subject: [ITK-users] question about wiki example ResampleDICOM
In-Reply-To: <B44044E0-7C64-41C0-8E8E-7DB61F7AFF95@gmail.com>
References: <C83078BB-3646-40C7-ABFA-DBB4BA55435F@gmail.com>
 <582F5FDC-3091-4EB9-B8A3-E11B80DCFF4B@gmail.com>
 <75058210-3021-4372-A59C-8880B69CABED@gmail.com>
 <CAK3qF+_B5PEYVJsn2QAJUBqz8vg0cBkRVjDs4E73sVSM87y7fw@mail.gmail.com>
 <B44044E0-7C64-41C0-8E8E-7DB61F7AFF95@gmail.com>
Message-ID: <CAK3qF+9K-jfU6C=YL-jKDJZFZHB41XhbxGwwLn8sKhY-nVRQHg@mail.gmail.com>

I have been modifying extensively this example...
Rescale slope/intercept are saved with expected values -1024 and 1.

Not sure if the error is in my code or in this example, but when I compare
inputs and outputs with the ShiftScale part all pixels are different (and
the difference is -1024)... that's why I am asking if this part is still
valid?

On Wed, Sep 17, 2014 at 3:06 PM, Nick Patterson <pattersonnp.work at gmail.com>
wrote:

> Ok thanks. When you say that it doesn?t work anymore would I be correct in
> assuming that you mean that the output rescale slope/intercept are written
> out as 1 and 0, rather than the expected value of -1024 and 1? Or do you
> mean not working in some other way?
>
> Nick.
>
>
>
> On 17 Sep 2014, at 14:04, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>
> Hi Nick,
>
> I work with CT images, Rescale Intercept / Slope: ( -1024, 1 )
>
> I use system gdcm (release branch from official git repository)
>
> Thanks
> Arnaud
>
> On Wed, Sep 17, 2014 at 3:01 PM, Nick Patterson <
> pattersonnp.work at gmail.com> wrote:
>
>> Arnauld,
>>
>>  Can you also say if you are using the version of GDCM bundled with ITK
>> release or have you compiled a system version of GDCM from the
>> git-repository?
>>
>> Nick.
>>
>>
>> On 17 Sep 2014, at 13:59, Nick Patterson <pattersonnp.work at gmail.com>
>> wrote:
>>
>> Arnauld,
>>
>> Which modality image are you working with, and what are the rescale slope
>> and intercept of the original image?
>>
>> Nick.
>>
>>
>>
>>
>> On 17 Sep 2014, at 14:02, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>>
>> Hi all,
>>
>> I have been looking at the following wiki example:
>>
>> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM
>>
>> It seems to me that the section to rescale the image is not valid anymore
>> with latest ITK version (?)
>>
>>
>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333
>>
>> Can anyone confirm?
>>
>> Is this code validated? are output images compared to input ones in the
>> corresponding test?
>>
>> Thanks
>> Arnaud
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>>
>>
>
>
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From blowekamp at mail.nih.gov  Wed Sep 17 09:13:12 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Wed, 17 Sep 2014 09:13:12 -0400
Subject: [ITK-users] question about wiki example ResampleDICOM
In-Reply-To: <C83078BB-3646-40C7-ABFA-DBB4BA55435F@gmail.com>
References: <C83078BB-3646-40C7-ABFA-DBB4BA55435F@gmail.com>
Message-ID: <7723535C-1110-4A62-BF59-EA02980C2E86@mail.nih.gov>

Arnaud,

If using shared libraries causes the dynamic cast to fail, than this may be a side effect of some recent changes [1].

Brad

[1] https://github.com/InsightSoftwareConsortium/ITK/commits/master/Modules/Core/Common/include/itkMetaDataObject.h

On Sep 17, 2014, at 9:02 AM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:

> Hi all,
> 
> I have been looking at the following wiki example:
> 
> 	http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM
> 
> It seems to me that the section to rescale the image is not valid anymore with latest ITK version (?)
> 
> 	https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333
> 
> Can anyone confirm?
> 
> Is this code validated? are output images compared to input ones in the corresponding test?
> 
> Thanks
> Arnaud
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

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From matimontg at gmail.com  Wed Sep 17 09:21:09 2014
From: matimontg at gmail.com (Matias Montroull)
Date: Wed, 17 Sep 2014 10:21:09 -0300
Subject: [ITK-users] question about wiki example ResampleDICOM
In-Reply-To: <C83078BB-3646-40C7-ABFA-DBB4BA55435F@gmail.com>
References: <C83078BB-3646-40C7-ABFA-DBB4BA55435F@gmail.com>
Message-ID: <CAKKNfuLiXhqQEP950jf4XhFj8KA-ge1BtFPDNa8iHdQRLfQv2A@mail.gmail.com>

I had an issue with the resampledicom example once (all my pixel values
were recalculated by adding rescaleintercept) and then downloaded the
latest ITK release (4.6) and worked fine.

The issue was with the GDCMIO class I beleive but was fixed somehow in the
4.6 version.

On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas <arnaudgelas at gmail.com>
wrote:

> Hi all,
>
> I have been looking at the following wiki example:
>
> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM
>
> It seems to me that the section to rescale the image is not valid anymore
> with latest ITK version (?)
>
>
> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333
>
> Can anyone confirm?
>
> Is this code validated? are output images compared to input ones in the
> corresponding test?
>
> Thanks
> Arnaud
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
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From yxp233 at postech.ac.kr  Wed Sep 17 09:23:50 2014
From: yxp233 at postech.ac.kr (Xiaopeng Yang)
Date: Wed, 17 Sep 2014 22:23:50 +0900
Subject: [ITK-users] Any instruction of compiling ITK with GPU support
In-Reply-To: <1410913163921868.021894.ptmail04@ptmail04>
References: <CAHoiV3ZGmbX7XT6ymjaeL0VLgQRtUR1=vcmdVcm6-7VEWh+LEQ@mail.gmail.com>
 <CAK3qF+_-3wsSVPNmutDzg6Dy=ME=APJZm_t7yPVHo4tpc_Ce7A@mail.gmail.com>
 <1410796270474129.115529.ptmail04@ptmail04>
 <1410878838500935.032749.ptmail04@ptmail04>
 <1410913163921868.021894.ptmail04@ptmail04>
Message-ID: <000c01cfd27a$9ed25020$dc76f060$@ac.kr>

By the way, I tried to compile ITK 4.6.0 with Visual Studio 2010, under windows 7 64 bit. I set USE_GPU on, but I got the error as follows:

 

Found OpenCL: C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v6.5\lib 

CMake Error at C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:304 (set):
Syntax error in cmake code at

C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:304

when parsing string

D:\Toolbox\ITK-4.6.0

Invalid escape sequence \T
Call Stack (most recent call first):
C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:516 (cpack_set_if_not_set)
CMake/ITKModuleEnablement.cmake:171 (include)
CMakeLists.txt:322 (include)

Configuring incomplete, errors occurred!

See also "D:/Toolbox/ITK-4.6.0/bin/CMakeFiles/CMakeOutput.log".

See also "D:/Toolbox/ITK-4.6.0/bin/CMakeFiles/CMakeError.log".

 

 

From: Insight-users [mailto:insight-users-bounces at itk.org] On Behalf Of Xiaopeng Yang
Sent: Wednesday, September 17, 2014 9:19 AM
To: 'insight-users'
Subject: [ITK-users] Any instruction of compiling ITK with GPU support

 

Hello,

 

Is there any detailed instructions of how to compile ITK with GPU module on? I had a hard time to get it work properly. Any information or help is appreciated. 

 

Thanks,

Xiaopeng

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From pattersonnp.work at gmail.com  Wed Sep 17 09:25:00 2014
From: pattersonnp.work at gmail.com (Nick Patterson)
Date: Wed, 17 Sep 2014 14:25:00 +0100
Subject: [ITK-users] question about wiki example ResampleDICOM
In-Reply-To: <7182E410-B1F7-4D3E-A5C9-B279A22468C7@gmail.com>
References: <C83078BB-3646-40C7-ABFA-DBB4BA55435F@gmail.com>
 <582F5FDC-3091-4EB9-B8A3-E11B80DCFF4B@gmail.com>
 <75058210-3021-4372-A59C-8880B69CABED@gmail.com>
 <CAK3qF+_B5PEYVJsn2QAJUBqz8vg0cBkRVjDs4E73sVSM87y7fw@mail.gmail.com>
 <B44044E0-7C64-41C0-8E8E-7DB61F7AFF95@gmail.com>
 <CAK3qF+9K-jfU6C=YL-jKDJZFZHB41XhbxGwwLn8sKhY-nVRQHg@mail.gmail.com>
 <F5FA2E64-CDFC-43AE-85A0-6AF74E007DBF@gmail.com>
 <7182E410-B1F7-4D3E-A5C9-B279A22468C7@gmail.com>
Message-ID: <EDB2DA4C-A389-42CF-8606-6099A22A64C4@gmail.com>


Ok thanks, 


I have had various issues with this examples before. If you can re-test your CT images with the unmodified ResampleDICOM example and let me know the results. If you see the same problem, get back to me.

Nick.

From arnaudgelas at gmail.com  Wed Sep 17 09:32:08 2014
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Wed, 17 Sep 2014 15:32:08 +0200
Subject: [ITK-users] question about wiki example ResampleDICOM
In-Reply-To: <CAKKNfuLiXhqQEP950jf4XhFj8KA-ge1BtFPDNa8iHdQRLfQv2A@mail.gmail.com>
References: <C83078BB-3646-40C7-ABFA-DBB4BA55435F@gmail.com>
 <CAKKNfuLiXhqQEP950jf4XhFj8KA-ge1BtFPDNa8iHdQRLfQv2A@mail.gmail.com>
Message-ID: <A903CE9B-1D91-494B-84BF-C3ADBDC858B7@gmail.com>

Hi Matias,

I guess you are referring to 

	https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e

$ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e
v4.6.0

I use the release branch of ITK

---

Matt,

Can you comment on this, please?

Thanks
Arnaud

On Sep 17, 2014, at 3:21 PM, Matias Montroull <matimontg at gmail.com> wrote:

> I had an issue with the resampledicom example once (all my pixel values were recalculated by adding rescaleintercept) and then downloaded the latest ITK release (4.6) and worked fine.
> 
> The issue was with the GDCMIO class I beleive but was fixed somehow in the 4.6 version.
> 
> On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
> Hi all,
> 
> I have been looking at the following wiki example:
> 
> 	http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM
> 
> It seems to me that the section to rescale the image is not valid anymore with latest ITK version (?)
> 
> 	https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333
> 
> Can anyone confirm?
> 
> Is this code validated? are output images compared to input ones in the corresponding test?
> 
> Thanks
> Arnaud
> 
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
> 
> 

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From matimontg at gmail.com  Wed Sep 17 09:27:44 2014
From: matimontg at gmail.com (Matias Montroull)
Date: Wed, 17 Sep 2014 10:27:44 -0300
Subject: [ITK-users] question about wiki example ResampleDICOM
In-Reply-To: <EDB2DA4C-A389-42CF-8606-6099A22A64C4@gmail.com>
References: <C83078BB-3646-40C7-ABFA-DBB4BA55435F@gmail.com>
 <582F5FDC-3091-4EB9-B8A3-E11B80DCFF4B@gmail.com>
 <75058210-3021-4372-A59C-8880B69CABED@gmail.com>
 <CAK3qF+_B5PEYVJsn2QAJUBqz8vg0cBkRVjDs4E73sVSM87y7fw@mail.gmail.com>
 <B44044E0-7C64-41C0-8E8E-7DB61F7AFF95@gmail.com>
 <CAK3qF+9K-jfU6C=YL-jKDJZFZHB41XhbxGwwLn8sKhY-nVRQHg@mail.gmail.com>
 <F5FA2E64-CDFC-43AE-85A0-6AF74E007DBF@gmail.com>
 <7182E410-B1F7-4D3E-A5C9-B279A22468C7@gmail.com>
 <EDB2DA4C-A389-42CF-8606-6099A22A64C4@gmail.com>
Message-ID: <CAKKNfuLks_B55sjc2FtQtKQ=a2KoShpFpnrLVNTa9fyQL8fwLg@mail.gmail.com>

Nick, what do you mean by "the unmodified resampleDICOM"?
thanks,

On Wed, Sep 17, 2014 at 10:25 AM, Nick Patterson <pattersonnp.work at gmail.com
> wrote:

>
> Ok thanks,
>
>
> I have had various issues with this examples before. If you can re-test
> your CT images with the unmodified ResampleDICOM example and let me know
> the results. If you see the same problem, get back to me.
>
> Nick.
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
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From chinander at gmail.com  Wed Sep 17 09:28:45 2014
From: chinander at gmail.com (Mike Chinander)
Date: Wed, 17 Sep 2014 08:28:45 -0500
Subject: [ITK-users] Any instruction of compiling ITK with GPU support
In-Reply-To: <000c01cfd27a$9ed25020$dc76f060$@ac.kr>
References: <CAHoiV3ZGmbX7XT6ymjaeL0VLgQRtUR1=vcmdVcm6-7VEWh+LEQ@mail.gmail.com>
 <CAK3qF+_-3wsSVPNmutDzg6Dy=ME=APJZm_t7yPVHo4tpc_Ce7A@mail.gmail.com>
 <1410796270474129.115529.ptmail04@ptmail04>
 <1410878838500935.032749.ptmail04@ptmail04>
 <1410913163921868.021894.ptmail04@ptmail04>
 <000c01cfd27a$9ed25020$dc76f060$@ac.kr>
Message-ID: <CAEb_q0dbn3uOAqoNxU6XZvVdy-rJ57X+Z7Psi=-Y0HfstodRtA@mail.gmail.com>

Did you manually set the path "D:\Toolbox\ITK-4.6.0" somewhere? Try it with
forward slashes instead, "D:/Toolbox/ITK-4.6.0"

On Wed, Sep 17, 2014 at 8:23 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:

> By the way, I tried to compile ITK 4.6.0 with Visual Studio 2010, under
> windows 7 64 bit. I set USE_GPU on, but I got the error as follows:
>
>
>
> Found OpenCL: C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v6.5\lib
>
> CMake Error at C:/Program Files
> (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:304 (set):
> Syntax error in cmake code at
>
> C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:304
>
> when parsing string
>
> D:\Toolbox\ITK-4.6.0
>
> Invalid escape sequence \T
> Call Stack (most recent call first):
> C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:516
> (cpack_set_if_not_set)
> CMake/ITKModuleEnablement.cmake:171 (include)
> CMakeLists.txt:322 (include)
>
> Configuring incomplete, errors occurred!
>
> See also "D:/Toolbox/ITK-4.6.0/bin/CMakeFiles/CMakeOutput.log".
>
> See also "D:/Toolbox/ITK-4.6.0/bin/CMakeFiles/CMakeError.log".
>
>
>
>
>
>
>
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From pattersonnp.work at gmail.com  Wed Sep 17 09:29:04 2014
From: pattersonnp.work at gmail.com (Nick Patterson)
Date: Wed, 17 Sep 2014 14:29:04 +0100
Subject: [ITK-users] question about wiki example ResampleDICOM
In-Reply-To: <A903CE9B-1D91-494B-84BF-C3ADBDC858B7@gmail.com>
References: <C83078BB-3646-40C7-ABFA-DBB4BA55435F@gmail.com>
 <CAKKNfuLiXhqQEP950jf4XhFj8KA-ge1BtFPDNa8iHdQRLfQv2A@mail.gmail.com>
 <A903CE9B-1D91-494B-84BF-C3ADBDC858B7@gmail.com>
Message-ID: <0B4FCE54-7AAA-4CE2-B55D-715EC601A553@gmail.com>

I should also mention Arnauld that I use ITK4.5.2.  I have had many issues with using ITK 4.6 with the latest GDCM from git, so rolled back to ITK4.5.2.

Nick.


On 17 Sep 2014, at 14:32, Arnaud Gelas <arnaudgelas at gmail.com> wrote:

> Hi Matias,
> 
> I guess you are referring to 
> 
> 	https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e
> 
> $ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e
> v4.6.0
> 
> I use the release branch of ITK
> 
> ---
> 
> Matt,
> 
> Can you comment on this, please?
> 
> Thanks
> Arnaud
> 
> On Sep 17, 2014, at 3:21 PM, Matias Montroull <matimontg at gmail.com> wrote:
> 
>> I had an issue with the resampledicom example once (all my pixel values were recalculated by adding rescaleintercept) and then downloaded the latest ITK release (4.6) and worked fine.
>> 
>> The issue was with the GDCMIO class I beleive but was fixed somehow in the 4.6 version.
>> 
>> On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>> Hi all,
>> 
>> I have been looking at the following wiki example:
>> 
>> 	http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM
>> 
>> It seems to me that the section to rescale the image is not valid anymore with latest ITK version (?)
>> 
>> 	https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333
>> 
>> Can anyone confirm?
>> 
>> Is this code validated? are output images compared to input ones in the corresponding test?
>> 
>> Thanks
>> Arnaud
>> 
>> _____________________________________
>> Powered by www.kitware.com
>> 
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>> 
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>> 
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>> 
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>> 
>> 
> 
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

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From arnaudgelas at gmail.com  Wed Sep 17 09:27:33 2014
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Wed, 17 Sep 2014 15:27:33 +0200
Subject: [ITK-users] question about wiki example ResampleDICOM
In-Reply-To: <F5FA2E64-CDFC-43AE-85A0-6AF74E007DBF@gmail.com>
References: <C83078BB-3646-40C7-ABFA-DBB4BA55435F@gmail.com>
 <582F5FDC-3091-4EB9-B8A3-E11B80DCFF4B@gmail.com>
 <75058210-3021-4372-A59C-8880B69CABED@gmail.com>
 <CAK3qF+_B5PEYVJsn2QAJUBqz8vg0cBkRVjDs4E73sVSM87y7fw@mail.gmail.com>
 <B44044E0-7C64-41C0-8E8E-7DB61F7AFF95@gmail.com>
 <CAK3qF+9K-jfU6C=YL-jKDJZFZHB41XhbxGwwLn8sKhY-nVRQHg@mail.gmail.com>
 <F5FA2E64-CDFC-43AE-85A0-6AF74E007DBF@gmail.com>
Message-ID: <7182E410-B1F7-4D3E-A5C9-B279A22468C7@gmail.com>

I have already done that change before sending the email?
Unfortunately, I can' share the code; so I'll rather get back to the example and validate with this one. I'll get back to you once I have made the same test with the example.

On Sep 17, 2014, at 3:13 PM, Nick Patterson <pattersonnp.work at gmail.com> wrote:

> Ok, I will probably need to see your code if you have heavily modified the example. However, could you try the following:-
> 
> after line 333 : shiftScale->SetShift( interceptShift );
> add   shiftScale->Update();
> 
> 
> and try again?
> 
> Let me know.
> 
> Nick.
> 
> 
> 
> On 17 Sep 2014, at 14:10, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
> 
>> I have been modifying extensively this example...
>> Rescale slope/intercept are saved with expected values -1024 and 1.
>> 
>> Not sure if the error is in my code or in this example, but when I compare inputs and outputs with the ShiftScale part all pixels are different (and the difference is -1024)... that's why I am asking if this part is still valid?
>> 
>> On Wed, Sep 17, 2014 at 3:06 PM, Nick Patterson <pattersonnp.work at gmail.com> wrote:
>> Ok thanks. When you say that it doesn?t work anymore would I be correct in assuming that you mean that the output rescale slope/intercept are written out as 1 and 0, rather than the expected value of -1024 and 1? Or do you mean not working in some other way?
>> 
>> Nick.
>> 
>> 
>> 
>> On 17 Sep 2014, at 14:04, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>> 
>>> Hi Nick,
>>> 
>>> I work with CT images, Rescale Intercept / Slope: ( -1024, 1 )
>>> 
>>> I use system gdcm (release branch from official git repository)
>>> 
>>> Thanks
>>> Arnaud 
>>> 
>>> On Wed, Sep 17, 2014 at 3:01 PM, Nick Patterson <pattersonnp.work at gmail.com> wrote:
>>> Arnauld,
>>> 
>>>  Can you also say if you are using the version of GDCM bundled with ITK release or have you compiled a system version of GDCM from the git-repository?
>>> 
>>> Nick.
>>> 
>>> 
>>> On 17 Sep 2014, at 13:59, Nick Patterson <pattersonnp.work at gmail.com> wrote:
>>> 
>>>> Arnauld,
>>>> 
>>>> Which modality image are you working with, and what are the rescale slope and intercept of the original image?
>>>> 
>>>> Nick.
>>>> 
>>>> 
>>>> 
>>>>  
>>>> On 17 Sep 2014, at 14:02, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>>>> 
>>>>> Hi all,
>>>>> 
>>>>> I have been looking at the following wiki example:
>>>>> 
>>>>> 	http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM
>>>>> 
>>>>> It seems to me that the section to rescale the image is not valid anymore with latest ITK version (?)
>>>>> 
>>>>> 	https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333
>>>>> 
>>>>> Can anyone confirm?
>>>>> 
>>>>> Is this code validated? are output images compared to input ones in the corresponding test?
>>>>> 
>>>>> Thanks
>>>>> Arnaud
>>>>> _____________________________________
>>>>> Powered by www.kitware.com
>>>>> 
>>>>> Visit other Kitware open-source projects at
>>>>> http://www.kitware.com/opensource/opensource.html
>>>>> 
>>>>> Kitware offers ITK Training Courses, for more information visit:
>>>>> http://www.kitware.com/products/protraining.php
>>>>> 
>>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>> 
>>>>> Follow this link to subscribe/unsubscribe:
>>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>> 
>>> 
>>> 
>> 
>> 
> 

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From arnaudgelas at gmail.com  Wed Sep 17 09:34:00 2014
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Wed, 17 Sep 2014 15:34:00 +0200
Subject: [ITK-users] question about wiki example ResampleDICOM
In-Reply-To: <0B4FCE54-7AAA-4CE2-B55D-715EC601A553@gmail.com>
References: <C83078BB-3646-40C7-ABFA-DBB4BA55435F@gmail.com>
 <CAKKNfuLiXhqQEP950jf4XhFj8KA-ge1BtFPDNa8iHdQRLfQv2A@mail.gmail.com>
 <A903CE9B-1D91-494B-84BF-C3ADBDC858B7@gmail.com>
 <0B4FCE54-7AAA-4CE2-B55D-715EC601A553@gmail.com>
Message-ID: <CAK3qF+-_t8N+0WpSXRFu-1fXFq+68FVQWEiRzkhYFZzunV27Aw@mail.gmail.com>

Nick,

I can't roll back to previous ITK version, important patches on
itkGDCMImageIO were very recently merged...


https://github.com/Kitware/ITK/commits/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx

e.g.


https://github.com/Kitware/ITK/commit/33a7e7162fc040f6c7346af5fc1ec15a80834273

https://github.com/Kitware/ITK/commit/2f86b89df192aa80793b2d7f09624a2e4a74ec3c


Arnaud

On Wed, Sep 17, 2014 at 3:29 PM, Nick Patterson <pattersonnp.work at gmail.com>
wrote:

> I should also mention Arnauld that I use ITK4.5.2.  I have had many issues
> with using ITK 4.6 with the latest GDCM from git, so rolled back to
> ITK4.5.2.
>
> Nick.
>
>
>
> On 17 Sep 2014, at 14:32, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>
> Hi Matias,
>
> I guess you are referring to
>
>
> https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e
>
> $ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e
> v4.6.0
>
> I use the release branch of ITK
>
> ---
>
> Matt,
>
> Can you comment on this, please?
>
> Thanks
> Arnaud
>
> On Sep 17, 2014, at 3:21 PM, Matias Montroull <matimontg at gmail.com> wrote:
>
> I had an issue with the resampledicom example once (all my pixel values
> were recalculated by adding rescaleintercept) and then downloaded the
> latest ITK release (4.6) and worked fine.
>
> The issue was with the GDCMIO class I beleive but was fixed somehow in the
> 4.6 version.
>
> On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas <arnaudgelas at gmail.com>
> wrote:
>
>> Hi all,
>>
>> I have been looking at the following wiki example:
>>
>> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM
>>
>> It seems to me that the section to rescale the image is not valid anymore
>> with latest ITK version (?)
>>
>>
>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333
>>
>> Can anyone confirm?
>>
>> Is this code validated? are output images compared to input ones in the
>> corresponding test?
>>
>> Thanks
>> Arnaud
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
>
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From pattersonnp.work at gmail.com  Wed Sep 17 09:35:49 2014
From: pattersonnp.work at gmail.com (Nick Patterson)
Date: Wed, 17 Sep 2014 14:35:49 +0100
Subject: [ITK-users] question about wiki example ResampleDICOM
In-Reply-To: <CAK3qF+-_t8N+0WpSXRFu-1fXFq+68FVQWEiRzkhYFZzunV27Aw@mail.gmail.com>
References: <C83078BB-3646-40C7-ABFA-DBB4BA55435F@gmail.com>
 <CAKKNfuLiXhqQEP950jf4XhFj8KA-ge1BtFPDNa8iHdQRLfQv2A@mail.gmail.com>
 <A903CE9B-1D91-494B-84BF-C3ADBDC858B7@gmail.com>
 <0B4FCE54-7AAA-4CE2-B55D-715EC601A553@gmail.com>
 <CAK3qF+-_t8N+0WpSXRFu-1fXFq+68FVQWEiRzkhYFZzunV27Aw@mail.gmail.com>
Message-ID: <AF25FDC2-8FFF-4BB1-8239-1EE1D9ACFF25@gmail.com>

OK, I will wait to hear the outcome of your run with the original example then.

