From gregthom992 at gmail.com  Sat Feb  3 01:39:33 2018
From: gregthom992 at gmail.com (G Tom)
Date: Sat, 3 Feb 2018 01:39:33 -0500
Subject: [ITK] [ITK-users] Extract Line/Intensity profile from image
 given start and stop points
In-Reply-To: <CAPf2UMRLQWgZfV8k1N7Jmxb_ROmNphiz4Ugt-zcrNdfj40NmZg@mail.gmail.com>
References: <CAFh_-OOCZY4FRfRH-51K2OiZAa69+CduOOyrifTh0SLhw+8h6w@mail.gmail.com>
 <CAPf2UMQ4DQhKm896u6amKA5vCJ_0c4mhB=9DbvXzOvYZ_M9h=w@mail.gmail.com>
 <1517433832235-0.post@n7.nabble.com>
 <CAPf2UMRLQWgZfV8k1N7Jmxb_ROmNphiz4Ugt-zcrNdfj40NmZg@mail.gmail.com>
Message-ID: <CAFh_-OOVbTQW8BQJTMyaDkhes6mxncU-4kbo2gPvdwvpmNy3JA@mail.gmail.com>

Do you have an idea how to do this averaging over the line with a radius ?

I am also looking at vtkprobefilter.

Thanks

GT

On Wed, Jan 31, 2018 at 6:01 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:

> Hi Tom,
>
> BresenhamLine does not have a radius, it is only one pixel wide. If you
> need some kind of averaging, you will probably need to resample the image.
> There was a similar question last year, that thread
> <https://public.kitware.com/pipermail/community/2017-April/012924.html>
> will probably be helpful.
>
> Regards,
> D?enan
>
> On Wed, Jan 31, 2018 at 4:23 PM, gregthom992 <gregthom992 at gmail.com>
> wrote:
>
>> Hi Dzenan,
>>
>> itk::BresenhamLine seems to be what I need. Thanks for pointing that out.
>> I
>> am going through the example, how do I give it a radius ?
>>
>> Thanks
>>
>> GT
>>
>>
>>
>> --
>> Sent from: http://itk-users.7.n7.nabble.com/
>> The ITK community is transitioning from this mailing list to
>> discourse.itk.org. Please join us there!
>> ________________________________
>> 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:
>> https://itk.org/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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From gregthom992 at gmail.com  Sat Feb  3 02:37:40 2018
From: gregthom992 at gmail.com (G Tom)
Date: Sat, 3 Feb 2018 02:37:40 -0500
Subject: [ITK] [ITK-users] Extract Line/Intensity profile from image
 given start and stop points
In-Reply-To: <CAFh_-OOVbTQW8BQJTMyaDkhes6mxncU-4kbo2gPvdwvpmNy3JA@mail.gmail.com>
References: <CAFh_-OOCZY4FRfRH-51K2OiZAa69+CduOOyrifTh0SLhw+8h6w@mail.gmail.com>
 <CAPf2UMQ4DQhKm896u6amKA5vCJ_0c4mhB=9DbvXzOvYZ_M9h=w@mail.gmail.com>
 <1517433832235-0.post@n7.nabble.com>
 <CAPf2UMRLQWgZfV8k1N7Jmxb_ROmNphiz4Ugt-zcrNdfj40NmZg@mail.gmail.com>
 <CAFh_-OOVbTQW8BQJTMyaDkhes6mxncU-4kbo2gPvdwvpmNy3JA@mail.gmail.com>
Message-ID: <CAFh_-OOK-yMPMVjLyq_a5yi-Gxib4=qTphDJYNziKdKe4jxK=A@mail.gmail.com>

Hi ,
I looked at the link you mentioned; the idea that comes to mind now is that
I first rotate my image so that one of the axis is aligned with the line,
then extract scan line along the rotated image axis possibly after re
sampling.
How do I rotate the image about a line defined by two points ?