Cheers, Nick.




On 17 Sep 2014, at 14:34, Arnaud Gelas <arnaudgelas at gmail.com> wrote:

> Nick,
> 
> I can't roll back to previous ITK version, important patches on itkGDCMImageIO were very recently merged...
> 
>     https://github.com/Kitware/ITK/commits/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx
> 
> e.g.
> 
>     https://github.com/Kitware/ITK/commit/33a7e7162fc040f6c7346af5fc1ec15a80834273
>     https://github.com/Kitware/ITK/commit/2f86b89df192aa80793b2d7f09624a2e4a74ec3c
> 
> 
> Arnaud
> 
> On Wed, Sep 17, 2014 at 3:29 PM, Nick Patterson <pattersonnp.work at gmail.com> wrote:
> I should also mention Arnauld that I use ITK4.5.2.  I have had many issues with using ITK 4.6 with the latest GDCM from git, so rolled back to ITK4.5.2.
> Nick.
> 
> 
> 
> On 17 Sep 2014, at 14:32, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
> 
>> Hi Matias,
>> 
>> I guess you are referring to 
>> 
>> 	https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e
>> 
>> $ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e
>> v4.6.0
>> 
>> I use the release branch of ITK
>> 
>> ---
>> 
>> Matt,
>> 
>> Can you comment on this, please?
>> 
>> Thanks
>> Arnaud
>> 
>> On Sep 17, 2014, at 3:21 PM, Matias Montroull <matimontg at gmail.com> wrote:
>> 
>>> I had an issue with the resampledicom example once (all my pixel values were recalculated by adding rescaleintercept) and then downloaded the latest ITK release (4.6) and worked fine.
>>> 
>>> The issue was with the GDCMIO class I beleive but was fixed somehow in the 4.6 version.
>>> 
>>> On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>>> Hi all,
>>> 
>>> I have been looking at the following wiki example:
>>> 
>>> 	http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM
>>> 
>>> It seems to me that the section to rescale the image is not valid anymore with latest ITK version (?)
>>> 
>>> 	https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333
>>> 
>>> Can anyone confirm?
>>> 
>>> Is this code validated? are output images compared to input ones in the corresponding test?
>>> 
>>> Thanks
>>> Arnaud
>>> 
>>> _____________________________________
>>> Powered by www.kitware.com
>>> 
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>> 
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>> 
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>> 
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>> 
>>> 
>> 
>> _____________________________________
>> Powered by www.kitware.com
>> 
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>> 
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>> 
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>> 
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
> 
> 

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From arnaudgelas at gmail.com  Wed Sep 17 10:15:11 2014
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Wed, 17 Sep 2014 16:15:11 +0200
Subject: [ITK-users] question about wiki example ResampleDICOM
In-Reply-To: <AF25FDC2-8FFF-4BB1-8239-1EE1D9ACFF25@gmail.com>
References: <C83078BB-3646-40C7-ABFA-DBB4BA55435F@gmail.com>
 <CAKKNfuLiXhqQEP950jf4XhFj8KA-ge1BtFPDNa8iHdQRLfQv2A@mail.gmail.com>
 <A903CE9B-1D91-494B-84BF-C3ADBDC858B7@gmail.com>
 <0B4FCE54-7AAA-4CE2-B55D-715EC601A553@gmail.com>
 <CAK3qF+-_t8N+0WpSXRFu-1fXFq+68FVQWEiRzkhYFZzunV27Aw@mail.gmail.com>
 <AF25FDC2-8FFF-4BB1-8239-1EE1D9ACFF25@gmail.com>
Message-ID: <CAK3qF+_bw6A7RUwd+DDbzPfhddX+i3m2xTw2RhEz5p86+wqQvw@mail.gmail.com>

Hi Nick,

I can confirm that with the example I get a difference of -1024 (+/- 1) in
between the input and the output, using the ShiftScaleImage part...
While without this part of code the difference is (+/-1)

I would like to make sure this is the expected behaviour!?

On Wed, Sep 17, 2014 at 3:35 PM, Nick Patterson <pattersonnp.work at gmail.com>
wrote:

> OK, I will wait to hear the outcome of your run with the original example
> then.
>
> Cheers, Nick.
>
>
>
>
> On 17 Sep 2014, at 14:34, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>
> Nick,
>
> I can't roll back to previous ITK version, important patches on
> itkGDCMImageIO were very recently merged...
>
>
> https://github.com/Kitware/ITK/commits/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx
>
> e.g.
>
>
> https://github.com/Kitware/ITK/commit/33a7e7162fc040f6c7346af5fc1ec15a80834273
>
> https://github.com/Kitware/ITK/commit/2f86b89df192aa80793b2d7f09624a2e4a74ec3c
>
>
> Arnaud
>
> On Wed, Sep 17, 2014 at 3:29 PM, Nick Patterson <
> pattersonnp.work at gmail.com> wrote:
>
>> I should also mention Arnauld that I use ITK4.5.2.  I have had many
>> issues with using ITK 4.6 with the latest GDCM from git, so rolled back to
>> ITK4.5.2.
>> Nick.
>>
>>
>>
>> On 17 Sep 2014, at 14:32, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>>
>> Hi Matias,
>>
>> I guess you are referring to
>>
>>
>> https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e
>>
>> $ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e
>> v4.6.0
>>
>> I use the release branch of ITK
>>
>> ---
>>
>> Matt,
>>
>> Can you comment on this, please?
>>
>> Thanks
>> Arnaud
>>
>> On Sep 17, 2014, at 3:21 PM, Matias Montroull <matimontg at gmail.com>
>> wrote:
>>
>> I had an issue with the resampledicom example once (all my pixel values
>> were recalculated by adding rescaleintercept) and then downloaded the
>> latest ITK release (4.6) and worked fine.
>>
>> The issue was with the GDCMIO class I beleive but was fixed somehow in
>> the 4.6 version.
>>
>> On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas <arnaudgelas at gmail.com>
>> wrote:
>>
>>> Hi all,
>>>
>>> I have been looking at the following wiki example:
>>>
>>> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM
>>>
>>> It seems to me that the section to rescale the image is not valid
>>> anymore with latest ITK version (?)
>>>
>>>
>>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333
>>>
>>> Can anyone confirm?
>>>
>>> Is this code validated? are output images compared to input ones in the
>>> corresponding test?
>>>
>>> Thanks
>>> Arnaud
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>>
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>>
>
>
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From bill.lorensen at gmail.com  Wed Sep 17 10:41:12 2014
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Wed, 17 Sep 2014 10:41:12 -0400
Subject: [ITK-users] question about wiki example ResampleDICOM
In-Reply-To: <CAK3qF+_bw6A7RUwd+DDbzPfhddX+i3m2xTw2RhEz5p86+wqQvw@mail.gmail.com>
References: <C83078BB-3646-40C7-ABFA-DBB4BA55435F@gmail.com>
 <CAKKNfuLiXhqQEP950jf4XhFj8KA-ge1BtFPDNa8iHdQRLfQv2A@mail.gmail.com>
 <A903CE9B-1D91-494B-84BF-C3ADBDC858B7@gmail.com>
 <0B4FCE54-7AAA-4CE2-B55D-715EC601A553@gmail.com>
 <CAK3qF+-_t8N+0WpSXRFu-1fXFq+68FVQWEiRzkhYFZzunV27Aw@mail.gmail.com>
 <AF25FDC2-8FFF-4BB1-8239-1EE1D9ACFF25@gmail.com>
 <CAK3qF+_bw6A7RUwd+DDbzPfhddX+i3m2xTw2RhEz5p86+wqQvw@mail.gmail.com>
Message-ID: <CADZJ4hPuoosTP0F=rcf=MLAedFxO82KneEFSH-YG2+LM9dd2XA@mail.gmail.com>

I wrote this example many years ago?
1) If the input has a non-trivial slope/intercept, the reader applies
the slope/intercept to the raw data.
2) Rather than setting the slope/intercept in the output dicom, I
apply the inverse of of the slope intercept to the resampled data
before writing. The output dicom should not have the origin
slope/intercept tags.

I'll try to verify this with Slicer, but I may be out of touch for 2 weeks?

Bill


On Wed, Sep 17, 2014 at 10:15 AM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
> Hi Nick,
>
> I can confirm that with the example I get a difference of -1024 (+/- 1) in
> between the input and the output, using the ShiftScaleImage part...
> While without this part of code the difference is (+/-1)
>
> I would like to make sure this is the expected behaviour!?
>
> On Wed, Sep 17, 2014 at 3:35 PM, Nick Patterson <pattersonnp.work at gmail.com>
> wrote:
>>
>> OK, I will wait to hear the outcome of your run with the original example
>> then.
>>
>> Cheers, Nick.
>>
>>
>>
>>
>> On 17 Sep 2014, at 14:34, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>>
>> Nick,
>>
>> I can't roll back to previous ITK version, important patches on
>> itkGDCMImageIO were very recently merged...
>>
>>
>> https://github.com/Kitware/ITK/commits/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx
>>
>> e.g.
>>
>>
>> https://github.com/Kitware/ITK/commit/33a7e7162fc040f6c7346af5fc1ec15a80834273
>>
>> https://github.com/Kitware/ITK/commit/2f86b89df192aa80793b2d7f09624a2e4a74ec3c
>>
>>
>> Arnaud
>>
>> On Wed, Sep 17, 2014 at 3:29 PM, Nick Patterson
>> <pattersonnp.work at gmail.com> wrote:
>>>
>>> I should also mention Arnauld that I use ITK4.5.2.  I have had many
>>> issues with using ITK 4.6 with the latest GDCM from git, so rolled back to
>>> ITK4.5.2.
>>> Nick.
>>>
>>>
>>>
>>> On 17 Sep 2014, at 14:32, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>>>
>>> Hi Matias,
>>>
>>> I guess you are referring to
>>>
>>>
>>> https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e
>>>
>>> $ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e
>>> v4.6.0
>>>
>>> I use the release branch of ITK
>>>
>>> ---
>>>
>>> Matt,
>>>
>>> Can you comment on this, please?
>>>
>>> Thanks
>>> Arnaud
>>>
>>> On Sep 17, 2014, at 3:21 PM, Matias Montroull <matimontg at gmail.com>
>>> wrote:
>>>
>>> I had an issue with the resampledicom example once (all my pixel values
>>> were recalculated by adding rescaleintercept) and then downloaded the latest
>>> ITK release (4.6) and worked fine.
>>>
>>> The issue was with the GDCMIO class I beleive but was fixed somehow in
>>> the 4.6 version.
>>>
>>> On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas <arnaudgelas at gmail.com>
>>> wrote:
>>>>
>>>> Hi all,
>>>>
>>>> I have been looking at the following wiki example:
>>>>
>>>> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM
>>>>
>>>> It seems to me that the section to rescale the image is not valid
>>>> anymore with latest ITK version (?)
>>>>
>>>>
>>>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333
>>>>
>>>> Can anyone confirm?
>>>>
>>>> Is this code validated? are output images compared to input ones in the
>>>> corresponding test?
>>>>
>>>> Thanks
>>>> Arnaud
>>>>
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>
>>>
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>>
>>
>>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>



-- 
Unpaid intern in BillsBasement at noware dot com

From matt.mccormick at kitware.com  Wed Sep 17 11:13:20 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 17 Sep 2014 11:13:20 -0400
Subject: [ITK-users] Opportunities to share, discuss, design,
 and learn with other ITK community members
Message-ID: <CALzTN-QF3BM63OzPf7xXM=URec3HDTyix85A757rEG1QWnCdfg@mail.gmail.com>

There are a couple of upcoming opportunities to share, discuss, design, and
learn with your fellow ITK community members.


On Thursday (tomorrow), 9:30 AM Eastern USA time, there will be a
Google+ Hangout
where we will be doing code reviews:

  https://plus.google.com/events/cg0n52cqd08ulpr6o9jgku32gj0?authkey=CJ-S7tP5s5_xAw


On Friday, 11:00 AM Eastern USA time, an ITK development conference,

  https://plus.google.com/events/ctabd8pd4oasc3p5ejat27jgko4?authkey=COjR69z2toGlIQ


For those that cannot join via Hangout, telephone call-in is also possible.
Dial:

  585-632-6296

Enter pin:

  31423


All are welcome.  Hope to talk to you then!

From matt.mccormick at kitware.com  Wed Sep 17 11:42:33 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 17 Sep 2014 11:42:33 -0400
Subject: [ITK-users] question about wiki example ResampleDICOM
In-Reply-To: <CADZJ4hPuoosTP0F=rcf=MLAedFxO82KneEFSH-YG2+LM9dd2XA@mail.gmail.com>
References: <C83078BB-3646-40C7-ABFA-DBB4BA55435F@gmail.com>
 <CAKKNfuLiXhqQEP950jf4XhFj8KA-ge1BtFPDNa8iHdQRLfQv2A@mail.gmail.com>
 <A903CE9B-1D91-494B-84BF-C3ADBDC858B7@gmail.com>
 <0B4FCE54-7AAA-4CE2-B55D-715EC601A553@gmail.com>
 <CAK3qF+-_t8N+0WpSXRFu-1fXFq+68FVQWEiRzkhYFZzunV27Aw@mail.gmail.com>
 <AF25FDC2-8FFF-4BB1-8239-1EE1D9ACFF25@gmail.com>
 <CAK3qF+_bw6A7RUwd+DDbzPfhddX+i3m2xTw2RhEz5p86+wqQvw@mail.gmail.com>
 <CADZJ4hPuoosTP0F=rcf=MLAedFxO82KneEFSH-YG2+LM9dd2XA@mail.gmail.com>
Message-ID: <CALzTN-Sw2+z6qwBtPt5xVTOOcVsM7_1ECqdR9-NrLfZ6a0DH8w@mail.gmail.com>

Hi,

Do to this fix [1], if the writer is re-using the GDCMImageIO, the
writer should apply the inverse rescale / slope intercept like the
reader applied the rescale / slope intercept when reading.  This was a
long-standing bug that I fixed in 4.6.0.  Arnaud, if the manual
inverse rescale / slope operation is removed, does the correct output
result?

Thanks,
Matt

[1] https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e

On Wed, Sep 17, 2014 at 10:41 AM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
> I wrote this example many years ago?
> 1) If the input has a non-trivial slope/intercept, the reader applies
> the slope/intercept to the raw data.
> 2) Rather than setting the slope/intercept in the output dicom, I
> apply the inverse of of the slope intercept to the resampled data
> before writing. The output dicom should not have the origin
> slope/intercept tags.
>
> I'll try to verify this with Slicer, but I may be out of touch for 2 weeks?
>
> Bill
>
>
> On Wed, Sep 17, 2014 at 10:15 AM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>> Hi Nick,
>>
>> I can confirm that with the example I get a difference of -1024 (+/- 1) in
>> between the input and the output, using the ShiftScaleImage part...
>> While without this part of code the difference is (+/-1)
>>
>> I would like to make sure this is the expected behaviour!?
>>
>> On Wed, Sep 17, 2014 at 3:35 PM, Nick Patterson <pattersonnp.work at gmail.com>
>> wrote:
>>>
>>> OK, I will wait to hear the outcome of your run with the original example
>>> then.
>>>
>>> Cheers, Nick.
>>>
>>>
>>>
>>>
>>> On 17 Sep 2014, at 14:34, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>>>
>>> Nick,
>>>
>>> I can't roll back to previous ITK version, important patches on
>>> itkGDCMImageIO were very recently merged...
>>>
>>>
>>> https://github.com/Kitware/ITK/commits/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx
>>>
>>> e.g.
>>>
>>>
>>> https://github.com/Kitware/ITK/commit/33a7e7162fc040f6c7346af5fc1ec15a80834273
>>>
>>> https://github.com/Kitware/ITK/commit/2f86b89df192aa80793b2d7f09624a2e4a74ec3c
>>>
>>>
>>> Arnaud
>>>
>>> On Wed, Sep 17, 2014 at 3:29 PM, Nick Patterson
>>> <pattersonnp.work at gmail.com> wrote:
>>>>
>>>> I should also mention Arnauld that I use ITK4.5.2.  I have had many
>>>> issues with using ITK 4.6 with the latest GDCM from git, so rolled back to
>>>> ITK4.5.2.
>>>> Nick.
>>>>
>>>>
>>>>
>>>> On 17 Sep 2014, at 14:32, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>>>>
>>>> Hi Matias,
>>>>
>>>> I guess you are referring to
>>>>
>>>>
>>>> https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e
>>>>
>>>> $ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e
>>>> v4.6.0
>>>>
>>>> I use the release branch of ITK
>>>>
>>>> ---
>>>>
>>>> Matt,
>>>>
>>>> Can you comment on this, please?
>>>>
>>>> Thanks
>>>> Arnaud
>>>>
>>>> On Sep 17, 2014, at 3:21 PM, Matias Montroull <matimontg at gmail.com>
>>>> wrote:
>>>>
>>>> I had an issue with the resampledicom example once (all my pixel values
>>>> were recalculated by adding rescaleintercept) and then downloaded the latest
>>>> ITK release (4.6) and worked fine.
>>>>
>>>> The issue was with the GDCMIO class I beleive but was fixed somehow in
>>>> the 4.6 version.
>>>>
>>>> On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas <arnaudgelas at gmail.com>
>>>> wrote:
>>>>>
>>>>> Hi all,
>>>>>
>>>>> I have been looking at the following wiki example:
>>>>>
>>>>> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM
>>>>>
>>>>> It seems to me that the section to rescale the image is not valid
>>>>> anymore with latest ITK version (?)
>>>>>
>>>>>
>>>>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333
>>>>>
>>>>> Can anyone confirm?
>>>>>
>>>>> Is this code validated? are output images compared to input ones in the
>>>>> corresponding test?
>>>>>
>>>>> Thanks
>>>>> Arnaud
>>>>>
>>>>> _____________________________________
>>>>> Powered by www.kitware.com
>>>>>
>>>>> Visit other Kitware open-source projects at
>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>
>>>>> Kitware offers ITK Training Courses, for more information visit:
>>>>> http://www.kitware.com/products/protraining.php
>>>>>
>>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>>
>>>>> Follow this link to subscribe/unsubscribe:
>>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>>
>>>>
>>>>
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>
>>>>
>>>
>>>
>>
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>
>
>
> --
> Unpaid intern in BillsBasement at noware dot com
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

From matt.mccormick at kitware.com  Wed Sep 17 16:16:27 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 17 Sep 2014 16:16:27 -0400
Subject: [ITK-users] Opportunities to share, discuss, design,
 and learn with other ITK community members
In-Reply-To: <CALzTN-QF3BM63OzPf7xXM=URec3HDTyix85A757rEG1QWnCdfg@mail.gmail.com>
References: <CALzTN-QF3BM63OzPf7xXM=URec3HDTyix85A757rEG1QWnCdfg@mail.gmail.com>
Message-ID: <CALzTN-TQKgGsCQU3tenFxSSYLMuT2d-UtTjXzYfo5Z7c9eywdw@mail.gmail.com>

On Wed, Sep 17, 2014 at 11:13 AM, Matt McCormick
<matt.mccormick at kitware.com> wrote:
> There are a couple of upcoming opportunities to share, discuss, design, and
> learn with your fellow ITK community members.
>
>
> On Thursday (tomorrow), 9:30 AM Eastern USA time, there will be a
> Google+ Hangout
> where we will be doing code reviews:
>
>   https://plus.google.com/events/cg0n52cqd08ulpr6o9jgku32gj0?authkey=CJ-S7tP5s5_xAw
>

Due to a conflict, this had to be changed to 1:00 PM Eastern USA time.
Sorry for schedule variation.

Matt

From yxp233 at postech.ac.kr  Wed Sep 17 20:11:55 2014
From: yxp233 at postech.ac.kr (Xiaopeng Yang)
Date: Thu, 18 Sep 2014 09:11:55 +0900
Subject: [ITK-users] Any instruction of compiling ITK with GPU support
In-Reply-To: <1410960535981899.04578.ptmail04@ptmail04>
References: <CAHoiV3ZGmbX7XT6ymjaeL0VLgQRtUR1=vcmdVcm6-7VEWh+LEQ@mail.gmail.com>
 <CAK3qF+_-3wsSVPNmutDzg6Dy=ME=APJZm_t7yPVHo4tpc_Ce7A@mail.gmail.com>
 <1410796270474129.115529.ptmail04@ptmail04>
 <1410878838500935.032749.ptmail04@ptmail04>
 <1410913163921868.021894.ptmail04@ptmail04>
 <000c01cfd27a$9ed25020$dc76f060$@ac.kr>
 <1410960535981899.04578.ptmail04@ptmail04>
Message-ID: <008301cfd2d5$27ecc890$77c659b0$@ac.kr>

Hi Mike,

 

If I turn USE_GPU off, then there is no CMake error. I guess there is something wrong with the GPU module. I am using CUDA toolkit 6.5 for compiling. Which version of CUDA toolkit should I use?

 

Thanks,

Xiaopeng

 

From: Insight-users [mailto:insight-users-bounces at itk.org] On Behalf Of Mike Chinander
Sent: Wednesday, September 17, 2014 10:29 PM
To: insight-users
Subject: Re: [ITK-users] Any instruction of compiling ITK with GPU support

 

Did you manually set the path "D:\Toolbox\ITK-4.6.0" somewhere? Try it with forward slashes instead, "D:/Toolbox/ITK-4.6.0"

 

On Wed, Sep 17, 2014 at 8:23 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:

By the way, I tried to compile ITK 4.6.0 with Visual Studio 2010, under windows 7 64 bit. I set USE_GPU on, but I got the error as follows:

 

Found OpenCL: C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v6.5\lib 

CMake Error at C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:304 (set):
Syntax error in cmake code at

C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:304

when parsing string

D:\Toolbox\ITK-4.6.0

Invalid escape sequence \T
Call Stack (most recent call first):
C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:516 (cpack_set_if_not_set)
CMake/ITKModuleEnablement.cmake:171 (include)
CMakeLists.txt:322 (include)

Configuring incomplete, errors occurred!

See also "D:/Toolbox/ITK-4.6.0/bin/CMakeFiles/CMakeOutput.log".

See also "D:/Toolbox/ITK-4.6.0/bin/CMakeFiles/CMakeError.log".

 

 

 

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From yxp233 at postech.ac.kr  Wed Sep 17 21:48:11 2014
From: yxp233 at postech.ac.kr (Xiaopeng Yang)
Date: Thu, 18 Sep 2014 10:48:11 +0900
Subject: [ITK-users] Any instruction of compiling ITK with GPU support
References: <CAHoiV3ZGmbX7XT6ymjaeL0VLgQRtUR1=vcmdVcm6-7VEWh+LEQ@mail.gmail.com>
 <CAK3qF+_-3wsSVPNmutDzg6Dy=ME=APJZm_t7yPVHo4tpc_Ce7A@mail.gmail.com>
 <1410796270474129.115529.ptmail04@ptmail04>
 <1410878838500935.032749.ptmail04@ptmail04>
 <1410913163921868.021894.ptmail04@ptmail04>
 <000c01cfd27a$9ed25020$dc76f060$@ac.kr>
 <1410960535981899.04578.ptmail04@ptmail04> 
Message-ID: <009401cfd2e2$9b13c640$d13b52c0$@ac.kr>

Hi Mike,

 

I found that you were right. I changed the forward slashes for the directories of OpenCL:

 

OPENCL_INCLUDE_DIRS  C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v6.5/include

OPENCL_LIBRARIES          C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v6.5/lib

 

There was no CMake error, but many warning messages:

 

WARNING: Target "ITKGPUCommon" requests linking to directory "C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v6.5/lib". Targets may link only to libraries. CMake is dropping the item.

WARNING: Target "ITKGPUCommon" requests linking to directory "C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v6.5/lib". Targets may link only to libraries. CMake is dropping the item.

WARNING: Target "ITKGPUCommon" requests linking to directory "C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v6.5/lib". Targets may link only to libraries. CMake is dropping the item.

WARNING: Target "ITKGPUCommon" requests linking to directory "C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v6.5/lib". Targets may link only to libraries. CMake is dropping the item.

WARNING: Target "ITKGPUCommon" requests linking to directory "C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v6.5/lib". Targets may link only to libraries. CMake is dropping the item.

 

And when I tried to debug ITK, errors occurred as ?cannot find CL/opencl.h?. 

 

Can you tell me where I made a mistake?

 

Thank you,

Xiaopeng

 

From: Xiaopeng Yang [mailto:yxp233 at postech.ac.kr] 
Sent: Thursday, September 18, 2014 9:12 AM
To: 'Mike Chinander'; 'insight-users'
Subject: RE: [ITK-users] Any instruction of compiling ITK with GPU support

 

Hi Mike,

 

If I turn USE_GPU off, then there is no CMake error. I guess there is something wrong with the GPU module. I am using CUDA toolkit 6.5 for compiling. Which version of CUDA toolkit should I use?

 

Thanks,

Xiaopeng

 

From: Insight-users [mailto:insight-users-bounces at itk.org] On Behalf Of Mike Chinander
Sent: Wednesday, September 17, 2014 10:29 PM
To: insight-users
Subject: Re: [ITK-users] Any instruction of compiling ITK with GPU support

 

Did you manually set the path "D:\Toolbox\ITK-4.6.0" somewhere? Try it with forward slashes instead, "D:/Toolbox/ITK-4.6.0"

 

On Wed, Sep 17, 2014 at 8:23 AM, Xiaopeng Yang <yxp233 at postech.ac.kr> wrote:

By the way, I tried to compile ITK 4.6.0 with Visual Studio 2010, under windows 7 64 bit. I set USE_GPU on, but I got the error as follows:

 

Found OpenCL: C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v6.5\lib 

CMake Error at C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:304 (set):
Syntax error in cmake code at

C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:304

when parsing string

D:\Toolbox\ITK-4.6.0

Invalid escape sequence \T
Call Stack (most recent call first):
C:/Program Files (x86)/CMake/share/cmake-3.0/Modules/CPack.cmake:516 (cpack_set_if_not_set)
CMake/ITKModuleEnablement.cmake:171 (include)
CMakeLists.txt:322 (include)

Configuring incomplete, errors occurred!

See also "D:/Toolbox/ITK-4.6.0/bin/CMakeFiles/CMakeOutput.log".

See also "D:/Toolbox/ITK-4.6.0/bin/CMakeFiles/CMakeError.log".

 

 

 

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From llliu at umich.edu  Wed Sep 17 21:54:06 2014
From: llliu at umich.edu (Lianli Liu)
Date: Wed, 17 Sep 2014 21:54:06 -0400
Subject: [ITK-users] Mask in metric calculation
Message-ID: <CAGKqDmc-HY3Pc8yoMvhsrJeS8uobXP0S1FtuvNzoiSGP3m8nag@mail.gmail.com>

Hi all,

I just wonder if I define two masks for fixed image and moving image that
are of differnt size, will voxels that fall in both the masks will
contribute to metric calculation? Thanks!

Regards,
Lianli
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From arnaudgelas at gmail.com  Thu Sep 18 02:36:05 2014
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Thu, 18 Sep 2014 08:36:05 +0200
Subject: [ITK-users] question about wiki example ResampleDICOM
In-Reply-To: <CALzTN-Sw2+z6qwBtPt5xVTOOcVsM7_1ECqdR9-NrLfZ6a0DH8w@mail.gmail.com>
References: <C83078BB-3646-40C7-ABFA-DBB4BA55435F@gmail.com>
 <CAKKNfuLiXhqQEP950jf4XhFj8KA-ge1BtFPDNa8iHdQRLfQv2A@mail.gmail.com>
 <A903CE9B-1D91-494B-84BF-C3ADBDC858B7@gmail.com>
 <0B4FCE54-7AAA-4CE2-B55D-715EC601A553@gmail.com>
 <CAK3qF+-_t8N+0WpSXRFu-1fXFq+68FVQWEiRzkhYFZzunV27Aw@mail.gmail.com>
 <AF25FDC2-8FFF-4BB1-8239-1EE1D9ACFF25@gmail.com>
 <CAK3qF+_bw6A7RUwd+DDbzPfhddX+i3m2xTw2RhEz5p86+wqQvw@mail.gmail.com>
 <CADZJ4hPuoosTP0F=rcf=MLAedFxO82KneEFSH-YG2+LM9dd2XA@mail.gmail.com>
 <CALzTN-Sw2+z6qwBtPt5xVTOOcVsM7_1ECqdR9-NrLfZ6a0DH8w@mail.gmail.com>
Message-ID: <CAK3qF+9t_hMnssUocOHYFe43frK9vTsOhOki4YDPTdUtXw5yPw@mail.gmail.com>

Hi Matt,

This is indeed the observed and, based on your answer, expected behaviour.
Thank you very much for the confirmation (that's exactly what I needed!).

To avoid confusion in future, I am going to modify the corresponding
example on github and on the wiki!

Best,
Arnaud

On Wed, Sep 17, 2014 at 5:42 PM, Matt McCormick <matt.mccormick at kitware.com>
wrote:

> Hi,
>
> Do to this fix [1], if the writer is re-using the GDCMImageIO, the
> writer should apply the inverse rescale / slope intercept like the
> reader applied the rescale / slope intercept when reading.  This was a
> long-standing bug that I fixed in 4.6.0.  Arnaud, if the manual
> inverse rescale / slope operation is removed, does the correct output
> result?
>
> Thanks,
> Matt
>
> [1]
> https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e
>
> On Wed, Sep 17, 2014 at 10:41 AM, Bill Lorensen <bill.lorensen at gmail.com>
> wrote:
> > I wrote this example many years ago?
> > 1) If the input has a non-trivial slope/intercept, the reader applies
> > the slope/intercept to the raw data.
> > 2) Rather than setting the slope/intercept in the output dicom, I
> > apply the inverse of of the slope intercept to the resampled data
> > before writing. The output dicom should not have the origin
> > slope/intercept tags.
> >
> > I'll try to verify this with Slicer, but I may be out of touch for 2
> weeks?
> >
> > Bill
> >
> >
> > On Wed, Sep 17, 2014 at 10:15 AM, Arnaud Gelas <arnaudgelas at gmail.com>
> wrote:
> >> Hi Nick,
> >>
> >> I can confirm that with the example I get a difference of -1024 (+/- 1)
> in
> >> between the input and the output, using the ShiftScaleImage part...
> >> While without this part of code the difference is (+/-1)
> >>
> >> I would like to make sure this is the expected behaviour!?
> >>
> >> On Wed, Sep 17, 2014 at 3:35 PM, Nick Patterson <
> pattersonnp.work at gmail.com>
> >> wrote:
> >>>
> >>> OK, I will wait to hear the outcome of your run with the original
> example
> >>> then.
> >>>
> >>> Cheers, Nick.
> >>>
> >>>
> >>>
> >>>
> >>> On 17 Sep 2014, at 14:34, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
> >>>
> >>> Nick,
> >>>
> >>> I can't roll back to previous ITK version, important patches on
> >>> itkGDCMImageIO were very recently merged...
> >>>
> >>>
> >>>
> https://github.com/Kitware/ITK/commits/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx
> >>>
> >>> e.g.
> >>>
> >>>
> >>>
> https://github.com/Kitware/ITK/commit/33a7e7162fc040f6c7346af5fc1ec15a80834273
> >>>
> >>>
> https://github.com/Kitware/ITK/commit/2f86b89df192aa80793b2d7f09624a2e4a74ec3c
> >>>
> >>>
> >>> Arnaud
> >>>
> >>> On Wed, Sep 17, 2014 at 3:29 PM, Nick Patterson
> >>> <pattersonnp.work at gmail.com> wrote:
> >>>>
> >>>> I should also mention Arnauld that I use ITK4.5.2.  I have had many
> >>>> issues with using ITK 4.6 with the latest GDCM from git, so rolled
> back to
> >>>> ITK4.5.2.
> >>>> Nick.
> >>>>
> >>>>
> >>>>
> >>>> On 17 Sep 2014, at 14:32, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
> >>>>
> >>>> Hi Matias,
> >>>>
> >>>> I guess you are referring to
> >>>>
> >>>>
> >>>>
> https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e
> >>>>
> >>>> $ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e
> >>>> v4.6.0
> >>>>
> >>>> I use the release branch of ITK
> >>>>
> >>>> ---
> >>>>
> >>>> Matt,
> >>>>
> >>>> Can you comment on this, please?
> >>>>
> >>>> Thanks
> >>>> Arnaud
> >>>>
> >>>> On Sep 17, 2014, at 3:21 PM, Matias Montroull <matimontg at gmail.com>
> >>>> wrote:
> >>>>
> >>>> I had an issue with the resampledicom example once (all my pixel
> values
> >>>> were recalculated by adding rescaleintercept) and then downloaded the
> latest
> >>>> ITK release (4.6) and worked fine.
> >>>>
> >>>> The issue was with the GDCMIO class I beleive but was fixed somehow in
> >>>> the 4.6 version.
> >>>>
> >>>> On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas <arnaudgelas at gmail.com
> >
> >>>> wrote:
> >>>>>
> >>>>> Hi all,
> >>>>>
> >>>>> I have been looking at the following wiki example:
> >>>>>
> >>>>> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM
> >>>>>
> >>>>> It seems to me that the section to rescale the image is not valid
> >>>>> anymore with latest ITK version (?)
> >>>>>
> >>>>>
> >>>>>
> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333
> >>>>>
> >>>>> Can anyone confirm?
> >>>>>
> >>>>> Is this code validated? are output images compared to input ones in
> the
> >>>>> corresponding test?
> >>>>>
> >>>>> Thanks
> >>>>> Arnaud
> >>>>>
> >>>>> _____________________________________
> >>>>> Powered by www.kitware.com
> >>>>>
> >>>>> Visit other Kitware open-source projects at
> >>>>> http://www.kitware.com/opensource/opensource.html
> >>>>>
> >>>>> Kitware offers ITK Training Courses, for more information visit:
> >>>>> http://www.kitware.com/products/protraining.php
> >>>>>
> >>>>> Please keep messages on-topic and check the ITK FAQ at:
> >>>>> http://www.itk.org/Wiki/ITK_FAQ
> >>>>>
> >>>>> Follow this link to subscribe/unsubscribe:
> >>>>> http://public.kitware.com/mailman/listinfo/insight-users
> >>>>>
> >>>>
> >>>>
> >>>> _____________________________________
> >>>> Powered by www.kitware.com
> >>>>
> >>>> Visit other Kitware open-source projects at
> >>>> http://www.kitware.com/opensource/opensource.html
> >>>>
> >>>> Kitware offers ITK Training Courses, for more information visit:
> >>>> http://www.kitware.com/products/protraining.php
> >>>>
> >>>> Please keep messages on-topic and check the ITK FAQ at:
> >>>> http://www.itk.org/Wiki/ITK_FAQ
> >>>>
> >>>> Follow this link to subscribe/unsubscribe:
> >>>> http://public.kitware.com/mailman/listinfo/insight-users
> >>>>
> >>>>
> >>>
> >>>
> >>
> >>
> >> _____________________________________
> >> Powered by www.kitware.com
> >>
> >> Visit other Kitware open-source projects at
> >> http://www.kitware.com/opensource/opensource.html
> >>
> >> Kitware offers ITK Training Courses, for more information visit:
> >> http://www.kitware.com/products/protraining.php
> >>
> >> Please keep messages on-topic and check the ITK FAQ at:
> >> http://www.itk.org/Wiki/ITK_FAQ
> >>
> >> Follow this link to subscribe/unsubscribe:
> >> http://public.kitware.com/mailman/listinfo/insight-users
> >>
> >
> >
> >
> > --
> > Unpaid intern in BillsBasement at noware dot com
> > _____________________________________
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Kitware offers ITK Training Courses, for more information visit:
> > http://www.kitware.com/products/protraining.php
> >
> > Please keep messages on-topic and check the ITK FAQ at:
> > http://www.itk.org/Wiki/ITK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://public.kitware.com/mailman/listinfo/insight-users
>
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From arnaudgelas at gmail.com  Thu Sep 18 02:43:36 2014
From: arnaudgelas at gmail.com (Arnaud Gelas)
Date: Thu, 18 Sep 2014 08:43:36 +0200
Subject: [ITK-users] question about wiki example ResampleDICOM
In-Reply-To: <CAK3qF+9t_hMnssUocOHYFe43frK9vTsOhOki4YDPTdUtXw5yPw@mail.gmail.com>
References: <C83078BB-3646-40C7-ABFA-DBB4BA55435F@gmail.com>
 <CAKKNfuLiXhqQEP950jf4XhFj8KA-ge1BtFPDNa8iHdQRLfQv2A@mail.gmail.com>
 <A903CE9B-1D91-494B-84BF-C3ADBDC858B7@gmail.com>
 <0B4FCE54-7AAA-4CE2-B55D-715EC601A553@gmail.com>
 <CAK3qF+-_t8N+0WpSXRFu-1fXFq+68FVQWEiRzkhYFZzunV27Aw@mail.gmail.com>
 <AF25FDC2-8FFF-4BB1-8239-1EE1D9ACFF25@gmail.com>
 <CAK3qF+_bw6A7RUwd+DDbzPfhddX+i3m2xTw2RhEz5p86+wqQvw@mail.gmail.com>
 <CADZJ4hPuoosTP0F=rcf=MLAedFxO82KneEFSH-YG2+LM9dd2XA@mail.gmail.com>
 <CALzTN-Sw2+z6qwBtPt5xVTOOcVsM7_1ECqdR9-NrLfZ6a0DH8w@mail.gmail.com>
 <CAK3qF+9t_hMnssUocOHYFe43frK9vTsOhOki4YDPTdUtXw5yPw@mail.gmail.com>
Message-ID: <CAK3qF+96eR4XiGcWiis+pAhTGtoq1iKwZ=9_+1W+NDui8nwCUg@mail.gmail.com>

Matt,

I guess there should be migration report for this fix?

Arnaud

On Thu, Sep 18, 2014 at 8:36 AM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:

> Hi Matt,
>
> This is indeed the observed and, based on your answer, expected behaviour.
> Thank you very much for the confirmation (that's exactly what I needed!).
>
> To avoid confusion in future, I am going to modify the corresponding
> example on github and on the wiki!
>
> Best,
> Arnaud
>
> On Wed, Sep 17, 2014 at 5:42 PM, Matt McCormick <
> matt.mccormick at kitware.com> wrote:
>
>> Hi,
>>
>> Do to this fix [1], if the writer is re-using the GDCMImageIO, the
>> writer should apply the inverse rescale / slope intercept like the
>> reader applied the rescale / slope intercept when reading.  This was a
>> long-standing bug that I fixed in 4.6.0.  Arnaud, if the manual
>> inverse rescale / slope operation is removed, does the correct output
>> result?
>>
>> Thanks,
>> Matt
>>
>> [1]
>> https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e
>>
>> On Wed, Sep 17, 2014 at 10:41 AM, Bill Lorensen <bill.lorensen at gmail.com>
>> wrote:
>> > I wrote this example many years ago?
>> > 1) If the input has a non-trivial slope/intercept, the reader applies
>> > the slope/intercept to the raw data.
>> > 2) Rather than setting the slope/intercept in the output dicom, I
>> > apply the inverse of of the slope intercept to the resampled data
>> > before writing. The output dicom should not have the origin
>> > slope/intercept tags.
>> >
>> > I'll try to verify this with Slicer, but I may be out of touch for 2
>> weeks?
>> >
>> > Bill
>> >
>> >
>> > On Wed, Sep 17, 2014 at 10:15 AM, Arnaud Gelas <arnaudgelas at gmail.com>
>> wrote:
>> >> Hi Nick,
>> >>
>> >> I can confirm that with the example I get a difference of -1024 (+/-
>> 1) in
>> >> between the input and the output, using the ShiftScaleImage part...
>> >> While without this part of code the difference is (+/-1)
>> >>
>> >> I would like to make sure this is the expected behaviour!?
>> >>
>> >> On Wed, Sep 17, 2014 at 3:35 PM, Nick Patterson <
>> pattersonnp.work at gmail.com>
>> >> wrote:
>> >>>
>> >>> OK, I will wait to hear the outcome of your run with the original
>> example
>> >>> then.
>> >>>
>> >>> Cheers, Nick.
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> On 17 Sep 2014, at 14:34, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>> >>>
>> >>> Nick,
>> >>>
>> >>> I can't roll back to previous ITK version, important patches on
>> >>> itkGDCMImageIO were very recently merged...
>> >>>
>> >>>
>> >>>
>> https://github.com/Kitware/ITK/commits/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx
>> >>>
>> >>> e.g.
>> >>>
>> >>>
>> >>>
>> https://github.com/Kitware/ITK/commit/33a7e7162fc040f6c7346af5fc1ec15a80834273
>> >>>
>> >>>
>> https://github.com/Kitware/ITK/commit/2f86b89df192aa80793b2d7f09624a2e4a74ec3c
>> >>>
>> >>>
>> >>> Arnaud
>> >>>
>> >>> On Wed, Sep 17, 2014 at 3:29 PM, Nick Patterson
>> >>> <pattersonnp.work at gmail.com> wrote:
>> >>>>
>> >>>> I should also mention Arnauld that I use ITK4.5.2.  I have had many
>> >>>> issues with using ITK 4.6 with the latest GDCM from git, so rolled
>> back to
>> >>>> ITK4.5.2.
>> >>>> Nick.
>> >>>>
>> >>>>
>> >>>>
>> >>>> On 17 Sep 2014, at 14:32, Arnaud Gelas <arnaudgelas at gmail.com>
>> wrote:
>> >>>>
>> >>>> Hi Matias,
>> >>>>
>> >>>> I guess you are referring to
>> >>>>
>> >>>>
>> >>>>
>> https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e
>> >>>>
>> >>>> $ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e
>> >>>> v4.6.0
>> >>>>
>> >>>> I use the release branch of ITK
>> >>>>
>> >>>> ---
>> >>>>
>> >>>> Matt,
>> >>>>
>> >>>> Can you comment on this, please?
>> >>>>
>> >>>> Thanks
>> >>>> Arnaud
>> >>>>
>> >>>> On Sep 17, 2014, at 3:21 PM, Matias Montroull <matimontg at gmail.com>
>> >>>> wrote:
>> >>>>
>> >>>> I had an issue with the resampledicom example once (all my pixel
>> values
>> >>>> were recalculated by adding rescaleintercept) and then downloaded
>> the latest
>> >>>> ITK release (4.6) and worked fine.
>> >>>>
>> >>>> The issue was with the GDCMIO class I beleive but was fixed somehow
>> in
>> >>>> the 4.6 version.
>> >>>>
>> >>>> On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas <
>> arnaudgelas at gmail.com>
>> >>>> wrote:
>> >>>>>
>> >>>>> Hi all,
>> >>>>>
>> >>>>> I have been looking at the following wiki example:
>> >>>>>
>> >>>>> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM
>> >>>>>
>> >>>>> It seems to me that the section to rescale the image is not valid
>> >>>>> anymore with latest ITK version (?)
>> >>>>>
>> >>>>>
>> >>>>>
>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333
>> >>>>>
>> >>>>> Can anyone confirm?
>> >>>>>
>> >>>>> Is this code validated? are output images compared to input ones in
>> the
>> >>>>> corresponding test?
>> >>>>>
>> >>>>> Thanks
>> >>>>> Arnaud
>> >>>>>
>> >>>>> _____________________________________
>> >>>>> Powered by www.kitware.com
>> >>>>>
>> >>>>> Visit other Kitware open-source projects at
>> >>>>> http://www.kitware.com/opensource/opensource.html
>> >>>>>
>> >>>>> Kitware offers ITK Training Courses, for more information visit:
>> >>>>> http://www.kitware.com/products/protraining.php
>> >>>>>
>> >>>>> Please keep messages on-topic and check the ITK FAQ at:
>> >>>>> http://www.itk.org/Wiki/ITK_FAQ
>> >>>>>
>> >>>>> Follow this link to subscribe/unsubscribe:
>> >>>>> http://public.kitware.com/mailman/listinfo/insight-users
>> >>>>>
>> >>>>
>> >>>>
>> >>>> _____________________________________
>> >>>> Powered by www.kitware.com
>> >>>>
>> >>>> Visit other Kitware open-source projects at
>> >>>> http://www.kitware.com/opensource/opensource.html
>> >>>>
>> >>>> Kitware offers ITK Training Courses, for more information visit:
>> >>>> http://www.kitware.com/products/protraining.php
>> >>>>
>> >>>> Please keep messages on-topic and check the ITK FAQ at:
>> >>>> http://www.itk.org/Wiki/ITK_FAQ
>> >>>>
>> >>>> Follow this link to subscribe/unsubscribe:
>> >>>> http://public.kitware.com/mailman/listinfo/insight-users
>> >>>>
>> >>>>
>> >>>
>> >>>
>> >>
>> >>
>> >> _____________________________________
>> >> Powered by www.kitware.com
>> >>
>> >> Visit other Kitware open-source projects at
>> >> http://www.kitware.com/opensource/opensource.html
>> >>
>> >> Kitware offers ITK Training Courses, for more information visit:
>> >> http://www.kitware.com/products/protraining.php
>> >>
>> >> Please keep messages on-topic and check the ITK FAQ at:
>> >> http://www.itk.org/Wiki/ITK_FAQ
>> >>
>> >> Follow this link to subscribe/unsubscribe:
>> >> http://public.kitware.com/mailman/listinfo/insight-users
>> >>
>> >
>> >
>> >
>> > --
>> > Unpaid intern in BillsBasement at noware dot com
>> > _____________________________________
>> > Powered by www.kitware.com
>> >
>> > Visit other Kitware open-source projects at
>> > http://www.kitware.com/opensource/opensource.html
>> >
>> > Kitware offers ITK Training Courses, for more information visit:
>> > http://www.kitware.com/products/protraining.php
>> >
>> > Please keep messages on-topic and check the ITK FAQ at:
>> > http://www.itk.org/Wiki/ITK_FAQ
>> >
>> > Follow this link to subscribe/unsubscribe:
>> > http://public.kitware.com/mailman/listinfo/insight-users
>>
>
>
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From joel.schaerer at laposte.net  Thu Sep 18 08:19:52 2014
From: joel.schaerer at laposte.net (=?UTF-8?B?Sm/Dq2wgU2NoYWVyZXI=?=)
Date: Thu, 18 Sep 2014 14:19:52 +0200
Subject: [ITK-users] Insight Journal template ITKv4 compatibilty
In-Reply-To: <CALzTN-R5pbYay1MQ8nQ6OBGMDow02FRe37m-bGdwXd-CmHc+mA@mail.gmail.com>
References: <541848B5.9060901@laposte.net>
 <CALzTN-R5pbYay1MQ8nQ6OBGMDow02FRe37m-bGdwXd-CmHc+mA@mail.gmail.com>
Message-ID: <541ACDE8.4080508@laposte.net>

Hi Matt,

I just sent you a github pull request:

https://github.com/InsightSoftwareConsortium/InsightJournalTemplate/pull/2

Note that I ditched my old fork and started with a clean clone of the 
template.

Jo?l


On 09/16/2014 07:26 PM, Matt McCormick wrote:
> Hi Jo?l,
>
> Yes, that the current best repository, and fixes are welcome!  Please
> add a pull request on the repository and ping the mailing list if it
> is not merged after a few days.
>
> Thanks,
> Matt
>
> On Tue, Sep 16, 2014 at 10:27 AM, Jo?l Schaerer
> <joel.schaerer at laposte.net> wrote:
>> Hi all,
>>
>> The template for Insight Journal submissions that is available on GitHub and
>> recommended on the Insight Journal website
>> (https://github.com/InsightSoftwareConsortium/InsightJournalTemplate) does
>> not build with ITK4.
>>
>> I can try to fix it, but before I do I would like to make sure it is still
>> the current version?
>>
>> Thanks!
>>
>> Jo?l
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users


From matt.mccormick at kitware.com  Thu Sep 18 13:02:55 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 18 Sep 2014 13:02:55 -0400
Subject: [ITK-users] question about wiki example ResampleDICOM
In-Reply-To: <CAK3qF+96eR4XiGcWiis+pAhTGtoq1iKwZ=9_+1W+NDui8nwCUg@mail.gmail.com>
References: <C83078BB-3646-40C7-ABFA-DBB4BA55435F@gmail.com>
 <CAKKNfuLiXhqQEP950jf4XhFj8KA-ge1BtFPDNa8iHdQRLfQv2A@mail.gmail.com>
 <A903CE9B-1D91-494B-84BF-C3ADBDC858B7@gmail.com>
 <0B4FCE54-7AAA-4CE2-B55D-715EC601A553@gmail.com>
 <CAK3qF+-_t8N+0WpSXRFu-1fXFq+68FVQWEiRzkhYFZzunV27Aw@mail.gmail.com>
 <AF25FDC2-8FFF-4BB1-8239-1EE1D9ACFF25@gmail.com>
 <CAK3qF+_bw6A7RUwd+DDbzPfhddX+i3m2xTw2RhEz5p86+wqQvw@mail.gmail.com>
 <CADZJ4hPuoosTP0F=rcf=MLAedFxO82KneEFSH-YG2+LM9dd2XA@mail.gmail.com>
 <CALzTN-Sw2+z6qwBtPt5xVTOOcVsM7_1ECqdR9-NrLfZ6a0DH8w@mail.gmail.com>
 <CAK3qF+9t_hMnssUocOHYFe43frK9vTsOhOki4YDPTdUtXw5yPw@mail.gmail.com>
 <CAK3qF+96eR4XiGcWiis+pAhTGtoq1iKwZ=9_+1W+NDui8nwCUg@mail.gmail.com>
Message-ID: <CALzTN-R=2i3GKT9Fuu7Qif3_y9oiaGOtbmpF3JyYWdePEQVTPA@mail.gmail.com>

Hi Arnaud,

Great to hear it is working!