On Sat, Feb 3, 2018 at 1:39 AM, G Tom <gregthom992 at gmail.com> wrote:

> Do you have an idea how to do this averaging over the line with a radius ?
>
> I am also looking at vtkprobefilter.
>
> Thanks
>
> GT
>
> On Wed, Jan 31, 2018 at 6:01 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>
>> Hi Tom,
>>
>> BresenhamLine does not have a radius, it is only one pixel wide. If you
>> need some kind of averaging, you will probably need to resample the image.
>> There was a similar question last year, that thread
>> <https://public.kitware.com/pipermail/community/2017-April/012924.html>
>> will probably be helpful.
>>
>> Regards,
>> D?enan
>>
>> On Wed, Jan 31, 2018 at 4:23 PM, gregthom992 <gregthom992 at gmail.com>
>> wrote:
>>
>>> Hi Dzenan,
>>>
>>> itk::BresenhamLine seems to be what I need. Thanks for pointing that
>>> out. I
>>> am going through the example, how do I give it a radius ?
>>>
>>> Thanks
>>>
>>> GT
>>>
>>>
>>>
>>> --
>>> Sent from: http://itk-users.7.n7.nabble.com/
>>> The ITK community is transitioning from this mailing list to
>>> discourse.itk.org. Please join us there!
>>> ________________________________
>>> 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:
>>> https://itk.org/mailman/listinfo/insight-users
>>>
>>
>>
>
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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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Follow this link to subscribe/unsubscribe:
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From dzenanz at gmail.com  Mon Feb  5 11:20:18 2018
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Mon, 5 Feb 2018 11:20:18 -0500
Subject: [ITK] [ITK-users] Extract Line/Intensity profile from image
 given start and stop points
In-Reply-To: <CAFh_-OOK-yMPMVjLyq_a5yi-Gxib4=qTphDJYNziKdKe4jxK=A@mail.gmail.com>
References: <CAFh_-OOCZY4FRfRH-51K2OiZAa69+CduOOyrifTh0SLhw+8h6w@mail.gmail.com>
 <CAPf2UMQ4DQhKm896u6amKA5vCJ_0c4mhB=9DbvXzOvYZ_M9h=w@mail.gmail.com>
 <1517433832235-0.post@n7.nabble.com>
 <CAPf2UMRLQWgZfV8k1N7Jmxb_ROmNphiz4Ugt-zcrNdfj40NmZg@mail.gmail.com>
 <CAFh_-OOVbTQW8BQJTMyaDkhes6mxncU-4kbo2gPvdwvpmNy3JA@mail.gmail.com>
 <CAFh_-OOK-yMPMVjLyq_a5yi-Gxib4=qTphDJYNziKdKe4jxK=A@mail.gmail.com>
Message-ID: <CAPf2UMQ2ynnzP-CkgeLo+8chdvJkgUaTM93=cW7PEeWNB0nN+A@mail.gmail.com>

Hi,

resample <https://itk.org/Doxygen/html/classitk_1_1ResampleImageFilter.html>
image filter can do the heavy lifting. But you do need to provide an
appropriate transform
<https://itk.org/Doxygen/html/classitk_1_1Rigid3DTransform.html>, relying
on linear algebra <https://en.wikipedia.org/wiki/Linear_algebra> - point
transformations etc.

Regards,
D?enan

On Sat, Feb 3, 2018 at 2:37 AM, G Tom <gregthom992 at gmail.com> wrote:

> Hi ,
> I looked at the link you mentioned; the idea that comes to mind now is
> that I first rotate my image so that one of the axis is aligned with the
> line, then extract scan line along the rotated image axis possibly after re
> sampling.
> How do I rotate the image about a line defined by two points ?
>
> On Sat, Feb 3, 2018 at 1:39 AM, G Tom <gregthom992 at gmail.com> wrote:
>
>> Do you have an idea how to do this averaging over the line with a radius ?
>>
>> I am also looking at vtkprobefilter.
>>
>> Thanks
>>
>> GT
>>
>> On Wed, Jan 31, 2018 at 6:01 PM, D?enan Zuki? <dzenanz at gmail.com> wrote:
>>
>>> Hi Tom,
>>>
>>> BresenhamLine does not have a radius, it is only one pixel wide. If you
>>> need some kind of averaging, you will probably need to resample the image.
>>> There was a similar question last year, that thread
>>> <https://public.kitware.com/pipermail/community/2017-April/012924.html>
>>> will probably be helpful.
>>>
>>> Regards,
>>> D?enan
>>>
>>> On Wed, Jan 31, 2018 at 4:23 PM, gregthom992 <gregthom992 at gmail.com>
>>> wrote:
>>>
>>>> Hi Dzenan,
>>>>
>>>> itk::BresenhamLine seems to be what I need. Thanks for pointing that
>>>> out. I
>>>> am going through the example, how do I give it a radius ?
>>>>
>>>> Thanks
>>>>
>>>> GT
>>>>
>>>>
>>>>
>>>> --
>>>> Sent from: http://itk-users.7.n7.nabble.com/
>>>> The ITK community is transitioning from this mailing list to
>>>> discourse.itk.org. Please join us there!
>>>> ________________________________
>>>> 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:
>>>> https://itk.org/mailman/listinfo/insight-users
>>>>
>>>
>>>
>>
>
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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:
http://www.itk.org/Wiki/ITK_FAQ