Yes, good idea on the migration guide to better communicate and
explain the development.  Here is a patch to review.

  http://review.source.kitware.com/#/c/17098/

Thanks,
Matt

On Thu, Sep 18, 2014 at 2:43 AM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
> Matt,
>
> I guess there should be migration report for this fix?
>
> Arnaud
>
> On Thu, Sep 18, 2014 at 8:36 AM, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>>
>> Hi Matt,
>>
>> This is indeed the observed and, based on your answer, expected behaviour.
>> Thank you very much for the confirmation (that's exactly what I needed!).
>>
>> To avoid confusion in future, I am going to modify the corresponding
>> example on github and on the wiki!
>>
>> Best,
>> Arnaud
>>
>> On Wed, Sep 17, 2014 at 5:42 PM, Matt McCormick
>> <matt.mccormick at kitware.com> wrote:
>>>
>>> Hi,
>>>
>>> Do to this fix [1], if the writer is re-using the GDCMImageIO, the
>>> writer should apply the inverse rescale / slope intercept like the
>>> reader applied the rescale / slope intercept when reading.  This was a
>>> long-standing bug that I fixed in 4.6.0.  Arnaud, if the manual
>>> inverse rescale / slope operation is removed, does the correct output
>>> result?
>>>
>>> Thanks,
>>> Matt
>>>
>>> [1]
>>> https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e
>>>
>>> On Wed, Sep 17, 2014 at 10:41 AM, Bill Lorensen <bill.lorensen at gmail.com>
>>> wrote:
>>> > I wrote this example many years ago?
>>> > 1) If the input has a non-trivial slope/intercept, the reader applies
>>> > the slope/intercept to the raw data.
>>> > 2) Rather than setting the slope/intercept in the output dicom, I
>>> > apply the inverse of of the slope intercept to the resampled data
>>> > before writing. The output dicom should not have the origin
>>> > slope/intercept tags.
>>> >
>>> > I'll try to verify this with Slicer, but I may be out of touch for 2
>>> > weeks?
>>> >
>>> > Bill
>>> >
>>> >
>>> > On Wed, Sep 17, 2014 at 10:15 AM, Arnaud Gelas <arnaudgelas at gmail.com>
>>> > wrote:
>>> >> Hi Nick,
>>> >>
>>> >> I can confirm that with the example I get a difference of -1024 (+/-
>>> >> 1) in
>>> >> between the input and the output, using the ShiftScaleImage part...
>>> >> While without this part of code the difference is (+/-1)
>>> >>
>>> >> I would like to make sure this is the expected behaviour!?
>>> >>
>>> >> On Wed, Sep 17, 2014 at 3:35 PM, Nick Patterson
>>> >> <pattersonnp.work at gmail.com>
>>> >> wrote:
>>> >>>
>>> >>> OK, I will wait to hear the outcome of your run with the original
>>> >>> example
>>> >>> then.
>>> >>>
>>> >>> Cheers, Nick.
>>> >>>
>>> >>>
>>> >>>
>>> >>>
>>> >>> On 17 Sep 2014, at 14:34, Arnaud Gelas <arnaudgelas at gmail.com> wrote:
>>> >>>
>>> >>> Nick,
>>> >>>
>>> >>> I can't roll back to previous ITK version, important patches on
>>> >>> itkGDCMImageIO were very recently merged...
>>> >>>
>>> >>>
>>> >>>
>>> >>> https://github.com/Kitware/ITK/commits/master/Modules/IO/GDCM/src/itkGDCMImageIO.cxx
>>> >>>
>>> >>> e.g.
>>> >>>
>>> >>>
>>> >>>
>>> >>> https://github.com/Kitware/ITK/commit/33a7e7162fc040f6c7346af5fc1ec15a80834273
>>> >>>
>>> >>>
>>> >>> https://github.com/Kitware/ITK/commit/2f86b89df192aa80793b2d7f09624a2e4a74ec3c
>>> >>>
>>> >>>
>>> >>> Arnaud
>>> >>>
>>> >>> On Wed, Sep 17, 2014 at 3:29 PM, Nick Patterson
>>> >>> <pattersonnp.work at gmail.com> wrote:
>>> >>>>
>>> >>>> I should also mention Arnauld that I use ITK4.5.2.  I have had many
>>> >>>> issues with using ITK 4.6 with the latest GDCM from git, so rolled
>>> >>>> back to
>>> >>>> ITK4.5.2.
>>> >>>> Nick.
>>> >>>>
>>> >>>>
>>> >>>>
>>> >>>> On 17 Sep 2014, at 14:32, Arnaud Gelas <arnaudgelas at gmail.com>
>>> >>>> wrote:
>>> >>>>
>>> >>>> Hi Matias,
>>> >>>>
>>> >>>> I guess you are referring to
>>> >>>>
>>> >>>>
>>> >>>>
>>> >>>> https://github.com/Kitware/ITK/commit/847ec2b79ac2cedaab6714678c0677793aa23a1e
>>> >>>>
>>> >>>> $ git tag --contains 847ec2b79ac2cedaab6714678c0677793aa23a1e
>>> >>>> v4.6.0
>>> >>>>
>>> >>>> I use the release branch of ITK
>>> >>>>
>>> >>>> ---
>>> >>>>
>>> >>>> Matt,
>>> >>>>
>>> >>>> Can you comment on this, please?
>>> >>>>
>>> >>>> Thanks
>>> >>>> Arnaud
>>> >>>>
>>> >>>> On Sep 17, 2014, at 3:21 PM, Matias Montroull <matimontg at gmail.com>
>>> >>>> wrote:
>>> >>>>
>>> >>>> I had an issue with the resampledicom example once (all my pixel
>>> >>>> values
>>> >>>> were recalculated by adding rescaleintercept) and then downloaded
>>> >>>> the latest
>>> >>>> ITK release (4.6) and worked fine.
>>> >>>>
>>> >>>> The issue was with the GDCMIO class I beleive but was fixed somehow
>>> >>>> in
>>> >>>> the 4.6 version.
>>> >>>>
>>> >>>> On Wed, Sep 17, 2014 at 10:02 AM, Arnaud Gelas
>>> >>>> <arnaudgelas at gmail.com>
>>> >>>> wrote:
>>> >>>>>
>>> >>>>> Hi all,
>>> >>>>>
>>> >>>>> I have been looking at the following wiki example:
>>> >>>>>
>>> >>>>> http://www.itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM
>>> >>>>>
>>> >>>>> It seems to me that the section to rescale the image is not valid
>>> >>>>> anymore with latest ITK version (?)
>>> >>>>>
>>> >>>>>
>>> >>>>>
>>> >>>>> https://github.com/InsightSoftwareConsortium/ITKWikiExamples/blob/master/DICOM/ResampleDICOM.cxx#L314-L333
>>> >>>>>
>>> >>>>> Can anyone confirm?
>>> >>>>>
>>> >>>>> Is this code validated? are output images compared to input ones in
>>> >>>>> the
>>> >>>>> corresponding test?
>>> >>>>>
>>> >>>>> Thanks
>>> >>>>> Arnaud
>>> >>>>>
>>> >>>>> _____________________________________
>>> >>>>> Powered by www.kitware.com
>>> >>>>>
>>> >>>>> Visit other Kitware open-source projects at
>>> >>>>> http://www.kitware.com/opensource/opensource.html
>>> >>>>>
>>> >>>>> Kitware offers ITK Training Courses, for more information visit:
>>> >>>>> http://www.kitware.com/products/protraining.php
>>> >>>>>
>>> >>>>> Please keep messages on-topic and check the ITK FAQ at:
>>> >>>>> http://www.itk.org/Wiki/ITK_FAQ
>>> >>>>>
>>> >>>>> Follow this link to subscribe/unsubscribe:
>>> >>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>> >>>>>
>>> >>>>
>>> >>>>
>>> >>>> _____________________________________
>>> >>>> Powered by www.kitware.com
>>> >>>>
>>> >>>> Visit other Kitware open-source projects at
>>> >>>> http://www.kitware.com/opensource/opensource.html
>>> >>>>
>>> >>>> Kitware offers ITK Training Courses, for more information visit:
>>> >>>> http://www.kitware.com/products/protraining.php
>>> >>>>
>>> >>>> Please keep messages on-topic and check the ITK FAQ at:
>>> >>>> http://www.itk.org/Wiki/ITK_FAQ
>>> >>>>
>>> >>>> Follow this link to subscribe/unsubscribe:
>>> >>>> http://public.kitware.com/mailman/listinfo/insight-users
>>> >>>>
>>> >>>>
>>> >>>
>>> >>>
>>> >>
>>> >>
>>> >> _____________________________________
>>> >> Powered by www.kitware.com
>>> >>
>>> >> Visit other Kitware open-source projects at
>>> >> http://www.kitware.com/opensource/opensource.html
>>> >>
>>> >> Kitware offers ITK Training Courses, for more information visit:
>>> >> http://www.kitware.com/products/protraining.php
>>> >>
>>> >> Please keep messages on-topic and check the ITK FAQ at:
>>> >> http://www.itk.org/Wiki/ITK_FAQ
>>> >>
>>> >> Follow this link to subscribe/unsubscribe:
>>> >> http://public.kitware.com/mailman/listinfo/insight-users
>>> >>
>>> >
>>> >
>>> >
>>> > --
>>> > Unpaid intern in BillsBasement at noware dot com
>>> > _____________________________________
>>> > Powered by www.kitware.com
>>> >
>>> > Visit other Kitware open-source projects at
>>> > http://www.kitware.com/opensource/opensource.html
>>> >
>>> > Kitware offers ITK Training Courses, for more information visit:
>>> > http://www.kitware.com/products/protraining.php
>>> >
>>> > Please keep messages on-topic and check the ITK FAQ at:
>>> > http://www.itk.org/Wiki/ITK_FAQ
>>> >
>>> > Follow this link to subscribe/unsubscribe:
>>> > http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>

From matt.mccormick at kitware.com  Thu Sep 18 13:03:57 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 18 Sep 2014 13:03:57 -0400
Subject: [ITK-users] Mask in metric calculation
In-Reply-To: <CAGKqDmc-HY3Pc8yoMvhsrJeS8uobXP0S1FtuvNzoiSGP3m8nag@mail.gmail.com>
References: <CAGKqDmc-HY3Pc8yoMvhsrJeS8uobXP0S1FtuvNzoiSGP3m8nag@mail.gmail.com>
Message-ID: <CALzTN-TjkRh4PduO0eHNNUopxFRQXU-pxG5PnuW2qt_iemz4WA@mail.gmail.com>

Hi Lianli,

Could you please specify in greater detail which metric class you are
using and how the masks are being applied.

Thanks,
Matt

On Wed, Sep 17, 2014 at 9:54 PM, Lianli Liu <llliu at umich.edu> wrote:
> Hi all,
>
> I just wonder if I define two masks for fixed image and moving image that
> are of differnt size, will voxels that fall in both the masks will
> contribute to metric calculation? Thanks!
>
> Regards,
> Lianli
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>

From matt.mccormick at kitware.com  Thu Sep 18 14:58:39 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 18 Sep 2014 14:58:39 -0400
Subject: [ITK-users] Insight Journal template ITKv4 compatibilty
In-Reply-To: <541ACDE8.4080508@laposte.net>
References: <541848B5.9060901@laposte.net>
 <CALzTN-R5pbYay1MQ8nQ6OBGMDow02FRe37m-bGdwXd-CmHc+mA@mail.gmail.com>
 <541ACDE8.4080508@laposte.net>
Message-ID: <CALzTN-RNNaz5fSgwV2oV7visPEXoQeeOw_y4m6w5mJo118wGmw@mail.gmail.com>

Thanks, merged!

Should the other pull request be closed?

On Thu, Sep 18, 2014 at 8:19 AM, Jo?l Schaerer
<joel.schaerer at laposte.net> wrote:
> Hi Matt,
>
> I just sent you a github pull request:
>
> https://github.com/InsightSoftwareConsortium/InsightJournalTemplate/pull/2
>
> Note that I ditched my old fork and started with a clean clone of the
> template.
>
> Jo?l
>
>
>
> On 09/16/2014 07:26 PM, Matt McCormick wrote:
>>
>> Hi Jo?l,
>>
>> Yes, that the current best repository, and fixes are welcome!  Please
>> add a pull request on the repository and ping the mailing list if it
>> is not merged after a few days.
>>
>> Thanks,
>> Matt
>>
>> On Tue, Sep 16, 2014 at 10:27 AM, Jo?l Schaerer
>> <joel.schaerer at laposte.net> wrote:
>>>
>>> Hi all,
>>>
>>> The template for Insight Journal submissions that is available on GitHub
>>> and
>>> recommended on the Insight Journal website
>>> (https://github.com/InsightSoftwareConsortium/InsightJournalTemplate)
>>> does
>>> not build with ITK4.
>>>
>>> I can try to fix it, but before I do I would like to make sure it is
>>> still
>>> the current version?
>>>
>>> Thanks!
>>>
>>> Jo?l
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>
>

From nikita at iitj.ac.in  Thu Sep 18 15:45:34 2014
From: nikita at iitj.ac.in (Nikita Chopra)
Date: Thu, 18 Sep 2014 15:45:34 -0400
Subject: [ITK-users] (no subject)
Message-ID: <CAKwC1z6mgyRg6dNBrFYh2dgN5Oz6LHWoYzPzWRp_wQwYDjrU_Q@mail.gmail.com>

Hello Admin
I wanted to post this question.
I have built the ITK  libraries on my computer and I have made new projects
using CMake but now I want to integarte  my project that includes QT ,
Opencv and other libs with ITK libs. is there any way by including file
paths in Visual Studio 2010 I would be able to use ITK functions.
Regards
Nikita
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From g.bogle at auckland.ac.nz  Thu Sep 18 15:50:57 2014
From: g.bogle at auckland.ac.nz (Gib Bogle)
Date: Thu, 18 Sep 2014 19:50:57 +0000
Subject: [ITK-users] (no subject)
In-Reply-To: <CAKwC1z6mgyRg6dNBrFYh2dgN5Oz6LHWoYzPzWRp_wQwYDjrU_Q@mail.gmail.com>
References: <CAKwC1z6mgyRg6dNBrFYh2dgN5Oz6LHWoYzPzWRp_wQwYDjrU_Q@mail.gmail.com>
Message-ID: <BD80F91C3E2E394894ED4780703D7F9E826C3DEE@uxcn10-tdc06.UoA.auckland.ac.nz>

Many people will tell you that it's much better to use cmake to create your VS projects.

Cheers
Gib
________________________________
From: Insight-users [insight-users-bounces at itk.org] on behalf of Nikita Chopra [nikita at iitj.ac.in]
Sent: Friday, 19 September 2014 7:45 a.m.
To: Insight-users at itk.org
Subject: [ITK-users] (no subject)

Hello Admin
I wanted to post this question.
I have built the ITK  libraries on my computer and I have made new projects using CMake but now I want to integarte  my project that includes QT , Opencv and other libs with ITK libs. is there any way by including file paths in Visual Studio 2010 I would be able to use ITK functions.
Regards
Nikita
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From chinander at gmail.com  Thu Sep 18 15:51:22 2014
From: chinander at gmail.com (Mike Chinander)
Date: Thu, 18 Sep 2014 14:51:22 -0500
Subject: [ITK-users] (no subject)
In-Reply-To: <CAKwC1z6mgyRg6dNBrFYh2dgN5Oz6LHWoYzPzWRp_wQwYDjrU_Q@mail.gmail.com>
References: <CAKwC1z6mgyRg6dNBrFYh2dgN5Oz6LHWoYzPzWRp_wQwYDjrU_Q@mail.gmail.com>
Message-ID: <CAEb_q0eyD+iK=koJ5z09gUGRR_ZzA6rDwmnFXSr5Sh58XihD3g@mail.gmail.com>

The easiest way is to use CMake to set up your VS project. Here's Qt's
documentation on use CMake with Qt.

On Thu, Sep 18, 2014 at 2:45 PM, Nikita Chopra <nikita at iitj.ac.in> wrote:

> Hello Admin
> I wanted to post this question.
> I have built the ITK  libraries on my computer and I have made new
> projects using CMake but now I want to integarte  my project that includes
> QT , Opencv and other libs with ITK libs. is there any way by including
> file paths in Visual Studio 2010 I would be able to use ITK functions.
> Regards
> Nikita
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
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From chinander at gmail.com  Thu Sep 18 15:51:57 2014
From: chinander at gmail.com (Mike Chinander)
Date: Thu, 18 Sep 2014 14:51:57 -0500
Subject: [ITK-users] (no subject)
In-Reply-To: <CAEb_q0eyD+iK=koJ5z09gUGRR_ZzA6rDwmnFXSr5Sh58XihD3g@mail.gmail.com>
References: <CAKwC1z6mgyRg6dNBrFYh2dgN5Oz6LHWoYzPzWRp_wQwYDjrU_Q@mail.gmail.com>
 <CAEb_q0eyD+iK=koJ5z09gUGRR_ZzA6rDwmnFXSr5Sh58XihD3g@mail.gmail.com>
Message-ID: <CAEb_q0dCkYSoYZ2WU51xqRXQXHfgA3ELLh3_3SrE71J=DQH8jw@mail.gmail.com>

Here's the link I forgot to include in my previous email:
http://qt-project.org/doc/qt-5/cmake-manual.html

On Thu, Sep 18, 2014 at 2:51 PM, Mike Chinander <chinander at gmail.com> wrote:

> The easiest way is to use CMake to set up your VS project. Here's Qt's
> documentation on use CMake with Qt.
>
> On Thu, Sep 18, 2014 at 2:45 PM, Nikita Chopra <nikita at iitj.ac.in> wrote:
>
>> Hello Admin
>> I wanted to post this question.
>> I have built the ITK  libraries on my computer and I have made new
>> projects using CMake but now I want to integarte  my project that includes
>> QT , Opencv and other libs with ITK libs. is there any way by including
>> file paths in Visual Studio 2010 I would be able to use ITK functions.
>> Regards
>> Nikita
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
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From indianzeppelin at gmail.com  Thu Sep 18 15:51:56 2014
From: indianzeppelin at gmail.com (Girish Mallya Udupi)
Date: Thu, 18 Sep 2014 20:51:56 +0100
Subject: [ITK-users] (no subject)
In-Reply-To: <CAKwC1z6mgyRg6dNBrFYh2dgN5Oz6LHWoYzPzWRp_wQwYDjrU_Q@mail.gmail.com>
References: <CAKwC1z6mgyRg6dNBrFYh2dgN5Oz6LHWoYzPzWRp_wQwYDjrU_Q@mail.gmail.com>
Message-ID: <CAA+VR6hBAYmCc_Qsy+fTGjSLzzsCWdGfQjfQpcms0PhJHSFA6Q@mail.gmail.com>

Hi,

Just to clarify, you want to use Qt, OpenCV and ITK together in a project.
Is that correct?

I use OpenCV and ITK together in my projects and use CMake to configure and
generate build files for MSVS 2010. Is that something you have tried?


On Thu, Sep 18, 2014 at 8:45 PM, Nikita Chopra <nikita at iitj.ac.in> wrote:

> Hello Admin
> I wanted to post this question.
> I have built the ITK  libraries on my computer and I have made new
> projects using CMake but now I want to integarte  my project that includes
> QT , Opencv and other libs with ITK libs. is there any way by including
> file paths in Visual Studio 2010 I would be able to use ITK functions.
> Regards
> Nikita
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>


-- 
Regards,
Girish
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From nikita at iitj.ac.in  Thu Sep 18 15:57:30 2014
From: nikita at iitj.ac.in (Nikita Chopra)
Date: Thu, 18 Sep 2014 15:57:30 -0400
Subject: [ITK-users] (no subject)
In-Reply-To: <CAA+VR6hBAYmCc_Qsy+fTGjSLzzsCWdGfQjfQpcms0PhJHSFA6Q@mail.gmail.com>
References: <CAKwC1z6mgyRg6dNBrFYh2dgN5Oz6LHWoYzPzWRp_wQwYDjrU_Q@mail.gmail.com>
 <CAA+VR6hBAYmCc_Qsy+fTGjSLzzsCWdGfQjfQpcms0PhJHSFA6Q@mail.gmail.com>
Message-ID: <CAKwC1z4vdsG+q6wsRyJX9QztnP9OG3gWGBV_FJdZQT9e1qD=FA@mail.gmail.com>

Hi
Thanks a lot for quick responses . Can you suggest me the changes I should
make in .pro file to add ITK libs there so I can use qmake to build the
project .Thanks again I'm new to ITK and any help would be really
appreciated. My .pro file is as follows.
# ------------------------------
-------------------
# Project created by QtCreator 2010-10-25T15:08:18
# -------------------------------------------------
QT += opengl
TARGET = Endoscopic3D
TEMPLATE = app
INCLUDEPATH += . \
    "C:\Program Files\Matrox Imaging\Mil\Include"
LIBS += "-LC:\Program Files\Matrox Imaging\Mil\LIB" \
        -lmil
SOURCES += main.cpp \
    mainwindow.cpp \
    thread.cpp \
    display3d.cpp \
    matroxmeteorii.cpp
HEADERS += mainwindow.h \
    thread.h \
    display3d.h \
    core.h \
    matroxmeteorii.h
FORMS += mainwindow.ui

On Thu, Sep 18, 2014 at 3:51 PM, Girish Mallya Udupi <
indianzeppelin at gmail.com> wrote:

> Hi,
>
> Just to clarify, you want to use Qt, OpenCV and ITK together in a project.
> Is that correct?
>
> I use OpenCV and ITK together in my projects and use CMake to configure
> and generate build files for MSVS 2010. Is that something you have tried?
>
>
> On Thu, Sep 18, 2014 at 8:45 PM, Nikita Chopra <nikita at iitj.ac.in> wrote:
>
>> Hello Admin
>> I wanted to post this question.
>> I have built the ITK  libraries on my computer and I have made new
>> projects using CMake but now I want to integarte  my project that includes
>> QT , Opencv and other libs with ITK libs. is there any way by including
>> file paths in Visual Studio 2010 I would be able to use ITK functions.
>> Regards
>> Nikita
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
>
> --
> Regards,
> Girish
>
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From indianzeppelin at gmail.com  Thu Sep 18 16:07:19 2014
From: indianzeppelin at gmail.com (Girish Mallya Udupi)
Date: Thu, 18 Sep 2014 21:07:19 +0100
Subject: [ITK-users] (no subject)
In-Reply-To: <CAKwC1z4vdsG+q6wsRyJX9QztnP9OG3gWGBV_FJdZQT9e1qD=FA@mail.gmail.com>
References: <CAKwC1z6mgyRg6dNBrFYh2dgN5Oz6LHWoYzPzWRp_wQwYDjrU_Q@mail.gmail.com>
 <CAA+VR6hBAYmCc_Qsy+fTGjSLzzsCWdGfQjfQpcms0PhJHSFA6Q@mail.gmail.com>
 <CAKwC1z4vdsG+q6wsRyJX9QztnP9OG3gWGBV_FJdZQT9e1qD=FA@mail.gmail.com>
Message-ID: <CAA+VR6h4RM=eamWdDHmiMZ+-YmnQjLzoxpdXvPhmSLaY=keJnA@mail.gmail.com>

Never used Qt myself, so can't help you with that.

But, have you considered using CMake? There are CMake 'find' modules
available for OpenCV, ITK and Qt (from what I see in the link sent by
Mike). That same link explains how to use Qt with CMake.

On Thu, Sep 18, 2014 at 8:57 PM, Nikita Chopra <nikita at iitj.ac.in> wrote:

> Hi
> Thanks a lot for quick responses . Can you suggest me the changes I should
> make in .pro file to add ITK libs there so I can use qmake to build the
> project .Thanks again I'm new to ITK and any help would be really
> appreciated. My .pro file is as follows.
> # ------------------------------
> -------------------
> # Project created by QtCreator 2010-10-25T15:08:18
> # -------------------------------------------------
> QT += opengl
> TARGET = Endoscopic3D
> TEMPLATE = app
> INCLUDEPATH += . \
>     "C:\Program Files\Matrox Imaging\Mil\Include"
> LIBS += "-LC:\Program Files\Matrox Imaging\Mil\LIB" \
>         -lmil
> SOURCES += main.cpp \
>     mainwindow.cpp \
>     thread.cpp \
>     display3d.cpp \
>     matroxmeteorii.cpp
> HEADERS += mainwindow.h \
>     thread.h \
>     display3d.h \
>     core.h \
>     matroxmeteorii.h
> FORMS += mainwindow.ui
>
> On Thu, Sep 18, 2014 at 3:51 PM, Girish Mallya Udupi <
> indianzeppelin at gmail.com> wrote:
>
>> Hi,
>>
>> Just to clarify, you want to use Qt, OpenCV and ITK together in a
>> project. Is that correct?
>>
>> I use OpenCV and ITK together in my projects and use CMake to configure
>> and generate build files for MSVS 2010. Is that something you have tried?
>>
>>
>> On Thu, Sep 18, 2014 at 8:45 PM, Nikita Chopra <nikita at iitj.ac.in> wrote:
>>
>>> Hello Admin
>>> I wanted to post this question.
>>> I have built the ITK  libraries on my computer and I have made new
>>> projects using CMake but now I want to integarte  my project that includes
>>> QT , Opencv and other libs with ITK libs. is there any way by including
>>> file paths in Visual Studio 2010 I would be able to use ITK functions.
>>> Regards
>>> Nikita
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>>
>>
>>
>> --
>> Regards,
>> Girish
>>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>


-- 
Regards,
Girish
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From joel.schaerer at gmail.com  Thu Sep 18 16:12:09 2014
From: joel.schaerer at gmail.com (=?UTF-8?B?Sm/Dq2wgU2NoYWVyZXI=?=)
Date: Thu, 18 Sep 2014 22:12:09 +0200
Subject: [ITK-users] Insight Journal template ITKv4 compatibilty
In-Reply-To: <CALzTN-RNNaz5fSgwV2oV7visPEXoQeeOw_y4m6w5mJo118wGmw@mail.gmail.com>
References: <541848B5.9060901@laposte.net>
 <CALzTN-R5pbYay1MQ8nQ6OBGMDow02FRe37m-bGdwXd-CmHc+mA@mail.gmail.com>
 <541ACDE8.4080508@laposte.net>
 <CALzTN-RNNaz5fSgwV2oV7visPEXoQeeOw_y4m6w5mJo118wGmw@mail.gmail.com>
Message-ID: <541B3C99.1070503@gmail.com>

Done!

On 09/18/2014 08:58 PM, Matt McCormick wrote:
> Thanks, merged!
>
> Should the other pull request be closed?
>
> On Thu, Sep 18, 2014 at 8:19 AM, Jo?l Schaerer
> <joel.schaerer at laposte.net> wrote:
>> Hi Matt,
>>
>> I just sent you a github pull request:
>>
>> https://github.com/InsightSoftwareConsortium/InsightJournalTemplate/pull/2
>>
>> Note that I ditched my old fork and started with a clean clone of the
>> template.
>>
>> Jo?l
>>
>>
>>
>> On 09/16/2014 07:26 PM, Matt McCormick wrote:
>>> Hi Jo?l,
>>>
>>> Yes, that the current best repository, and fixes are welcome!  Please
>>> add a pull request on the repository and ping the mailing list if it
>>> is not merged after a few days.
>>>
>>> Thanks,
>>> Matt
>>>
>>> On Tue, Sep 16, 2014 at 10:27 AM, Jo?l Schaerer
>>> <joel.schaerer at laposte.net> wrote:
>>>> Hi all,
>>>>
>>>> The template for Insight Journal submissions that is available on GitHub
>>>> and
>>>> recommended on the Insight Journal website
>>>> (https://github.com/InsightSoftwareConsortium/InsightJournalTemplate)
>>>> does
>>>> not build with ITK4.
>>>>
>>>> I can try to fix it, but before I do I would like to make sure it is
>>>> still
>>>> the current version?
>>>>
>>>> Thanks!
>>>>
>>>> Jo?l
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users


From chinander at gmail.com  Thu Sep 18 16:46:51 2014
From: chinander at gmail.com (Mike Chinander)
Date: Thu, 18 Sep 2014 15:46:51 -0500
Subject: [ITK-users] (no subject)
In-Reply-To: <CAKwC1z4vdsG+q6wsRyJX9QztnP9OG3gWGBV_FJdZQT9e1qD=FA@mail.gmail.com>
References: <CAKwC1z6mgyRg6dNBrFYh2dgN5Oz6LHWoYzPzWRp_wQwYDjrU_Q@mail.gmail.com>
 <CAA+VR6hBAYmCc_Qsy+fTGjSLzzsCWdGfQjfQpcms0PhJHSFA6Q@mail.gmail.com>
 <CAKwC1z4vdsG+q6wsRyJX9QztnP9OG3gWGBV_FJdZQT9e1qD=FA@mail.gmail.com>
Message-ID: <CAEb_q0frKAGq7W6pE5m-Mp5pD40698SzQ_1KpAFu_zaQmsggBQ@mail.gmail.com>

A CMakeLists.txt files replaces your .pro project file. Yours would look
something like the following. I don't use Qt Designer so I'm not quite sure
about the .ui-related configuration (or the OpenGL module).

cmake_minimum_required(VERSION 2.8.12)
PROJECT(Endoscopic3D)
set(CMAKE_AUTOMOC ON)
set(CMAKE_INCLUDE_CURRENT_DIR ON)

SET(ITK_DIR "C:/Program Files/ITK/lib/cmake/ITK-4.5")
FIND_PACKAGE(Qt5Core REQUIRED )
FIND_PACKAGE(Qt5Widgets REQUIRED)
FIND_PACKAGE(Qt5OpenGL REQUIRED)
find_package(ITK REQUIRED)
include(${ITK_USE_FILE})
include_directories (${CMAKE_CURRENT_BINARY_DIR})

SET (SRCS main.cpp
    mainwindow.cpp
    thread.cpp
    display3d.cpp
    matroxmeteorii.cpp)

SET (MOC_SRCS mainwindow.h
    thread.h
    display3d.h
    core.h
    matroxmeteorii.h)

QT5_WRAP_UI(UIS_HDRS
    mainwindow.ui)

ADD_EXECUTABLE(Endoscopic3D WIN32 ${SRCS} ${UIS_HDRS} )
TARGET_LINK_LIBRARIES(Endoscopic3D  Qt5::Widgets Qt5::OpenGL
${ITK_LIBRARIES})

On Thu, Sep 18, 2014 at 2:57 PM, Nikita Chopra <nikita at iitj.ac.in> wrote:

> Hi
> Thanks a lot for quick responses . Can you suggest me the changes I should
> make in .pro file to add ITK libs there so I can use qmake to build the
> project .Thanks again I'm new to ITK and any help would be really
> appreciated. My .pro file is as follows.
> # ------------------------------
> -------------------
> # Project created by QtCreator 2010-10-25T15:08:18
> # -------------------------------------------------
> QT += opengl
> TARGET = Endoscopic3D
> TEMPLATE = app
> INCLUDEPATH += . \
>     "C:\Program Files\Matrox Imaging\Mil\Include"
> LIBS += "-LC:\Program Files\Matrox Imaging\Mil\LIB" \
>         -lmil
> SOURCES += main.cpp \
>     mainwindow.cpp \
>     thread.cpp \
>     display3d.cpp \
>     matroxmeteorii.cpp
> HEADERS += mainwindow.h \
>     thread.h \
>     display3d.h \
>     core.h \
>     matroxmeteorii.h
> FORMS += mainwindow.ui
>
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From llliu at umich.edu  Sun Sep 21 22:30:37 2014
From: llliu at umich.edu (Lianli Liu)
Date: Sun, 21 Sep 2014 22:30:37 -0400
Subject: [ITK-users] B spline multi grid registration
Message-ID: <CAGKqDmddUvrXV=xTfVx7G9+-k3Q5NdASqg1VEVjbhpvp=O9hsw@mail.gmail.com>

Hi all,

I am trying to use the B spline multi grid registration method in ITK, as
given by the example code deformableregistration7.cxx. I used to 3D MRI
images in analyze format (.img). I received the following error information:

terminate called after throwing an instance of 'std::bad_alloc'

I was wondering what is wrong and how to fix it?

Thanks!

Lianli
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From nikita at iitj.ac.in  Sun Sep 21 22:44:38 2014
From: nikita at iitj.ac.in (Nikita Chopra)
Date: Sun, 21 Sep 2014 22:44:38 -0400
Subject: [ITK-users] B spline multi grid registration
In-Reply-To: <CAGKqDmddUvrXV=xTfVx7G9+-k3Q5NdASqg1VEVjbhpvp=O9hsw@mail.gmail.com>
References: <CAGKqDmddUvrXV=xTfVx7G9+-k3Q5NdASqg1VEVjbhpvp=O9hsw@mail.gmail.com>
Message-ID: <CAKwC1z5Mo0bX5qs_rjGGtAV_0TtK0jBTDtd5KQo0w5x6_3+4Ng@mail.gmail.com>

Did you tr to debug it , Can you share the specific line in code where the
error occurs ? I have used the same example to register CT scans with
slight modification.

On Sun, Sep 21, 2014 at 10:30 PM, Lianli Liu <llliu at umich.edu> wrote:

> Hi all,
>
> I am trying to use the B spline multi grid registration method in ITK, as
> given by the example code deformableregistration7.cxx. I used to 3D MRI
> images in analyze format (.img). I received the following error information:
>
> terminate called after throwing an instance of 'std::bad_alloc'
>
> I was wondering what is wrong and how to fix it?
>
> Thanks!
>
> Lianli
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
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From matt.mccormick at kitware.com  Sun Sep 21 22:58:59 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Sun, 21 Sep 2014 22:58:59 -0400
Subject: [ITK-users] B spline multi grid registration
In-Reply-To: <CAGKqDmddUvrXV=xTfVx7G9+-k3Q5NdASqg1VEVjbhpvp=O9hsw@mail.gmail.com>
References: <CAGKqDmddUvrXV=xTfVx7G9+-k3Q5NdASqg1VEVjbhpvp=O9hsw@mail.gmail.com>
Message-ID: <CALzTN-Qvk7Wk=u89gFSp-pHEQAwGVM1qF=zNRKxcmJKc+OfDbA@mail.gmail.com>

Hi Lianli,

On Sun, Sep 21, 2014 at 10:30 PM, Lianli Liu <llliu at umich.edu> wrote:
> Hi all,
>
> I am trying to use the B spline multi grid registration method in ITK, as
> given by the example code deformableregistration7.cxx. I used to 3D MRI
> images in analyze format (.img). I received the following error information:
>
> terminate called after throwing an instance of 'std::bad_alloc'
>
> I was wondering what is wrong and how to fix it?

Are you running out of memory?

HTH,
Matt

From llliu at umich.edu  Sun Sep 21 23:13:09 2014
From: llliu at umich.edu (Lianli Liu)
Date: Sun, 21 Sep 2014 23:13:09 -0400
Subject: [ITK-users] B spline multi grid registration
In-Reply-To: <CALzTN-Qvk7Wk=u89gFSp-pHEQAwGVM1qF=zNRKxcmJKc+OfDbA@mail.gmail.com>
References: <CAGKqDmddUvrXV=xTfVx7G9+-k3Q5NdASqg1VEVjbhpvp=O9hsw@mail.gmail.com>
 <CALzTN-Qvk7Wk=u89gFSp-pHEQAwGVM1qF=zNRKxcmJKc+OfDbA@mail.gmail.com>
Message-ID: <CAGKqDmdR_cRbeMzdO345tpE-w+aBFoMw3Pre=gPHxUxCzsx6ZQ@mail.gmail.com>

Hi all,

Thanks for help. The program runs after I change the metric from mean
square error to mutual information. But the new problem is the transformed
image looks really wired. Seems the intensity is distorted a lot. I was
wondering what may be the possible cause of this?

Regards,
Lianli

On Sun, Sep 21, 2014 at 10:58 PM, Matt McCormick <matt.mccormick at kitware.com
> wrote:

> Hi Lianli,
>
> On Sun, Sep 21, 2014 at 10:30 PM, Lianli Liu <llliu at umich.edu> wrote:
> > Hi all,
> >
> > I am trying to use the B spline multi grid registration method in ITK, as
> > given by the example code deformableregistration7.cxx. I used to 3D MRI
> > images in analyze format (.img). I received the following error
> information:
> >
> > terminate called after throwing an instance of 'std::bad_alloc'
> >
> > I was wondering what is wrong and how to fix it?
>
> Are you running out of memory?
>
> HTH,
> Matt
>
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From vijayarani.shanmugavadivu at appasamy.com  Mon Sep 22 07:52:36 2014
From: vijayarani.shanmugavadivu at appasamy.com (vijayarani)
Date: Mon, 22 Sep 2014 04:52:36 -0700 (PDT)
Subject: [ITK-users] Picking 10000 samples from a larger mha image using
 ImageRandomNonRepeatingConstIteratorWithIndex and finding histogram.
Message-ID: <1411386756138-7586255.post@n2.nabble.com>

Hi
I tried to pick 10000 samples from a larger mha image (which size is 167 MB)
using ImageRandomNonRepeatingConstIteratorWithIndex class and tried to find
the histogram and percentile
values for the resultant image. However it gives 0 to all the percentiles.
When I do the same for a small image it gives the valid percentile
values.How to achieve finding histogram and percentiles for a larger mha
image by picking up only 10000 samples from the original image?

Thanks & Regards
Vijaya Rani S



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Picking-10000-samples-from-a-larger-mha-image-using-ImageRandomNonRepeatingConstIteratorWithIndex-an-tp7586255.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From blowekamp at mail.nih.gov  Mon Sep 22 09:08:11 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Mon, 22 Sep 2014 09:08:11 -0400
Subject: [ITK-users] Picking 10000 samples from a larger mha image using
	ImageRandomNonRepeatingConstIteratorWithIndex and finding histogram.
In-Reply-To: <1411386756138-7586255.post@n2.nabble.com>
References: <1411386756138-7586255.post@n2.nabble.com>
Message-ID: <C5BE2793-3E83-41C6-B963-D570782930E7@mail.nih.gov>

Hello,

Do you have a small compilable example of this problem? It's really impossible to give specific information without any code.

The most frequent reason for this type of issue is that the Update method to the reader has not been called before a manual iteration over the image. So the size of the image is zero during iteration.

Brad

On Sep 22, 2014, at 7:52 AM, vijayarani <vijayarani.shanmugavadivu at appasamy.com> wrote:

> Hi
> I tried to pick 10000 samples from a larger mha image (which size is 167 MB)
> using ImageRandomNonRepeatingConstIteratorWithIndex class and tried to find
> the histogram and percentile
> values for the resultant image. However it gives 0 to all the percentiles.
> When I do the same for a small image it gives the valid percentile
> values.How to achieve finding histogram and percentiles for a larger mha
> image by picking up only 10000 samples from the original image?
> 
> Thanks & Regards
> Vijaya Rani S
> 
> 
> 
> --
> View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Picking-10000-samples-from-a-larger-mha-image-using-ImageRandomNonRepeatingConstIteratorWithIndex-an-tp7586255.html
> Sent from the ITK Insight Users mailing list archive at Nabble.com.
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users


From genet at biomed.ee.ethz.ch  Mon Sep 22 15:49:25 2014
From: genet at biomed.ee.ethz.ch (Martin Genet)
Date: Mon, 22 Sep 2014 21:49:25 +0200
Subject: [ITK-users] FEMRegistration
Message-ID: <54207D45.9070409@biomed.ee.ethz.ch>

Dear all:

Trying to use FEMRegistration on a bunch of images. Still trying to 
figure out the following:

  - What is the simplest way to convert an external mesh (e.g., 
vtkUnstructuredGrid, or GMSH) into an FEMObject (for registration), and 
vice versa (for post-treatment, vizualization)?

  - If the mesh covers only a subset of the image, what happens to the 
rest of the image?

Any help would be super appreciated. Sorry if that's too trivial. Thanks 
in advance.

Martin


From matt.mccormick at kitware.com  Mon Sep 22 16:54:40 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 22 Sep 2014 16:54:40 -0400
Subject: [ITK-users] FEMRegistration
In-Reply-To: <54207D45.9070409@biomed.ee.ethz.ch>
References: <54207D45.9070409@biomed.ee.ethz.ch>
Message-ID: <CALzTN-Qo6hbgL8mxVWUA8VKV3p0e_4NH5=Q_+tyuVjSeg_Y3Nw@mail.gmail.com>

Hi Martin,

itk::MeshFileReader and itk::MeshFileWriter are great classes for
importing / exporting meshes.

HTH,
Matt

On Mon, Sep 22, 2014 at 3:49 PM, Martin Genet <genet at biomed.ee.ethz.ch> wrote:
> Dear all:
>
> Trying to use FEMRegistration on a bunch of images. Still trying to figure
> out the following:
>
>  - What is the simplest way to convert an external mesh (e.g.,
> vtkUnstructuredGrid, or GMSH) into an FEMObject (for registration), and vice
> versa (for post-treatment, vizualization)?
>
>  - If the mesh covers only a subset of the image, what happens to the rest
> of the image?
>
> Any help would be super appreciated. Sorry if that's too trivial. Thanks in
> advance.
>
> Martin
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

From vijayarani.shanmugavadivu at appasamy.com  Tue Sep 23 02:10:56 2014
From: vijayarani.shanmugavadivu at appasamy.com (vijayarani)
Date: Mon, 22 Sep 2014 23:10:56 -0700 (PDT)
Subject: [ITK-users] Picking 10000 samples from a larger mha image using
 ImageRandomNonRepeatingConstIteratorWithIndex and finding histogram.
In-Reply-To: <C5BE2793-3E83-41C6-B963-D570782930E7@mail.nih.gov>
References: <1411386756138-7586255.post@n2.nabble.com>
 <C5BE2793-3E83-41C6-B963-D570782930E7@mail.nih.gov>
Message-ID: <1411452656592-7586259.post@n2.nabble.com>

Hi,
Thanks for your reply.Here is my code and the output

#include "itkImage.h"
#include "itkImageFileReader.h"
#include <itkScalarImageToHistogramGenerator.h>
#include <itkMetaImageIO.h>
#include <itkTIFFImageIO.h>
#include "itkImageFileWriter.h"
#include "itkImageRandomNonRepeatingConstIteratorWithIndex.h"
 
int main(int argc, char*argv[])
{
   const    unsigned int    Dimension = 3;
   typedef unsigned short PixelType;
   typedef itk::Image<PixelType, Dimension>  ImageType;

   typedef itk::ImageFileReader< ImageType  > ImageReaderType;
   typedef itk::ImageFileWriter< ImageType  > ImageWriterType;

   ImageReaderType::Pointer ImageReader   = ImageReaderType::New();
   ImageWriterType::Pointer ImageWriter =  ImageWriterType::New();

   ImageReader->SetFileName( "SampleMha.mha" );
   ImageWriter->SetFileName( "RandomIterator.mha" );

   ImageType::Pointer Image = ImageReader->GetOutput();
   Image->Update();

   ImageType::RegionType region=Image->GetRequestedRegion();
   ImageType::SizeType size=region.GetSize();
   ImageType::IndexType index=region.GetIndex();
   ImageType::IndexType start = index;
   ImageType::SpacingType   spacing   = Image->GetSpacing();
   ImageType::DirectionType direction = Image->GetDirection();

   ImageType::RegionType newregion;
   newregion.SetSize(size);
   newregion.SetIndex(start);
   std::cout << "The size of the image is " << size <<std::endl;
   
   //Define Output Image
   ImageType::Pointer output = ImageType::New();
   output->SetRegions(newregion);
   output->SetSpacing(spacing);
   output->SetDirection(direction);
   output->Allocate();
   output->FillBuffer(0);
   output->Update();
 
   typedef itk::ImageRandomNonRepeatingConstIteratorWithIndex<ImageType >
ConstIteratorType;                                

   ConstIteratorType inputIt(  Image,  region );

   unsigned int number = 10000;
   inputIt.SetNumberOfSamples( number  ); 
   std::cout << "The number of samples is " << number  << std::endl;
   inputIt.ReinitializeSeed();
   inputIt.GoToBegin();

   while(!inputIt.IsAtEnd())  
   {    
     output->SetPixel(inputIt.GetIndex(), inputIt.Get());
     ++inputIt;
   }
   output->Update();
   ImageWriter->SetInput( output );
   ImageWriter->Update();
   calculatePercentile("RandomIterator.mha"); 
   return EXIT_SUCCESS;
}
void calculatePercentile(QString file)
{ 
  qDebug()<<"Calling:  calculatePercentile";
  //Define the pixel type and dimension for reader
  typedef int InternalPixelType;
  const unsigned int    Dimension=3;
  typedef itk::Image<InternalPixelType, Dimension>    InternalImageType;

  //Define the reader
  typedef itk::ImageFileReader<InternalImageType>  ReaderType;
  ReaderType::Pointer reader = ReaderType::New();

  typedef InternalPixelType HistogramMeasurementType;
  typedef itk::Statistics::Histogram< HistogramMeasurementType >
HistogramType;
  typedef itk::Statistics::ImageToListSampleAdaptor< InternalImageType >  
AdaptorType;
  AdaptorType::Pointer adaptor = AdaptorType::New();
  typedef
itk::Statistics::SampleToHistogramFilter<AdaptorType,HistogramType>
FilterType;
  FilterType::Pointer filter = FilterType::New();

  if(QFileInfo(file).suffix()=="mha")
  {
    typedef itk::MetaImageIO    MetaImageIOType;
	MetaImageIOType::Pointer metaIO=MetaImageIOType::New();
	metaIO->SetFileName(file.toLocal8Bit().data());  
	reader->SetFileName(file.toLocal8Bit().data());	
	metaIO->ReadImageInformation();	
	qDebug()<<"No of dimesnsions "<<metaIO->GetNumberOfDimensions()<<"No of
Comps "<<metaIO->GetNumberOfComponents()<<"Comp size
"<<metaIO->GetComponentSize();
    qDebug()<<"Image size in bytes "<<metaIO->GetImageSizeInBytes()<<"Image
size in Comps "<<metaIO->GetImageSizeInComponents()<<"Image size in Pixels
"<<metaIO->GetImageSizeInPixels();
 
	adaptor->SetImage(reader->GetOutput() );
	try
	{
	  reader->Update();
	}
	catch( itk::ExceptionObject & excp )
	{
	  std::cerr << "Problem reading image file" << std::endl;
	  std::cerr << excp << std::endl;  
	}
	const unsigned int numberOfComponents = metaIO->GetNumberOfComponents();
	HistogramType::SizeType size(numberOfComponents);
	size.Fill( metaIO->GetImageSizeInPixels() );	
	filter->SetInput( adaptor );
	filter->SetHistogramSize( size );
	filter->SetMarginalScale( 10 );
	HistogramType::MeasurementVectorType min( numberOfComponents );
	HistogramType::MeasurementVectorType max( numberOfComponents );
	min.Fill( 0 );
	max.Fill( metaIO->GetImageSizeInComponents() );	
	filter->SetHistogramBinMinimum( min );
	filter->SetHistogramBinMaximum( max );
	filter->Update();
  }  
  HistogramType::ConstPointer histogram = filter->GetOutput();
  qDebug()<<"5th percentile is "<< histogram->Quantile( 0, 0.05 ) <<" 25th
percentile is  "<<histogram->Quantile( 0, 0.25 )<<" 50th percentile is 
"<<histogram->Quantile( 0, 0.50 )<<" 75th percentile is 
"<<histogram->Quantile( 0, 0.75 )<<" 95th percentile is
"<<histogram->Quantile( 0, 0.95 );
}

And the output is:
The size of the image is [650, 450, 300]
The number of samples is 10000
Calling:  calculatePercentile
No of dimesnsions  3 No of Comps  1 Comp size  2
Image size in bytes  175500000 Image size in Comps  87750000 Image size in
Pixels  87750000
5th percentile is  0  25th percentile is   0   50th percentile is  0   75th
percentile is  0   95th percentile is 0

I have uploaded the SampleMha.mha file.