Follow this link to subscribe/unsubscribe:
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From julien.jomier at kitware.com  Tue Feb  6 02:39:03 2018
From: julien.jomier at kitware.com (Julien Jomier)
Date: Tue, 6 Feb 2018 08:39:03 +0100
Subject: [ITK] [ITK-users] [ANN] CMake Training Course in Singapore - March
 27-28
In-Reply-To: <2d50072b-a62a-a58a-19a2-dd2747a38b39@kitware.com>
References: <2d50072b-a62a-a58a-19a2-dd2747a38b39@kitware.com>
Message-ID: <8f00f380-bba3-4436-c368-4d97dfb7cdb6@kitware.com>

Kitware will be holding a CMake training course on March 27 and 28, 2018 
in Singapore. This two-days course will cover the best practice for 
CMake, CTest, CPack and CDash as well as advanced features of the tool

Please visit our website for more information and registration details:

     https://training.kitware.fr/browse/182

Note that the course will be taught in English. If you have any
questions, please contact us at training at kitware.fr or email me directly.

We are looking forward to seeing you in Singapore,
Julien
-- 
Kitware SAS
26 rue Louis Gu?rin
69100 Villeurbanne, France
http://www.kitware.eu
The ITK community is transitioning from this mailing list to discourse.itk.org. Please join us there!
________________________________
Powered by www.kitware.com

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From dzenanz at gmail.com  Thu Feb  8 09:36:36 2018
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 8 Feb 2018 09:36:36 -0500
Subject: [ITK] [ITK-users] ResampleDICOM example and DCMTK
In-Reply-To: <1518086204763-0.post@n7.nabble.com>
References: <95FBA78F-1DFC-4F33-9572-DA0DD9DE1E73@gmail.com>
 <1409515613801-7586158.post@n2.nabble.com>
 <CALzTN-TBe7P43_vCantDDGXXNT_H9oLhaZ6EXT6Fmfe5qWVuRQ@mail.gmail.com>
 <CALzTN-RHz0=MnvJDGHoRpDTwnRXR-uGp7qNfm67NLrjLKtpxQQ@mail.gmail.com>
 <1518086204763-0.post@n7.nabble.com>
Message-ID: <CAPf2UMS9TGHq7Y0NtYxC6j0NwAcu_b_W4YjLE2ZoZ0JE5DDDMw@mail.gmail.com>

Hi Ibraheem,

we are moving away from a mailing list, and into a forum
<https://discourse.itk.org/>. Could you repost your question there?

Thanks,
D?enan

On Thu, Feb 8, 2018 at 5:36 AM, Ibraheem via Insight-users <
insight-users at itk.org> wrote:

> Hi Matt,
> I have the same problem. I don't understand your answer. Part 3 of the code
> extract and create the meta data. The writer uses DCMTKImageIO as in :
> seriesWriter->SetImageIO(gdcmIO );
>
> Could you please add more explaination!
> Best!
> Ibraheem
>
>
>
>
> --
> Sent from: http://itk-users.7.n7.nabble.com/
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ________________________________
> 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:
> https://itk.org/mailman/listinfo/insight-users
>
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Kitware offers ITK Training Courses, for more information visit:
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From dclunie at dclunie.com  Thu Feb  8 10:11:46 2018
From: dclunie at dclunie.com (David Clunie)
Date: Thu, 8 Feb 2018 10:11:46 -0500
Subject: [ITK] [ITK-users] Forums suck, long live email,
 was Re:  ResampleDICOM example and DCMTK
In-Reply-To: <CAPf2UMS9TGHq7Y0NtYxC6j0NwAcu_b_W4YjLE2ZoZ0JE5DDDMw@mail.gmail.com>
References: <95FBA78F-1DFC-4F33-9572-DA0DD9DE1E73@gmail.com>
 <1409515613801-7586158.post@n2.nabble.com>
 <CALzTN-TBe7P43_vCantDDGXXNT_H9oLhaZ6EXT6Fmfe5qWVuRQ@mail.gmail.com>
 <CALzTN-RHz0=MnvJDGHoRpDTwnRXR-uGp7qNfm67NLrjLKtpxQQ@mail.gmail.com>
 <1518086204763-0.post@n7.nabble.com>
 <CAPf2UMS9TGHq7Y0NtYxC6j0NwAcu_b_W4YjLE2ZoZ0JE5DDDMw@mail.gmail.com>
Message-ID: <86a1fc0e-2c66-0e5c-5941-c348f99658f0@dclunie.com>

That's a bummer ... now I won't be able to have all the mail
to the list archived and indexed in a standard format along
with all the other lists that I subscribe to, so that I can
search everything at once, and instead it will be hidden on
some inaccessible proprietary system with dubious longevity.