Thanks & Regards
Vijaya Rani S



--
View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Picking-10000-samples-from-a-larger-mha-image-using-ImageRandomNonRepeatingConstIteratorWithIndex-an-tp7586255p7586259.html
Sent from the ITK Insight Users mailing list archive at Nabble.com.

From noreply at insightsoftwareconsortium.org  Tue Sep 23 02:40:01 2014
From: noreply at insightsoftwareconsortium.org (Insight Journal)
Date: Tue, 23 Sep 2014 02:40:01 -0400 (EDT)
Subject: [ITK-users] New Submission: InsightToolkit Kinetic Analysis
	(itk::ka) Library
Message-ID: <20140923064001.A66743D6C194@insightsoftwareconsortium.org>

Hello,

A new submission has been added to the Insight Journal.

Title: InsightToolkit Kinetic Analysis (itk::ka) Library
Authors: Dowson N., Baker C., Raffelt D., Smith J., Thomas P., Salvado O., Rose S.
Abstract: This paper describes how to compile and use the Insight Toolkit Kinetic Analysis library (itk::ka), to perform analysis of dynamic medical images, along with a brief overview of the library source code. A set of interfaces to facilitate application development (koala) and an application using Powell???s Dogleg optimisation (koalaDogleg) are also supplied, along with some sample data. Only versions of ITK4 and higher are currently supported.


Download and review this publication at: http://hdl.handle.net/10380/3469

Generated by the Insight Journal

You are receiving this email because you asked to be informed by the Insight Journal for new submissions. To change your email preference visit http://www.insight-journal.org/ .

From karl.diedrich at azetech.com  Tue Sep 23 11:59:22 2014
From: karl.diedrich at azetech.com (Karl Diedrich)
Date: Tue, 23 Sep 2014 11:59:22 -0400
Subject: [ITK-users] looking for itk:DomainThreader example
Message-ID: <542198DA.2070604@azetech.com>

Hello,

Does anyone know where an example program using the itk::DomainThreader 
is?  There is a missing link [ 
http://itk.org/ITKExamples/Examples/Core/Common/DoDataParallelThreading/DoDataParallelThreading.html 
] to an example on an ITKBar camp website here
http://insightsoftwareconsortium.github.io/ITKBarCamp-doc/ITK/WriteMultiThreadedCode/index.html

Thanks,

Karl

-- 
Karl Diedrich, Ph.D.
Principal Engineer
AZE Technology, Inc.
1 Broadway 14th Floor
Cambridge, MA 02142, USA
Phone: 1-617-475-1502
Fax: 1-617-588-1889
http://www.azetech.com/


From matt.mccormick at kitware.com  Tue Sep 23 14:24:11 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 23 Sep 2014 14:24:11 -0400
Subject: [ITK-users] looking for itk:DomainThreader example
In-Reply-To: <542198DA.2070604@azetech.com>
References: <542198DA.2070604@azetech.com>
Message-ID: <CALzTN-RKUjCT9OgGF+x69NMPUWHBnrQm6nMZb3Df1Tf2FJZBKg@mail.gmail.com>

Hii Karl,

The example is here:

 http://itk.org/ITKExamples/src/Core/Common/DoDataParallelThreading/Documentation.html

I have also fixed the link.

Thanks,
Matt

On Tue, Sep 23, 2014 at 11:59 AM, Karl Diedrich
<karl.diedrich at azetech.com> wrote:
> Hello,
>
> Does anyone know where an example program using the itk::DomainThreader is?
> There is a missing link [
> http://itk.org/ITKExamples/Examples/Core/Common/DoDataParallelThreading/DoDataParallelThreading.html
> ] to an example on an ITKBar camp website here
> http://insightsoftwareconsortium.github.io/ITKBarCamp-doc/ITK/WriteMultiThreadedCode/index.html
>
> Thanks,
>
> Karl
>
> --
> Karl Diedrich, Ph.D.
> Principal Engineer
> AZE Technology, Inc.
> 1 Broadway 14th Floor
> Cambridge, MA 02142, USA
> Phone: 1-617-475-1502
> Fax: 1-617-588-1889
> http://www.azetech.com/
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

From llliu at umich.edu  Tue Sep 23 21:51:17 2014
From: llliu at umich.edu (Lianli Liu)
Date: Tue, 23 Sep 2014 21:51:17 -0400
Subject: [ITK-users] format of mask file
Message-ID: <CAGKqDmfLY+2SwWJshQ4=cg0mS4VDKaC7-6P4VXDeTBFXh9=cdA@mail.gmail.com>

Hi all,

I am a bit unclear about the format of mask file. Is it fine if I use an
image of analyze format that has 0,1 value, but of integer type not boolean
type?

The reason I am asking is that when I use this mask in the mutual
information metric, there is an error : joint PDF summed to zero...

Thanks!
Lianli
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From eryanvtk at yahoo.com  Wed Sep 24 07:27:00 2014
From: eryanvtk at yahoo.com (Emma Ryan)
Date: Wed, 24 Sep 2014 04:27:00 -0700
Subject: [ITK-users] Image Rotation while preserving image
Message-ID: <1411558020.53437.YahooMailNeo@web120605.mail.ne1.yahoo.com>

Hi,

  I would like to rotate an input mage by a few degrees. I was able to easily do this using rigid transforms available in itk. But the output image is cropped. The extent of cropping is directly related to the angle of rotation. How can one disallow this kind of cropping ?

Thank you for your help.
regards,
Emma
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From eryanvtk at yahoo.com  Wed Sep 24 13:06:26 2014
From: eryanvtk at yahoo.com (Emma Ryan)
Date: Wed, 24 Sep 2014 10:06:26 -0700
Subject: [ITK-users] Image Rotation while preserving image
In-Reply-To: <CALzTN-RKi4kfR3DhN8AWs_Y0Q33+1n+PFu7=s=zgOK2SFhpDOA@mail.gmail.com>
References: <1411558020.53437.YahooMailNeo@web120605.mail.ne1.yahoo.com>
 <CALzTN-RKi4kfR3DhN8AWs_Y0Q33+1n+PFu7=s=zgOK2SFhpDOA@mail.gmail.com>
Message-ID: <1411578386.9555.YahooMailNeo@web120603.mail.ne1.yahoo.com>

HI Matt,

 Thank you for your reply. Attached is a snapshot of what is happening. The square needs to rotate and become a diamond. But after rotation, I get a chopped image. Ideally, I would just expect a larger sized matrix holding the larger image. So I'm not sure I understand how the 'content' could be missing.

I couldn't experiment with SetExtrapolator as it is probably not available in the version of itk that I am using . Version 3.X.

Are you suggesting that using Extrapolation, I would be able to address this specific problem ?

regards,
Emma








On Wednesday, September 24, 2014 7:44 AM, Matt McCormick <matt.mccormick at kitware.com> wrote:
 


Hi Emma,

If there is no content to resample from after the transformation, then
a default pixel value is used.  To use extrapolation instead, call
SetExtrapolator() [1] on the ResampleImageFilter.

HTH,
Matt

[1] http://www.itk.org/Insight/Doxygen/html/classitk_1_1ResampleImageFilter.html#a89d912b5608fbe73a9a2ca0ebcfebb69


On Wed, Sep 24, 2014 at 7:27 AM, Emma Ryan via Insight-users
<insight-users at itk.org> wrote:
> Hi,
>
>   I would like to rotate an input mage by a few degrees. I was able to
> easily do this using rigid transforms available in itk. But the output image
> is cropped. The extent of cropping is directly related to the angle of
> rotation. How can one disallow this kind of cropping ?
>
> Thank you for your help.
> regards,
> Emma
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

>
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From matt.mccormick at kitware.com  Wed Sep 24 13:39:55 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 24 Sep 2014 13:39:55 -0400
Subject: [ITK-users] Image Rotation while preserving image
In-Reply-To: <1411578386.9555.YahooMailNeo@web120603.mail.ne1.yahoo.com>
References: <1411558020.53437.YahooMailNeo@web120605.mail.ne1.yahoo.com>
 <CALzTN-RKi4kfR3DhN8AWs_Y0Q33+1n+PFu7=s=zgOK2SFhpDOA@mail.gmail.com>
 <1411578386.9555.YahooMailNeo@web120603.mail.ne1.yahoo.com>
Message-ID: <CALzTN-RNKoNuLyAwVt8LnqF2CzmoW2NFFzWqo_-hGtJ4MUo7wA@mail.gmail.com>

Hi Emma,

The resampled image will be sampled at the locations specified for the
output image by setting the desired parameters on ResampleImageFilter.
It does not does resize based on the transformation.  To get a
different output image domain, use SetOutputOrigin() and SetSize() on
the ResampleImageFilter.

Hope this helps,
Matt

On Wed, Sep 24, 2014 at 1:06 PM, Emma Ryan <eryanvtk at yahoo.com> wrote:
> HI Matt,
>
>  Thank you for your reply. Attached is a snapshot of what is happening. The
> square needs to rotate and become a diamond. But after rotation, I get a
> chopped image. Ideally, I would just expect a larger sized matrix holding
> the larger image. So I'm not sure I understand how the 'content' could be
> missing.
>
> I couldn't experiment with SetExtrapolator as it is probably not available
> in the version of itk that I am using . Version 3.X.
>
> Are you suggesting that using Extrapolation, I would be able to address this
> specific problem ?
>
> regards,
> Emma
>
>
>
>
>
>
>
> On Wednesday, September 24, 2014 7:44 AM, Matt McCormick
> <matt.mccormick at kitware.com> wrote:
>
>
> Hi Emma,
>
> If there is no content to resample from after the transformation, then
> a default pixel value is used.  To use extrapolation instead, call
> SetExtrapolator() [1] on the ResampleImageFilter.
>
> HTH,
> Matt
>
> [1]
> http://www.itk.org/Insight/Doxygen/html/classitk_1_1ResampleImageFilter.html#a89d912b5608fbe73a9a2ca0ebcfebb69
>
> On Wed, Sep 24, 2014 at 7:27 AM, Emma Ryan via Insight-users
> <insight-users at itk.org> wrote:
>> Hi,
>>
>>  I would like to rotate an input mage by a few degrees. I was able to
>> easily do this using rigid transforms available in itk. But the output
>> image
>> is cropped. The extent of cropping is directly related to the angle of
>> rotation. How can one disallow this kind of cropping ?
>>
>> Thank you for your help.
>> regards,
>> Emma
>
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>
>>
>
>

From eryanvtk at yahoo.com  Wed Sep 24 14:00:30 2014
From: eryanvtk at yahoo.com (Emma Ryan)
Date: Wed, 24 Sep 2014 11:00:30 -0700
Subject: [ITK-users] Image Rotation while preserving image
In-Reply-To: <CALzTN-RNKoNuLyAwVt8LnqF2CzmoW2NFFzWqo_-hGtJ4MUo7wA@mail.gmail.com>
References: <1411558020.53437.YahooMailNeo@web120605.mail.ne1.yahoo.com>	<CALzTN-RKi4kfR3DhN8AWs_Y0Q33+1n+PFu7=s=zgOK2SFhpDOA@mail.gmail.com>	<1411578386.9555.YahooMailNeo@web120603.mail.ne1.yahoo.com>
 <CALzTN-RNKoNuLyAwVt8LnqF2CzmoW2NFFzWqo_-hGtJ4MUo7wA@mail.gmail.com>
Message-ID: <1411581630.97652.YahooMailNeo@web120605.mail.ne1.yahoo.com>

Hi Matt,

You were right.  Thanks again. Turns out my input indeed was cropped out by another process !.  I had experimented with sizes and origins too, but if input is garbage ....

regards,
Emma



On Wednesday, September 24, 2014 10:39 AM, Matt McCormick <matt.mccormick at kitware.com> wrote:
 


Hi Emma,

The resampled image will be sampled at the locations specified for the
output image by setting the desired parameters on ResampleImageFilter.
It does not does resize based on the transformation.  To get a
different output image domain, use SetOutputOrigin() and SetSize() on
the ResampleImageFilter.

Hope this helps,
Matt


On Wed, Sep 24, 2014 at 1:06 PM, Emma Ryan <eryanvtk at yahoo.com> wrote:
> HI Matt,
>
>  Thank you for your reply. Attached is a snapshot of what is happening. The
> square needs to rotate and become a diamond. But after rotation, I get a
> chopped image. Ideally, I would just expect a larger sized matrix holding
> the larger image. So I'm not sure I understand how the 'content' could be
> missing.
>
> I couldn't experiment with SetExtrapolator as it is probably not available
> in the version of itk that I am using . Version 3.X.
>
> Are you suggesting that using Extrapolation, I would be able to address this
> specific problem ?
>
> regards,
> Emma
>
>
>
>
>
>
>
> On Wednesday, September 24, 2014 7:44 AM, Matt McCormick
> <matt.mccormick at kitware.com> wrote:
>
>
> Hi Emma,
>
> If there is no content to resample from after the transformation, then
> a default pixel value is used.  To use extrapolation instead, call
> SetExtrapolator() [1] on the ResampleImageFilter.
>
> HTH,
> Matt
>
> [1]
> http://www.itk.org/Insight/Doxygen/html/classitk_1_1ResampleImageFilter.html#a89d912b5608fbe73a9a2ca0ebcfebb69
>
> On Wed, Sep 24, 2014 at 7:27 AM, Emma Ryan via Insight-users
> <insight-users at itk.org> wrote:
>> Hi,
>>
>>  I would like to rotate an input mage by a few degrees. I was able to
>> easily do this using rigid transforms available in itk. But the output
>> image
>> is cropped. The extent of cropping is directly related to the angle of
>> rotation. How can one disallow this kind of cropping ?
>>
>> Thank you for your help.
>> regards,
>> Emma
>
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>
>>
>
>
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From matt.mccormick at kitware.com  Wed Sep 24 14:14:38 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 24 Sep 2014 14:14:38 -0400
Subject: [ITK-users] format of mask file
In-Reply-To: <CAGKqDmfLY+2SwWJshQ4=cg0mS4VDKaC7-6P4VXDeTBFXh9=cdA@mail.gmail.com>
References: <CAGKqDmfLY+2SwWJshQ4=cg0mS4VDKaC7-6P4VXDeTBFXh9=cdA@mail.gmail.com>
Message-ID: <CALzTN-SZaDmDey2HrqOY0ZNpY2u6fDhJYXyNcRL3_vouuQRu0A@mail.gmail.com>

Hi Lianli,

Any integer pixel type should work in the mask.  To check how the mask
applies to the image, the MaskImageFilter [1] can be applied.

HTH,
Matt

[1] http://www.itk.org/Doxygen/html/classitk_1_1MaskImageFilter.html

On Tue, Sep 23, 2014 at 9:51 PM, Lianli Liu <llliu at umich.edu> wrote:
> Hi all,
>
> I am a bit unclear about the format of mask file. Is it fine if I use an
> image of analyze format that has 0,1 value, but of integer type not boolean
> type?
>
> The reason I am asking is that when I use this mask in the mutual
> information metric, there is an error : joint PDF summed to zero...
>
> Thanks!
> Lianli
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>

From matt.mccormick at kitware.com  Wed Sep 24 17:53:03 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 24 Sep 2014 17:53:03 -0400
Subject: [ITK-users] Opportunities to share, discuss, design,
 and learn with other ITK community members
Message-ID: <CALzTN-SoV8MnMMye+KYSt3UL+YWgG=hdNvAdTv+02ryfRy7dNA@mail.gmail.com>

There are a couple of upcoming opportunities to share, discuss, design, and
learn with your fellow ITK community members.


On Thursday (tomorrow), 9:30 AM Eastern USA time, there will be a
Google+ Hangout
where we will be doing code reviews:

  https://plus.google.com/u/1/events/c4jelvrtfg0l9v01d1sfub79fgk


On Friday, 11:00 AM Eastern USA time, an ITK development conference,

  https://plus.google.com/u/1/events/ctabd8pd4oasc3p5ejat27jgko4

For those that cannot join via Hangout, telephone call-in is also possible.
Dial:

  585-632-6296

Enter pin:

  31423


All are welcome.  Hope to talk to you then!

From blowekamp at mail.nih.gov  Thu Sep 25 10:43:51 2014
From: blowekamp at mail.nih.gov (Bradley Lowekamp)
Date: Thu, 25 Sep 2014 10:43:51 -0400
Subject: [ITK-users] Opportunities to share, discuss, design,
	and learn with other ITK community members
In-Reply-To: <CALzTN-SoV8MnMMye+KYSt3UL+YWgG=hdNvAdTv+02ryfRy7dNA@mail.gmail.com>
References: <CALzTN-SoV8MnMMye+KYSt3UL+YWgG=hdNvAdTv+02ryfRy7dNA@mail.gmail.com>
Message-ID: <7FC6FBA0-E666-4ADB-A9D9-6B5346982D2A@mail.nih.gov>

Matt,

The URL for the Confab is from last week, I think this is the URL for the one tomorrow:

https://plus.google.com/u/0/events/c5snoqnkhtkcv1tebfo1cl9quo4

On Sep 24, 2014, at 5:53 PM, Matt McCormick <matt.mccormick at kitware.com> wrote:

> There are a couple of upcoming opportunities to share, discuss, design, and
> learn with your fellow ITK community members.
> 
> 
> On Thursday (tomorrow), 9:30 AM Eastern USA time, there will be a
> Google+ Hangout
> where we will be doing code reviews:
> 
>  https://plus.google.com/u/1/events/c4jelvrtfg0l9v01d1sfub79fgk
> 
> 
> On Friday, 11:00 AM Eastern USA time, an ITK development conference,
> 
>  https://plus.google.com/u/1/events/ctabd8pd4oasc3p5ejat27jgko4
> 
> For those that cannot join via Hangout, telephone call-in is also possible.
> Dial:
> 
>  585-632-6296
> 
> Enter pin:
> 
>  31423
> 
> 
> All are welcome.  Hope to talk to you then!
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users


From matt.mccormick at kitware.com  Thu Sep 25 10:45:45 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 25 Sep 2014 10:45:45 -0400
Subject: [ITK-users] Opportunities to share, discuss, design,
 and learn with other ITK community members
In-Reply-To: <7FC6FBA0-E666-4ADB-A9D9-6B5346982D2A@mail.nih.gov>
References: <CALzTN-SoV8MnMMye+KYSt3UL+YWgG=hdNvAdTv+02ryfRy7dNA@mail.gmail.com>
 <7FC6FBA0-E666-4ADB-A9D9-6B5346982D2A@mail.nih.gov>
Message-ID: <CALzTN-S-mFMrX-q54y9xvk2ANqbrZ3v==RnxmCVwJCpNmsLFqA@mail.gmail.com>

Thanks for the correction!

On Thu, Sep 25, 2014 at 10:43 AM, Bradley Lowekamp
<blowekamp at mail.nih.gov> wrote:
> Matt,
>
> The URL for the Confab is from last week, I think this is the URL for the one tomorrow:
>
> https://plus.google.com/u/0/events/c5snoqnkhtkcv1tebfo1cl9quo4
>
> On Sep 24, 2014, at 5:53 PM, Matt McCormick <matt.mccormick at kitware.com> wrote:
>
>> There are a couple of upcoming opportunities to share, discuss, design, and
>> learn with your fellow ITK community members.
>>
>>
>> On Thursday (tomorrow), 9:30 AM Eastern USA time, there will be a
>> Google+ Hangout
>> where we will be doing code reviews:
>>
>>  https://plus.google.com/u/1/events/c4jelvrtfg0l9v01d1sfub79fgk
>>
>>
>> On Friday, 11:00 AM Eastern USA time, an ITK development conference,
>>
>>  https://plus.google.com/u/1/events/ctabd8pd4oasc3p5ejat27jgko4
>>
>> For those that cannot join via Hangout, telephone call-in is also possible.
>> Dial:
>>
>>  585-632-6296
>>
>> Enter pin:
>>
>>  31423
>>
>>
>> All are welcome.  Hope to talk to you then!
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>

From elena.bresciani87 at gmail.com  Fri Sep 26 10:23:18 2014
From: elena.bresciani87 at gmail.com (elena bresciani)
Date: Fri, 26 Sep 2014 16:23:18 +0200
Subject: [ITK-users] OpenCV - ITK project
Message-ID: <CACxk=WwqRBiJ1crphwH=WsdMVJxLtVbtn+rhUmDP+dnNj_V3oQ@mail.gmail.com>

Hello to everybody,

for the project I'm working on I need to integrate ITK and OpenCV.
I've read the dedicated tutorial here
<http://www.na-mic.org/Wiki/images/4/4a/ITKOpenCVBridgeTutorial.pdf>, but I
can't find informations on how the CmakeList.txt file should be created or
if I have to change some kind of building configuration of ITK and/or
OpenCV.

Can you please explain me what I have to do?

Cheers
Elena
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From indianzeppelin at gmail.com  Fri Sep 26 10:35:18 2014
From: indianzeppelin at gmail.com (Girish Mallya Udupi)
Date: Fri, 26 Sep 2014 15:35:18 +0100
Subject: [ITK-users] OpenCV - ITK project
In-Reply-To: <CACxk=WwqRBiJ1crphwH=WsdMVJxLtVbtn+rhUmDP+dnNj_V3oQ@mail.gmail.com>
References: <CACxk=WwqRBiJ1crphwH=WsdMVJxLtVbtn+rhUmDP+dnNj_V3oQ@mail.gmail.com>
Message-ID: <CAA+VR6jGjS59VMvu1-9+Siww3rYydZea=mT7xgdR96apZByRbA@mail.gmail.com>

Hi Elena,

I use OpenCV and ITK together. The general procedure is to build OpenCV
from source using CMake, and then build ITK from source using CMake,
checking the "Module_ITKVideoBridgeOpenCV" option so that it is built.
During both the builds you generally do not have to modify the
CMakeLists.txt

For a project which uses the libraries, the CMakeLists.txt would simply
look like -

----
cmake_minimum_required(VERSION 2.8)

project(myProject)

find_package(ITK REQUIRED)
find_package(OpenCV REQUIRED)

include(${ITK_USE_FILE})

add_executable(myProject test.cpp)

target_link_libraries(myProject ${ITK_LIBRARIES} ${OpenCV_LIBS})
----

Is there a specific problem you are facing while trying this?

On Fri, Sep 26, 2014 at 3:23 PM, elena bresciani <
elena.bresciani87 at gmail.com> wrote:

> Hello to everybody,
>
> for the project I'm working on I need to integrate ITK and OpenCV.
> I've read the dedicated tutorial here
> <http://www.na-mic.org/Wiki/images/4/4a/ITKOpenCVBridgeTutorial.pdf>, but
> I can't find informations on how the CmakeList.txt file should be created
> or if I have to change some kind of building configuration of ITK and/or
> OpenCV.
>
> Can you please explain me what I have to do?
>
> Cheers
> Elena
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>


-- 
Regards,
Girish
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From elena.bresciani87 at gmail.com  Fri Sep 26 11:28:25 2014
From: elena.bresciani87 at gmail.com (elena bresciani)
Date: Fri, 26 Sep 2014 17:28:25 +0200
Subject: [ITK-users] OpenCV - ITK project
In-Reply-To: <CAA+VR6jGjS59VMvu1-9+Siww3rYydZea=mT7xgdR96apZByRbA@mail.gmail.com>
References: <CACxk=WwqRBiJ1crphwH=WsdMVJxLtVbtn+rhUmDP+dnNj_V3oQ@mail.gmail.com>
 <CAA+VR6jGjS59VMvu1-9+Siww3rYydZea=mT7xgdR96apZByRbA@mail.gmail.com>
Message-ID: <CACxk=WzxL2h-L5BKFJWrcKAAgOXEaVz+g7w8TVB4JNJ3QXKsAg@mail.gmail.com>

I get the CMake error " Error in configuration files. Project Files may be
invalid "

I think that my problem is with the module "Module_ITKVideoBridgeOpenCV", I
have to rebuild ITK by checking that option (I don't think I had done this
when I compiled ITK), and I hope that then it will work.
I installed OpenCV with brew on Mac, you suggest to recompile it from
source or it should be good as well?

Thank you so much

Elena

2014-09-26 16:35 GMT+02:00 Girish Mallya Udupi <indianzeppelin at gmail.com>:

> Hi Elena,
>
> I use OpenCV and ITK together. The general procedure is to build OpenCV
> from source using CMake, and then build ITK from source using CMake,
> checking the "Module_ITKVideoBridgeOpenCV" option so that it is built.
> During both the builds you generally do not have to modify the
> CMakeLists.txt
>
> For a project which uses the libraries, the CMakeLists.txt would simply
> look like -
>
> ----
> cmake_minimum_required(VERSION 2.8)
>
> project(myProject)
>
> find_package(ITK REQUIRED)
> find_package(OpenCV REQUIRED)
>
> include(${ITK_USE_FILE})
>
> add_executable(myProject test.cpp)
>
> target_link_libraries(myProject ${ITK_LIBRARIES} ${OpenCV_LIBS})
> ----
>
> Is there a specific problem you are facing while trying this?
>
> On Fri, Sep 26, 2014 at 3:23 PM, elena bresciani <
> elena.bresciani87 at gmail.com> wrote:
>
>> Hello to everybody,
>>
>> for the project I'm working on I need to integrate ITK and OpenCV.
>> I've read the dedicated tutorial here
>> <http://www.na-mic.org/Wiki/images/4/4a/ITKOpenCVBridgeTutorial.pdf>,
>> but I can't find informations on how the CmakeList.txt file should be
>> created or if I have to change some kind of building configuration of ITK
>> and/or OpenCV.
>>
>> Can you please explain me what I have to do?
>>
>> Cheers
>> Elena
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
>
> --
> Regards,
> Girish
>
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From indianzeppelin at gmail.com  Fri Sep 26 11:35:23 2014
From: indianzeppelin at gmail.com (Girish Mallya Udupi)
Date: Fri, 26 Sep 2014 16:35:23 +0100
Subject: [ITK-users] OpenCV - ITK project
In-Reply-To: <CACxk=WzxL2h-L5BKFJWrcKAAgOXEaVz+g7w8TVB4JNJ3QXKsAg@mail.gmail.com>
References: <CACxk=WwqRBiJ1crphwH=WsdMVJxLtVbtn+rhUmDP+dnNj_V3oQ@mail.gmail.com>
 <CAA+VR6jGjS59VMvu1-9+Siww3rYydZea=mT7xgdR96apZByRbA@mail.gmail.com>
 <CACxk=WzxL2h-L5BKFJWrcKAAgOXEaVz+g7w8TVB4JNJ3QXKsAg@mail.gmail.com>
Message-ID: <CAA+VR6jKni0CjJ20EGdXYMPXWSdKr9vRNO8QwgQZ7anKDjut8g@mail.gmail.com>

Yes, you do need to enable "Module_ITKVideoBridgeOpenCV" when you build
ITK.
I am not familiar with OpenCV installations on Mac. Do projects build fine
when you use OpenCV alone?

On Fri, Sep 26, 2014 at 4:28 PM, elena bresciani <
elena.bresciani87 at gmail.com> wrote:

> I get the CMake error " Error in configuration files. Project Files may be
> invalid "
>
> I think that my problem is with the module "Module_ITKVideoBridgeOpenCV",
> I have to rebuild ITK by checking that option (I don't think I had done
> this when I compiled ITK), and I hope that then it will work.
> I installed OpenCV with brew on Mac, you suggest to recompile it from
> source or it should be good as well?
>
> Thank you so much
>
> Elena
>
> 2014-09-26 16:35 GMT+02:00 Girish Mallya Udupi <indianzeppelin at gmail.com>:
>
>> Hi Elena,
>>
>> I use OpenCV and ITK together. The general procedure is to build OpenCV
>> from source using CMake, and then build ITK from source using CMake,
>> checking the "Module_ITKVideoBridgeOpenCV" option so that it is built.
>> During both the builds you generally do not have to modify the
>> CMakeLists.txt
>>
>> For a project which uses the libraries, the CMakeLists.txt would simply
>> look like -
>>
>> ----
>> cmake_minimum_required(VERSION 2.8)
>>
>> project(myProject)
>>
>> find_package(ITK REQUIRED)
>> find_package(OpenCV REQUIRED)
>>
>> include(${ITK_USE_FILE})
>>
>> add_executable(myProject test.cpp)
>>
>> target_link_libraries(myProject ${ITK_LIBRARIES} ${OpenCV_LIBS})
>> ----
>>
>> Is there a specific problem you are facing while trying this?
>>
>> On Fri, Sep 26, 2014 at 3:23 PM, elena bresciani <
>> elena.bresciani87 at gmail.com> wrote:
>>
>>> Hello to everybody,
>>>
>>> for the project I'm working on I need to integrate ITK and OpenCV.
>>> I've read the dedicated tutorial here
>>> <http://www.na-mic.org/Wiki/images/4/4a/ITKOpenCVBridgeTutorial.pdf>,
>>> but I can't find informations on how the CmakeList.txt file should be
>>> created or if I have to change some kind of building configuration of ITK
>>> and/or OpenCV.
>>>
>>> Can you please explain me what I have to do?
>>>
>>> Cheers
>>> Elena
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>>
>>
>>
>> --
>> Regards,
>> Girish
>>
>
>


-- 
Regards,
Girish
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From elena.bresciani87 at gmail.com  Fri Sep 26 11:53:12 2014
From: elena.bresciani87 at gmail.com (elena bresciani)
Date: Fri, 26 Sep 2014 17:53:12 +0200
Subject: [ITK-users] OpenCV - ITK project
In-Reply-To: <CAA+VR6jKni0CjJ20EGdXYMPXWSdKr9vRNO8QwgQZ7anKDjut8g@mail.gmail.com>
References: <CACxk=WwqRBiJ1crphwH=WsdMVJxLtVbtn+rhUmDP+dnNj_V3oQ@mail.gmail.com>
 <CAA+VR6jGjS59VMvu1-9+Siww3rYydZea=mT7xgdR96apZByRbA@mail.gmail.com>
 <CACxk=WzxL2h-L5BKFJWrcKAAgOXEaVz+g7w8TVB4JNJ3QXKsAg@mail.gmail.com>
 <CAA+VR6jKni0CjJ20EGdXYMPXWSdKr9vRNO8QwgQZ7anKDjut8g@mail.gmail.com>
Message-ID: <CACxk=WwP2ujvwDZg5_i+Grq1KBNeL-Ge-HDaZuFb1sarfZTtHA@mail.gmail.com>

Yes, I don't have problems with it alone, so I will leave it as it as and
only try rebuilding itk with the "Module_ITKVideoBridgeOpenCV" flag on.

Thanks

2014-09-26 17:35 GMT+02:00 Girish Mallya Udupi <indianzeppelin at gmail.com>:

> Yes, you do need to enable "Module_ITKVideoBridgeOpenCV" when you build
> ITK.
> I am not familiar with OpenCV installations on Mac. Do projects build fine
> when you use OpenCV alone?
>
> On Fri, Sep 26, 2014 at 4:28 PM, elena bresciani <
> elena.bresciani87 at gmail.com> wrote:
>
>> I get the CMake error " Error in configuration files. Project Files may
>> be invalid "
>>
>> I think that my problem is with the module "Module_ITKVideoBridgeOpenCV",
>> I have to rebuild ITK by checking that option (I don't think I had done
>> this when I compiled ITK), and I hope that then it will work.
>> I installed OpenCV with brew on Mac, you suggest to recompile it from
>> source or it should be good as well?
>>
>> Thank you so much
>>
>> Elena
>>
>> 2014-09-26 16:35 GMT+02:00 Girish Mallya Udupi <indianzeppelin at gmail.com>
>> :
>>
>>> Hi Elena,
>>>
>>> I use OpenCV and ITK together. The general procedure is to build OpenCV
>>> from source using CMake, and then build ITK from source using CMake,
>>> checking the "Module_ITKVideoBridgeOpenCV" option so that it is built.
>>> During both the builds you generally do not have to modify the
>>> CMakeLists.txt
>>>
>>> For a project which uses the libraries, the CMakeLists.txt would simply
>>> look like -
>>>
>>> ----
>>> cmake_minimum_required(VERSION 2.8)
>>>
>>> project(myProject)
>>>
>>> find_package(ITK REQUIRED)
>>> find_package(OpenCV REQUIRED)
>>>
>>> include(${ITK_USE_FILE})
>>>
>>> add_executable(myProject test.cpp)
>>>
>>> target_link_libraries(myProject ${ITK_LIBRARIES} ${OpenCV_LIBS})
>>> ----
>>>
>>> Is there a specific problem you are facing while trying this?
>>>
>>> On Fri, Sep 26, 2014 at 3:23 PM, elena bresciani <
>>> elena.bresciani87 at gmail.com> wrote:
>>>
>>>> Hello to everybody,
>>>>
>>>> for the project I'm working on I need to integrate ITK and OpenCV.
>>>> I've read the dedicated tutorial here
>>>> <http://www.na-mic.org/Wiki/images/4/4a/ITKOpenCVBridgeTutorial.pdf>,
>>>> but I can't find informations on how the CmakeList.txt file should be
>>>> created or if I have to change some kind of building configuration of ITK
>>>> and/or OpenCV.
>>>>
>>>> Can you please explain me what I have to do?
>>>>
>>>> Cheers
>>>> Elena
>>>>
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>
>>>>
>>>
>>>
>>> --
>>> Regards,
>>> Girish
>>>
>>
>>
>
>
> --
> Regards,
> Girish
>
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From matt.mccormick at kitware.com  Fri Sep 26 14:39:13 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 26 Sep 2014 14:39:13 -0400
Subject: [ITK-users] OpenCV - ITK project
In-Reply-To: <CACxk=WwP2ujvwDZg5_i+Grq1KBNeL-Ge-HDaZuFb1sarfZTtHA@mail.gmail.com>
References: <CACxk=WwqRBiJ1crphwH=WsdMVJxLtVbtn+rhUmDP+dnNj_V3oQ@mail.gmail.com>
 <CAA+VR6jGjS59VMvu1-9+Siww3rYydZea=mT7xgdR96apZByRbA@mail.gmail.com>
 <CACxk=WzxL2h-L5BKFJWrcKAAgOXEaVz+g7w8TVB4JNJ3QXKsAg@mail.gmail.com>
 <CAA+VR6jKni0CjJ20EGdXYMPXWSdKr9vRNO8QwgQZ7anKDjut8g@mail.gmail.com>
 <CACxk=WwP2ujvwDZg5_i+Grq1KBNeL-Ge-HDaZuFb1sarfZTtHA@mail.gmail.com>
Message-ID: <CALzTN-QCXwk48B9h0rc31WNfFFkCULfiS6COOZsfGH=csGT11w@mail.gmail.com>

Hi Elena,

This example may be helpful [1].

Matt

[1] http://itk.org/ITKExamples/src/Video/BridgeOpenCV/ConvertAnITKGrayScaleImageToCVMat/Documentation.html?highlight=opencv

On Fri, Sep 26, 2014 at 11:53 AM, elena bresciani
<elena.bresciani87 at gmail.com> wrote:
> Yes, I don't have problems with it alone, so I will leave it as it as and
> only try rebuilding itk with the "Module_ITKVideoBridgeOpenCV" flag on.
>
> Thanks
>
> 2014-09-26 17:35 GMT+02:00 Girish Mallya Udupi <indianzeppelin at gmail.com>:
>>
>> Yes, you do need to enable "Module_ITKVideoBridgeOpenCV" when you build
>> ITK.
>> I am not familiar with OpenCV installations on Mac. Do projects build fine
>> when you use OpenCV alone?
>>
>> On Fri, Sep 26, 2014 at 4:28 PM, elena bresciani
>> <elena.bresciani87 at gmail.com> wrote:
>>>
>>> I get the CMake error " Error in configuration files. Project Files may
>>> be invalid "
>>>
>>> I think that my problem is with the module "Module_ITKVideoBridgeOpenCV",
>>> I have to rebuild ITK by checking that option (I don't think I had done this
>>> when I compiled ITK), and I hope that then it will work.
>>> I installed OpenCV with brew on Mac, you suggest to recompile it from
>>> source or it should be good as well?
>>>
>>> Thank you so much
>>>
>>> Elena
>>>
>>> 2014-09-26 16:35 GMT+02:00 Girish Mallya Udupi
>>> <indianzeppelin at gmail.com>:
>>>>
>>>> Hi Elena,
>>>>
>>>> I use OpenCV and ITK together. The general procedure is to build OpenCV
>>>> from source using CMake, and then build ITK from source using CMake,
>>>> checking the "Module_ITKVideoBridgeOpenCV" option so that it is built.
>>>> During both the builds you generally do not have to modify the
>>>> CMakeLists.txt
>>>>
>>>> For a project which uses the libraries, the CMakeLists.txt would simply
>>>> look like -
>>>>
>>>> ----
>>>> cmake_minimum_required(VERSION 2.8)
>>>>
>>>> project(myProject)
>>>>
>>>> find_package(ITK REQUIRED)
>>>> find_package(OpenCV REQUIRED)
>>>>
>>>> include(${ITK_USE_FILE})
>>>>
>>>> add_executable(myProject test.cpp)
>>>>
>>>> target_link_libraries(myProject ${ITK_LIBRARIES} ${OpenCV_LIBS})
>>>> ----
>>>>
>>>> Is there a specific problem you are facing while trying this?
>>>>
>>>> On Fri, Sep 26, 2014 at 3:23 PM, elena bresciani
>>>> <elena.bresciani87 at gmail.com> wrote:
>>>>>
>>>>> Hello to everybody,
>>>>>
>>>>> for the project I'm working on I need to integrate ITK and OpenCV.
>>>>> I've read the dedicated tutorial here, but I can't find informations on
>>>>> how the CmakeList.txt file should be created or if I have to change some
>>>>> kind of building configuration of ITK and/or OpenCV.
>>>>>
>>>>> Can you please explain me what I have to do?
>>>>>
>>>>> Cheers
>>>>> Elena
>>>>>
>>>>> _____________________________________
>>>>> Powered by www.kitware.com
>>>>>
>>>>> Visit other Kitware open-source projects at
>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>
>>>>> Kitware offers ITK Training Courses, for more information visit:
>>>>> http://www.kitware.com/products/protraining.php
>>>>>
>>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>>
>>>>> Follow this link to subscribe/unsubscribe:
>>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Regards,
>>>> Girish
>>>
>>>
>>
>>
>>
>> --
>> Regards,
>> Girish
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>

From genet at biomed.ee.ethz.ch  Fri Sep 26 16:46:46 2014
From: genet at biomed.ee.ethz.ch (Martin Genet)
Date: Fri, 26 Sep 2014 22:46:46 +0200
Subject: [ITK-users] FEMRegistration
In-Reply-To: <CALzTN-Qo6hbgL8mxVWUA8VKV3p0e_4NH5=Q_+tyuVjSeg_Y3Nw@mail.gmail.com>
References: <54207D45.9070409@biomed.ee.ethz.ch>
 <CALzTN-Qo6hbgL8mxVWUA8VKV3p0e_4NH5=Q_+tyuVjSeg_Y3Nw@mail.gmail.com>
Message-ID: <5425D0B6.1000009@biomed.ee.ethz.ch>

Thanks a lot, Matt. I'm still a little confused though. I can access the 
mesh using:
> typedef itk::fem::FEMObject< 2 > MeshType;
> MeshType::Pointer mesh =  registrationFilter->GetInputFEMObject();

However, when trying to create a writer using
 > typedef itk::MeshFileWriter< MeshType > MeshWriterType;
 > MeshWriterType::Pointer meshWriter = MeshWriterType::New();
, it complains that InputMeshType (itk::fem::FEMObject< 2 > I guess) is 
missing a lot of stuff (e.g., RegionType, PixelType, GetPoints, etc.).

If I use
 > typedef itk::Mesh< float, 2 > MeshType;
instead, I can define the writer, but then I can't access the mesh from 
the registration filter of course.

Is there a way to write registrationFilter->GetInputFEMObject() into a 
vtk file? Thanks again, and sorry again for the confusion.

Martin

On 09/22/2014 10:54 PM, Matt McCormick wrote:
> Hi Martin,
>
> itk::MeshFileReader and itk::MeshFileWriter are great classes for
> importing / exporting meshes.
>
> HTH,
> Matt
>
> On Mon, Sep 22, 2014 at 3:49 PM, Martin Genet <genet at biomed.ee.ethz.ch> wrote:
>> Dear all:
>>
>> Trying to use FEMRegistration on a bunch of images. Still trying to figure
>> out the following:
>>
>>   - What is the simplest way to convert an external mesh (e.g.,
>> vtkUnstructuredGrid, or GMSH) into an FEMObject (for registration), and vice
>> versa (for post-treatment, vizualization)?
>>
>>   - If the mesh covers only a subset of the image, what happens to the rest
>> of the image?
>>
>> Any help would be super appreciated. Sorry if that's too trivial. Thanks in
>> advance.
>>
>> Martin
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users


From matt.mccormick at kitware.com  Fri Sep 26 17:11:11 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Fri, 26 Sep 2014 17:11:11 -0400
Subject: [ITK-users] FEMRegistration
In-Reply-To: <5425D0B6.1000009@biomed.ee.ethz.ch>
References: <54207D45.9070409@biomed.ee.ethz.ch>
 <CALzTN-Qo6hbgL8mxVWUA8VKV3p0e_4NH5=Q_+tyuVjSeg_Y3Nw@mail.gmail.com>
 <5425D0B6.1000009@biomed.ee.ethz.ch>
Message-ID: <CALzTN-SFT9o0cq+LLMB0aNXB4g2=1nRtpYVFqqZbRt3H-=t+vQ@mail.gmail.com>

Hi Martin,

An itk::Mesh will need to be constructed from the the
itk::fem::FEMObject manually.  We could use a set of converter
classes.

HTH,
Matt

On Fri, Sep 26, 2014 at 4:46 PM, Martin Genet <genet at biomed.ee.ethz.ch> wrote:
> Thanks a lot, Matt. I'm still a little confused though. I can access the
> mesh using:
>>
>> typedef itk::fem::FEMObject< 2 > MeshType;
>> MeshType::Pointer mesh =  registrationFilter->GetInputFEMObject();
>
>
> However, when trying to create a writer using
>> typedef itk::MeshFileWriter< MeshType > MeshWriterType;
>> MeshWriterType::Pointer meshWriter = MeshWriterType::New();
> , it complains that InputMeshType (itk::fem::FEMObject< 2 > I guess) is
> missing a lot of stuff (e.g., RegionType, PixelType, GetPoints, etc.).
>
> If I use
>> typedef itk::Mesh< float, 2 > MeshType;
> instead, I can define the writer, but then I can't access the mesh from the
> registration filter of course.
>
> Is there a way to write registrationFilter->GetInputFEMObject() into a vtk
> file? Thanks again, and sorry again for the confusion.
>
> Martin
>
>
> On 09/22/2014 10:54 PM, Matt McCormick wrote:
>>
>> Hi Martin,
>>
>> itk::MeshFileReader and itk::MeshFileWriter are great classes for
>> importing / exporting meshes.
>>
>> HTH,
>> Matt
>>
>> On Mon, Sep 22, 2014 at 3:49 PM, Martin Genet <genet at biomed.ee.ethz.ch>
>> wrote:
>>>
>>> Dear all:
>>>
>>> Trying to use FEMRegistration on a bunch of images. Still trying to
>>> figure
>>> out the following:
>>>
>>>   - What is the simplest way to convert an external mesh (e.g.,
>>> vtkUnstructuredGrid, or GMSH) into an FEMObject (for registration), and
>>> vice
>>> versa (for post-treatment, vizualization)?
>>>
>>>   - If the mesh covers only a subset of the image, what happens to the
>>> rest
>>> of the image?
>>>
>>> Any help would be super appreciated. Sorry if that's too trivial. Thanks
>>> in
>>> advance.
>>>
>>> Martin
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>
>

From llliu at umich.edu  Sun Sep 28 18:18:40 2014
From: llliu at umich.edu (Lianli Liu)
Date: Sun, 28 Sep 2014 18:18:40 -0400
Subject: [ITK-users] build itkvtkglue
Message-ID: <CAGKqDmeFgMD0yWmO-cuqSGwK=sddKW88a0est2wRx3chLC_8kw@mail.gmail.com>

Hi all,

I want to use vtk with itk and I set the BUILD_SHARED_LIBS option as ON. My
cmake file looks like this

# This is the root ITK CMakeLists file.
cmake_minimum_required(VERSION 2.4)
if(COMMAND CMAKE_POLICY)
  cmake_policy(SET CMP0003 NEW)
endif()


# This project is designed to be built outside the Insight source tree.
project(vtiPCA)

# Find ITK.
find_package(ITK REQUIRED)
include(${ITK_USE_FILE})

if (ITKVtkGlue_LOADED)
  find_package(VTK REQUIRED)
  include(${VTK_USE_FILE})
else()
  find_package(ItkVtkGlue REQUIRED)
  include(${ItkVtkGlue_USE_FILE})
  set(Glue ItkVtkGlue)
endif()

add_executable(vtiPCA vtiPCA.cxx )

target_link_libraries(vtiPCA ${ITK_LIBRARIES})

But I receivde the error saying

By not providing "FindItkVtkGlue.cmake" in CMAKE_MODULE_PATH this project
   has asked CMake to find a package configuration file provided by
   "ItkVtkGlue", but CMake did not find one.
.

Can anyone help with this? Thanks!

Best,
Lianli
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From bill.lorensen at gmail.com  Sun Sep 28 22:01:57 2014
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Sun, 28 Sep 2014 22:01:57 -0400
Subject: [ITK-users] build itkvtkglue
In-Reply-To: <CAGKqDmeFgMD0yWmO-cuqSGwK=sddKW88a0est2wRx3chLC_8kw@mail.gmail.com>
References: <CAGKqDmeFgMD0yWmO-cuqSGwK=sddKW88a0est2wRx3chLC_8kw@mail.gmail.com>
Message-ID: <CADZJ4hPHkDVNxTY0fMNeiNDDhFnjTcwAW6TCh-W9f+XC23Xg_A@mail.gmail.com>

Remove these lines:
else()
  find_package(ItkVtkGlue REQUIRED)
  include(${ItkVtkGlue_USE_FILE})
  set(Glue ItkVtkGlue)

On Sun, Sep 28, 2014 at 6:18 PM, Lianli Liu <llliu at umich.edu> wrote:
> Hi all,
>
> I want to use vtk with itk and I set the BUILD_SHARED_LIBS option as ON. My
> cmake file looks like this
>
> # This is the root ITK CMakeLists file.
> cmake_minimum_required(VERSION 2.4)
> if(COMMAND CMAKE_POLICY)
>   cmake_policy(SET CMP0003 NEW)
> endif()
>
>
> # This project is designed to be built outside the Insight source tree.
> project(vtiPCA)
>
> # Find ITK.
> find_package(ITK REQUIRED)
> include(${ITK_USE_FILE})
>
> if (ITKVtkGlue_LOADED)
>   find_package(VTK REQUIRED)
>   include(${VTK_USE_FILE})
> else()
>   find_package(ItkVtkGlue REQUIRED)
>   include(${ItkVtkGlue_USE_FILE})
>   set(Glue ItkVtkGlue)
> endif()
>
> add_executable(vtiPCA vtiPCA.cxx )
>
> target_link_libraries(vtiPCA ${ITK_LIBRARIES})
>
> But I receivde the error saying
>
> By not providing "FindItkVtkGlue.cmake" in CMAKE_MODULE_PATH this project
>    has asked CMake to find a package configuration file provided by
>    "ItkVtkGlue", but CMake did not find one.
> .
>
> Can anyone help with this? Thanks!
>
> Best,
> Lianli
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>



-- 
Unpaid intern in BillsBasement at noware dot com

From emmasaunders123 at gmail.com  Mon Sep 29 15:25:16 2014
From: emmasaunders123 at gmail.com (Emma Saunders)
Date: Mon, 29 Sep 2014 20:25:16 +0100
Subject: [ITK-users] Push forward Pull Back Euler Lagrangian Frame
Message-ID: <CABQY8kTDKG1GE=B-yUBwmMeAWqcRAp9r7wx_hnJa8kGOkzw1vw@mail.gmail.com>

Hi List

I am experiencing some confusion with terms above, if someone could clarify
that would be great:

Does registration using a Eulerian frame correspond to a pull back
framework of registration

similarly:

Does registration using a Lagrangian frame correspond to a push forward
framework for registration?

Thanks for any help

Kind regards

Emma
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From llliu at umich.edu  Mon Sep 29 18:24:39 2014
From: llliu at umich.edu (Lianli Liu)
Date: Mon, 29 Sep 2014 18:24:39 -0400
Subject: [ITK-users] segmentation error in PCA estimator
Message-ID: <CAGKqDmd8H+zbQLZaShGYsO2sRMejCYHX39TM6x+rqabhzU1+6w@mail.gmail.com>

Hi all,

I am applying the itk example code for PCA estimator
(EstimatePCAModel.cxx). I have 10 training images and I intend to output
all components (i.e. 10). But after writing 4 components, I get the
segmentation fault. I was wondering what is the cause of this? I would
really appreciate any help. Thanks!

Regards,
Lianli
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From michkapopoff at gmail.com  Tue Sep 30 07:03:33 2014
From: michkapopoff at gmail.com (Michka Popoff)
Date: Tue, 30 Sep 2014 13:03:33 +0200
Subject: [ITK-users] ITK 4.6.0 Python Wrapping (swig?) problem
In-Reply-To: <542A8B2E.6020404@utu.fi>
References: <542A8B2E.6020404@utu.fi>
Message-ID: <34E373F2-8FC0-4E7F-9D64-D99158AFBC43@gmail.com>

Hi

once ITK is compiled, there is no more need for Swig at runtime.

For the syntax, you should use the new wrapping syntax.
Look at how it is done in this example, at the end there is python code [1]

I would recommend you not to use system swig, this is mostly an option for people wanting to play around with external versions of swig.
If you want to be sure it works, just set ITK_USE_SYSTEM_SWIG=OFF. ITK will download, compile and use an internal swig.
You can find a detailed tutorial for the installation here : http://www.itk.org/Wiki/ITK/WrapITKInstallFedora

The tutorial should work for Ubuntu 14, I never tried but one user reported being able to install ITK wrappings with this tutorial.

[1] http://itk.org/ITKExamples/src/Filtering/AnisotropicSmoothing/ComputeCurvatureAnisotropicDiffusion/Documentation.html

Michka

On 30 sept. 2014, at 12:51, Sami Koho <sakoho at utu.fi> wrote:

> Hello,
> 
> this week I tried to upgrade my ITK installation on my Ubuntu 14.04 (64 bit) to the 4.6.0 release version, as it promised much improved Python wrapping. I had previously been using some pre-4.6 build from GIT. The library compiles fine, but now the Python wrapping does not work on my computer.
> 
> I am able to load itk in Python, but every time I try to execute anything, the following error appears:
> 
>> <ipython-input-12-8e289c4078ab> in <module>()
>> ----> 1 reader = itk.ImageFileReader.IUC3.New()
>> 
>> /usr/local/lib/ITK-4.6/Python/itkLazy.py in __getattribute__(self, attr)
>>     40             module = self.__lazy_attributes[attr]
>>     41             namespace = {}
>> ---> 42             itkBase.LoadModule(module, namespace)
>>     43             # Load into 'namespace' first, then self.__dict__ (via setattr) to
>>     44             # prevent the warnings about overwriting the 'NotLoaded' values
>> 
>> /usr/local/lib/ITK-4.6/Python/itkBase.py in LoadModule(name, namespace)
>>     51         if namespace is not None:
>>     52             swig = namespace.setdefault('swig', imp.new_module('swig'))
>> ---> 53 swig.__dict__.update(this_module.swig.__dict__)
>>     54
>>     55             # don't worry about overwriting the symbols in namespace -- any
>> 
>> AttributeError: 'module' object has no attribute 'swig'
> 
> I have had this problem before, but previously on Ubuntu I solved it by selecting USE SYSTEM SWIG in CMAKE before compiling. Now, as the version 4.6.0 requires a newer version of swig, this does not work. As a further detail, if I try to manually insert a command, for example in iPython,  tab-completion works until the module names e.g. itk.ImageFileReader, but then stops. It seems that the swig can not be found or is not working properly.
> 
> Should I manually set a path to swig? Or is something else wrong instead?
> 
> I have installed ITK in the default path /usr/local/lib, as can be seen from the example.
> 
> Best,
> 
> Sami


From sami.koho at gmail.com  Tue Sep 30 08:51:32 2014
From: sami.koho at gmail.com (Sami Koho)
Date: Tue, 30 Sep 2014 15:51:32 +0300
Subject: [ITK-users] ITK 4.6.0 Python Wrapping (swig?) problem
In-Reply-To: <34E373F2-8FC0-4E7F-9D64-D99158AFBC43@gmail.com>
References: <542A8B2E.6020404@utu.fi>
 <34E373F2-8FC0-4E7F-9D64-D99158AFBC43@gmail.com>
Message-ID: <E3FC494D-2A0D-41A7-B9E4-C102789888EA@gmail.com>

Thank you Michka! The solution was in the ldconfig file creation:

> ITK will install by default in /usr/local/lib. Now, you have to tell the system that the files have been installed here.
> cd /etc/ld.so.conf.d/
> add a file called itk-46.conf, which should contain only one line: /usr/local/lib
> ldconfig # tells the system to read the files in ld.so.conf.d

On Ubuntu 14 the Python directory configuration is a bit different than in the Fedora guide:

> /Path to a program.
> PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python
> 
> //Path to a file.
> PYTHON_INCLUDE_DIR:PATH=/usr/include/python2.7
> 
> //Path to a file.
> PYTHON_INCLUDE_DIR2:PATH=/usr/include/x86_64-linux-gnu/python2.7
> 
> //Path to a library.
> PYTHON_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libpython2.7.so.1.0
> 
> //Path to a library.
> PYTHON_LIBRARY_DEBUG:FILEPATH=PYTHON_LIBRARY_DEBUG-NOTFOUND
> 
> //Directory where the arrayobject.h header file can be found. This
> // file is part of the numarray package
> PYTHON_NUMARRAY_INCLUDE_DIR:PATH=/usr/lib/python2.7/dist-packages/numpy/core/include/numpy
> 
> //Python site-packages directory to install a .pth file pointing
> // at WrapITK Python modules.
> PY_SITE_PACKAGES_PATH:PATH=/usr/lib/python2.7/dist-packages


Best,

Sami

On Sep 30, 2014, at 14:03, Michka Popoff <michkapopoff at gmail.com> wrote:

> Hi
> 
> once ITK is compiled, there is no more need for Swig at runtime.
> 
> For the syntax, you should use the new wrapping syntax.
> Look at how it is done in this example, at the end there is python code [1]
> 
> I would recommend you not to use system swig, this is mostly an option for people wanting to play around with external versions of swig.
> If you want to be sure it works, just set ITK_USE_SYSTEM_SWIG=OFF. ITK will download, compile and use an internal swig.
> You can find a detailed tutorial for the installation here : http://www.itk.org/Wiki/ITK/WrapITKInstallFedora
> 
> The tutorial should work for Ubuntu 14, I never tried but one user reported being able to install ITK wrappings with this tutorial.
> 
> [1] http://itk.org/ITKExamples/src/Filtering/AnisotropicSmoothing/ComputeCurvatureAnisotropicDiffusion/Documentation.html
> 
> Michka
> 
> On 30 sept. 2014, at 12:51, Sami Koho <sakoho at utu.fi> wrote:
> 
>> Hello,
>> 
>> this week I tried to upgrade my ITK installation on my Ubuntu 14.04 (64 bit) to the 4.6.0 release version, as it promised much improved Python wrapping. I had previously been using some pre-4.6 build from GIT. The library compiles fine, but now the Python wrapping does not work on my computer.
>> 
>> I am able to load itk in Python, but every time I try to execute anything, the following error appears:
>> 
>>> <ipython-input-12-8e289c4078ab> in <module>()
>>> ----> 1 reader = itk.ImageFileReader.IUC3.New()
>>> 
>>> /usr/local/lib/ITK-4.6/Python/itkLazy.py in __getattribute__(self, attr)
>>>    40             module = self.__lazy_attributes[attr]
>>>    41             namespace = {}
>>> ---> 42             itkBase.LoadModule(module, namespace)
>>>    43             # Load into 'namespace' first, then self.__dict__ (via setattr) to
>>>    44             # prevent the warnings about overwriting the 'NotLoaded' values
>>> 
>>> /usr/local/lib/ITK-4.6/Python/itkBase.py in LoadModule(name, namespace)
>>>    51         if namespace is not None:
>>>    52             swig = namespace.setdefault('swig', imp.new_module('swig'))
>>> ---> 53 swig.__dict__.update(this_module.swig.__dict__)
>>>    54
>>>    55             # don't worry about overwriting the symbols in namespace -- any
>>> 
>>> AttributeError: 'module' object has no attribute 'swig'
>> 
>> I have had this problem before, but previously on Ubuntu I solved it by selecting USE SYSTEM SWIG in CMAKE before compiling. Now, as the version 4.6.0 requires a newer version of swig, this does not work. As a further detail, if I try to manually insert a command, for example in iPython,  tab-completion works until the module names e.g. itk.ImageFileReader, but then stops. It seems that the swig can not be found or is not working properly.
>> 
>> Should I manually set a path to swig? Or is something else wrong instead?
>> 
>> I have installed ITK in the default path /usr/local/lib, as can be seen from the example.
>> 
>> Best,
>> 
>> Sami
> 
> _____________________________________
> Powered by www.kitware.com
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
> 
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
> 
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
> 
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users

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From michkapopoff at gmail.com  Tue Sep 30 09:14:21 2014
From: michkapopoff at gmail.com (Michka Popoff)
Date: Tue, 30 Sep 2014 15:14:21 +0200
Subject: [ITK-users] ITK 4.6.0 Python Wrapping (swig?) problem
In-Reply-To: <E3FC494D-2A0D-41A7-B9E4-C102789888EA@gmail.com>
References: <542A8B2E.6020404@utu.fi>
 <34E373F2-8FC0-4E7F-9D64-D99158AFBC43@gmail.com>
 <E3FC494D-2A0D-41A7-B9E4-C102789888EA@gmail.com>
Message-ID: <D7D2F0C4-D6EB-4ED1-AE7E-6D760BDA69EE@gmail.com>

Would it be possible for you to write this down for me, so I can update the guide on the wiki ?

Michka

On 30 sept. 2014, at 14:51, Sami Koho <sami.koho at gmail.com> wrote:

> Thank you Michka! The solution was in the ldconfig file creation:
> 
>> ITK will install by default in /usr/local/lib. Now, you have to tell the system that the files have been installed here.
>> cd /etc/ld.so.conf.d/
>> add a file called itk-46.conf, which should contain only one line: /usr/local/lib
>> ldconfig # tells the system to read the files in ld.so.conf.d
> 
> On Ubuntu 14 the Python directory configuration is a bit different than in the Fedora guide:
> 
>> /Path to a program.
>> PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python
>> 
>> //Path to a file.
>> PYTHON_INCLUDE_DIR:PATH=/usr/include/python2.7
>> 
>> //Path to a file.
>> PYTHON_INCLUDE_DIR2:PATH=/usr/include/x86_64-linux-gnu/python2.7
>> 
>> //Path to a library.
>> PYTHON_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libpython2.7.so.1.0
>> 
>> //Path to a library.
>> PYTHON_LIBRARY_DEBUG:FILEPATH=PYTHON_LIBRARY_DEBUG-NOTFOUND
>> 
>> //Directory where the arrayobject.h header file can be found. This
>> // file is part of the numarray package
>> PYTHON_NUMARRAY_INCLUDE_DIR:PATH=/usr/lib/python2.7/dist-packages/numpy/core/include/numpy
>> 
>> //Python site-packages directory to install a .pth file pointing
>> // at WrapITK Python modules.
>> PY_SITE_PACKAGES_PATH:PATH=/usr/lib/python2.7/dist-packages
> 
> 
> Best,
> 
> Sami
> 
> On Sep 30, 2014, at 14:03, Michka Popoff <michkapopoff at gmail.com> wrote:
> 
>> Hi
>> 
>> once ITK is compiled, there is no more need for Swig at runtime.
>> 
>> For the syntax, you should use the new wrapping syntax.
>> Look at how it is done in this example, at the end there is python code [1]
>> 
>> I would recommend you not to use system swig, this is mostly an option for people wanting to play around with external versions of swig.
>> If you want to be sure it works, just set ITK_USE_SYSTEM_SWIG=OFF. ITK will download, compile and use an internal swig.
>> You can find a detailed tutorial for the installation here : http://www.itk.org/Wiki/ITK/WrapITKInstallFedora
>> 
>> The tutorial should work for Ubuntu 14, I never tried but one user reported being able to install ITK wrappings with this tutorial.
>> 
>> [1] http://itk.org/ITKExamples/src/Filtering/AnisotropicSmoothing/ComputeCurvatureAnisotropicDiffusion/Documentation.html
>> 
>> Michka
>> 
>> On 30 sept. 2014, at 12:51, Sami Koho <sakoho at utu.fi> wrote:
>> 
>>> Hello,
>>> 
>>> this week I tried to upgrade my ITK installation on my Ubuntu 14.04 (64 bit) to the 4.6.0 release version, as it promised much improved Python wrapping. I had previously been using some pre-4.6 build from GIT. The library compiles fine, but now the Python wrapping does not work on my computer.
>>> 
>>> I am able to load itk in Python, but every time I try to execute anything, the following error appears:
>>> 
>>>> <ipython-input-12-8e289c4078ab> in <module>()
>>>> ----> 1 reader = itk.ImageFileReader.IUC3.New()
>>>> 
>>>> /usr/local/lib/ITK-4.6/Python/itkLazy.py in __getattribute__(self, attr)
>>>>    40             module = self.__lazy_attributes[attr]
>>>>    41             namespace = {}
>>>> ---> 42             itkBase.LoadModule(module, namespace)
>>>>    43             # Load into 'namespace' first, then self.__dict__ (via setattr) to
>>>>    44             # prevent the warnings about overwriting the 'NotLoaded' values
>>>> 
>>>> /usr/local/lib/ITK-4.6/Python/itkBase.py in LoadModule(name, namespace)
>>>>    51         if namespace is not None:
>>>>    52             swig = namespace.setdefault('swig', imp.new_module('swig'))
>>>> ---> 53 swig.__dict__.update(this_module.swig.__dict__)
>>>>    54
>>>>    55             # don't worry about overwriting the symbols in namespace -- any
>>>> 
>>>> AttributeError: 'module' object has no attribute 'swig'
>>> 
>>> I have had this problem before, but previously on Ubuntu I solved it by selecting USE SYSTEM SWIG in CMAKE before compiling. Now, as the version 4.6.0 requires a newer version of swig, this does not work. As a further detail, if I try to manually insert a command, for example in iPython,  tab-completion works until the module names e.g. itk.ImageFileReader, but then stops. It seems that the swig can not be found or is not working properly.
>>> 
>>> Should I manually set a path to swig? Or is something else wrong instead?
>>> 
>>> I have installed ITK in the default path /usr/local/lib, as can be seen from the example.
>>> 
>>> Best,
>>> 
>>> Sami
>> 
>> _____________________________________
>> Powered by www.kitware.com
>> 
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>> 
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>> 
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>> 
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
> 

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From michkapopoff at gmail.com  Tue Sep 30 09:51:06 2014
From: michkapopoff at gmail.com (Michka Popoff)
Date: Tue, 30 Sep 2014 15:51:06 +0200
Subject: [ITK-users] ITK 4.6.0 Python Wrapping (swig?) problem
In-Reply-To: <D7D2F0C4-D6EB-4ED1-AE7E-6D760BDA69EE@gmail.com>
References: <542A8B2E.6020404@utu.fi>
 <34E373F2-8FC0-4E7F-9D64-D99158AFBC43@gmail.com>
 <E3FC494D-2A0D-41A7-B9E4-C102789888EA@gmail.com>
 <D7D2F0C4-D6EB-4ED1-AE7E-6D760BDA69EE@gmail.com>
Message-ID: <AAE3F7D1-0A5A-439A-B425-B70936648575@gmail.com>

Just writing this down for the list archives

Sami, thank you very much for all the informations.
I updated an created a new page, for Fedora and Ubuntu, with all the details.

http://www.itk.org/Wiki/ITK/WrapITKInstallLinux

For the moment this page is somewhat hidden, because you need to click 3-4 links through the FAQ and multiple pages to get to it.
I will maybe reorganize the wiki a little bit to move the installation procedures to the front page.

Thanks again

Michka

On 30 sept. 2014, at 15:14, Michka Popoff <michkapopoff at gmail.com> wrote:

> Would it be possible for you to write this down for me, so I can update the guide on the wiki ?
> 
> Michka
> 
> On 30 sept. 2014, at 14:51, Sami Koho <sami.koho at gmail.com> wrote:
> 
>> Thank you Michka! The solution was in the ldconfig file creation:
>> 
>>> ITK will install by default in /usr/local/lib. Now, you have to tell the system that the files have been installed here.
>>> cd /etc/ld.so.conf.d/
>>> add a file called itk-46.conf, which should contain only one line: /usr/local/lib
>>> ldconfig # tells the system to read the files in ld.so.conf.d
>> 
>> On Ubuntu 14 the Python directory configuration is a bit different than in the Fedora guide:
>> 
>>> /Path to a program.
>>> PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python
>>> 
>>> //Path to a file.
>>> PYTHON_INCLUDE_DIR:PATH=/usr/include/python2.7
>>> 
>>> //Path to a file.
>>> PYTHON_INCLUDE_DIR2:PATH=/usr/include/x86_64-linux-gnu/python2.7
>>> 
>>> //Path to a library.
>>> PYTHON_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libpython2.7.so.1.0
>>> 
>>> //Path to a library.
>>> PYTHON_LIBRARY_DEBUG:FILEPATH=PYTHON_LIBRARY_DEBUG-NOTFOUND
>>> 
>>> //Directory where the arrayobject.h header file can be found. This
>>> // file is part of the numarray package
>>> PYTHON_NUMARRAY_INCLUDE_DIR:PATH=/usr/lib/python2.7/dist-packages/numpy/core/include/numpy
>>> 
>>> //Python site-packages directory to install a .pth file pointing
>>> // at WrapITK Python modules.
>>> PY_SITE_PACKAGES_PATH:PATH=/usr/lib/python2.7/dist-packages
>> 
>> 
>> Best,
>> 
>> Sami
>> 
>> On Sep 30, 2014, at 14:03, Michka Popoff <michkapopoff at gmail.com> wrote:
>> 
>>> Hi
>>> 
>>> once ITK is compiled, there is no more need for Swig at runtime.
>>> 
>>> For the syntax, you should use the new wrapping syntax.
>>> Look at how it is done in this example, at the end there is python code [1]
>>> 
>>> I would recommend you not to use system swig, this is mostly an option for people wanting to play around with external versions of swig.
>>> If you want to be sure it works, just set ITK_USE_SYSTEM_SWIG=OFF. ITK will download, compile and use an internal swig.
>>> You can find a detailed tutorial for the installation here : http://www.itk.org/Wiki/ITK/WrapITKInstallFedora
>>> 
>>> The tutorial should work for Ubuntu 14, I never tried but one user reported being able to install ITK wrappings with this tutorial.
>>> 
>>> [1] http://itk.org/ITKExamples/src/Filtering/AnisotropicSmoothing/ComputeCurvatureAnisotropicDiffusion/Documentation.html
>>> 
>>> Michka
>>> 
>>> On 30 sept. 2014, at 12:51, Sami Koho <sakoho at utu.fi> wrote:
>>> 
>>>> Hello,
>>>> 
>>>> this week I tried to upgrade my ITK installation on my Ubuntu 14.04 (64 bit) to the 4.6.0 release version, as it promised much improved Python wrapping. I had previously been using some pre-4.6 build from GIT. The library compiles fine, but now the Python wrapping does not work on my computer.
>>>> 
>>>> I am able to load itk in Python, but every time I try to execute anything, the following error appears:
>>>> 
>>>>> <ipython-input-12-8e289c4078ab> in <module>()
>>>>> ----> 1 reader = itk.ImageFileReader.IUC3.New()
>>>>> 
>>>>> /usr/local/lib/ITK-4.6/Python/itkLazy.py in __getattribute__(self, attr)
>>>>>    40             module = self.__lazy_attributes[attr]
>>>>>    41             namespace = {}
>>>>> ---> 42             itkBase.LoadModule(module, namespace)
>>>>>    43             # Load into 'namespace' first, then self.__dict__ (via setattr) to
>>>>>    44             # prevent the warnings about overwriting the 'NotLoaded' values
>>>>> 
>>>>> /usr/local/lib/ITK-4.6/Python/itkBase.py in LoadModule(name, namespace)
>>>>>    51         if namespace is not None:
>>>>>    52             swig = namespace.setdefault('swig', imp.new_module('swig'))
>>>>> ---> 53 swig.__dict__.update(this_module.swig.__dict__)
>>>>>    54
>>>>>    55             # don't worry about overwriting the symbols in namespace -- any
>>>>> 
>>>>> AttributeError: 'module' object has no attribute 'swig'
>>>> 
>>>> I have had this problem before, but previously on Ubuntu I solved it by selecting USE SYSTEM SWIG in CMAKE before compiling. Now, as the version 4.6.0 requires a newer version of swig, this does not work. As a further detail, if I try to manually insert a command, for example in iPython,  tab-completion works until the module names e.g. itk.ImageFileReader, but then stops. It seems that the swig can not be found or is not working properly.
>>>> 
>>>> Should I manually set a path to swig? Or is something else wrong instead?
>>>> 
>>>> I have installed ITK in the default path /usr/local/lib, as can be seen from the example.
>>>> 
>>>> Best,
>>>> 
>>>> Sami
>>> 
>>> _____________________________________
>>> Powered by www.kitware.com
>>> 
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>> 
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>> 
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>> 
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>> 
> 

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From noreply at insightsoftwareconsortium.org  Tue Sep 30 09:57:58 2014
From: noreply at insightsoftwareconsortium.org (MIDAS Journal)
Date: Tue, 30 Sep 2014 09:57:58 -0400 (EDT)
Subject: [ITK-users] New Submission: On the Importance of Location and
	Features for the Patch-Based Segmentation of Parotid Glands
Message-ID: <20140930135758.AC11E3D6C169@insightsoftwareconsortium.org>

Hello,

A new submission has been added to the MIDAS Journal.

Title: On the Importance of Location and Features for the Patch-Based Segmentation of Parotid Glands
Authors: Wachinger C., Brennan M., Sharp G., Golland P.
Abstract: The segmentation of parotid glands in CT scans of patients with head and neck cancer is an essential part of treatment planning. We introduce a new method for the automatic segmentation of parotid glands that extends existing patch-based approaches in three ways: (1) we promote the use of image features in combination with patch intensity values to increase discrimination; (2) we work with larger search windows than established methods by using an approximate nearest neighbor search; and (3) we demonstrate that location information is a crucial discriminator and add it explicitly to the description. In our experiments, we compare a large number of features and introduce a new multi-scale descriptor. The best performance is achieved with entropy image features in combination with patches and location information.

Download and review this publication at: http://hdl.handle.net/10380/3472

Generated by the MIDAS Journal

You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ .

From matt.mccormick at kitware.com  Tue Sep 30 10:17:27 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 30 Sep 2014 10:17:27 -0400
Subject: [ITK-users] Push forward Pull Back Euler Lagrangian Frame
In-Reply-To: <CABQY8kTDKG1GE=B-yUBwmMeAWqcRAp9r7wx_hnJa8kGOkzw1vw@mail.gmail.com>
References: <CABQY8kTDKG1GE=B-yUBwmMeAWqcRAp9r7wx_hnJa8kGOkzw1vw@mail.gmail.com>
Message-ID: <CALzTN-Smw__ucooqOy547Zue+vG0x51W2qR+pjRtnwLsQ5KgdQ@mail.gmail.com>

Hi Emma,

Yes, that sounds correct.  Is there some context to where this
language is being used?

Thanks,
Matt

On Mon, Sep 29, 2014 at 3:25 PM, Emma Saunders
<emmasaunders123 at gmail.com> wrote:
> Hi List
>
> I am experiencing some confusion with terms above, if someone could clarify
> that would be great:
>
> Does registration using a Eulerian frame correspond to a pull back framework
> of registration
>
> similarly:
>
> Does registration using a Lagrangian frame correspond to a push forward
> framework for registration?
>
> Thanks for any help
>
> Kind regards
>
> Emma
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>

From matt.mccormick at kitware.com  Tue Sep 30 10:21:26 2014
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 30 Sep 2014 10:21:26 -0400
Subject: [ITK-users] segmentation error in PCA estimator
In-Reply-To: <CAGKqDmd8H+zbQLZaShGYsO2sRMejCYHX39TM6x+rqabhzU1+6w@mail.gmail.com>
References: <CAGKqDmd8H+zbQLZaShGYsO2sRMejCYHX39TM6x+rqabhzU1+6w@mail.gmail.com>
Message-ID: <CALzTN-QG0q=9g9Prt3476Y-zkGeExoWBExeK+BT_t6qcoJ9tyg@mail.gmail.com>

Hi Lianli,

Building the program with debugging symbols and running the executable
in a debugger should shed more light.  Or, sharing a SSCCE [1], i.e.
the code and images and command (CTest test), should help others debug
your issue.

Thanks,
Matt

[1] http://sscce.org/

On Mon, Sep 29, 2014 at 6:24 PM, Lianli Liu <llliu at umich.edu> wrote:
> Hi all,
>
> I am applying the itk example code for PCA estimator (EstimatePCAModel.cxx).
> I have 10 training images and I intend to output all components (i.e. 10).
> But after writing 4 components, I get the segmentation fault. I was
> wondering what is the cause of this? I would really appreciate any help.
> Thanks!
>
> Regards,
> Lianli
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>