Is there a way to have discourse.itk.org forward every message
by email? I couldn't find one.

David

On 2/8/18 9:36 AM, D?enan Zuki? wrote:
> Hi Ibraheem,
> 
> we are moving away from a mailing list, and into a forum <https://discourse.itk.org/>. Could you repost your question there?
> 
> Thanks,
> D?enan
The ITK community is transitioning from this mailing list to discourse.itk.org. Please join us there!
________________________________
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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Follow this link to subscribe/unsubscribe:
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From dzenanz at gmail.com  Thu Feb  8 10:46:31 2018
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Thu, 8 Feb 2018 10:46:31 -0500
Subject: [ITK] [ITK-users] Forums suck, long live email,
 was Re: ResampleDICOM example and DCMTK
In-Reply-To: <86a1fc0e-2c66-0e5c-5941-c348f99658f0@dclunie.com>
References: <95FBA78F-1DFC-4F33-9572-DA0DD9DE1E73@gmail.com>
 <1409515613801-7586158.post@n2.nabble.com>
 <CALzTN-TBe7P43_vCantDDGXXNT_H9oLhaZ6EXT6Fmfe5qWVuRQ@mail.gmail.com>
 <CALzTN-RHz0=MnvJDGHoRpDTwnRXR-uGp7qNfm67NLrjLKtpxQQ@mail.gmail.com>
 <1518086204763-0.post@n7.nabble.com>
 <CAPf2UMS9TGHq7Y0NtYxC6j0NwAcu_b_W4YjLE2ZoZ0JE5DDDMw@mail.gmail.com>
 <86a1fc0e-2c66-0e5c-5941-c348f99658f0@dclunie.com>
Message-ID: <CAPf2UMSWJnL9xv1G3ZXymsFRP0-MqhH8ThR7oDusA2tM8d-W1w@mail.gmail.com>

Yes, there is. For me, the "mailing list mode" is found on this page:
https://discourse.itk.org/u/dzenanz/preferences/emails

Regards,
D?enan

On Thu, Feb 8, 2018 at 10:11 AM, David Clunie <dclunie at dclunie.com> wrote:

> That's a bummer ... now I won't be able to have all the mail
> to the list archived and indexed in a standard format along
> with all the other lists that I subscribe to, so that I can
> search everything at once, and instead it will be hidden on
> some inaccessible proprietary system with dubious longevity.
>
> Is there a way to have discourse.itk.org forward every message
> by email? I couldn't find one.
>
> David
>
> On 2/8/18 9:36 AM, D?enan Zuki? wrote:
> > Hi Ibraheem,
> >
> > we are moving away from a mailing list, and into a forum <
> https://discourse.itk.org/>. Could you repost your question there?
> >
> > Thanks,
> > D?enan
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ________________________________
> 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:
> https://itk.org/mailman/listinfo/insight-users
>
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________________________________
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Kitware offers ITK Training Courses, for more information visit:
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From matt.mccormick at kitware.com  Thu Feb  8 10:47:55 2018
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Thu, 8 Feb 2018 10:47:55 -0500
Subject: [ITK] [ITK-users] Forums suck, long live email,
 was Re: ResampleDICOM example and DCMTK
In-Reply-To: <86a1fc0e-2c66-0e5c-5941-c348f99658f0@dclunie.com>
References: <95FBA78F-1DFC-4F33-9572-DA0DD9DE1E73@gmail.com>
 <1409515613801-7586158.post@n2.nabble.com>
 <CALzTN-TBe7P43_vCantDDGXXNT_H9oLhaZ6EXT6Fmfe5qWVuRQ@mail.gmail.com>
 <CALzTN-RHz0=MnvJDGHoRpDTwnRXR-uGp7qNfm67NLrjLKtpxQQ@mail.gmail.com>
 <1518086204763-0.post@n7.nabble.com>
 <CAPf2UMS9TGHq7Y0NtYxC6j0NwAcu_b_W4YjLE2ZoZ0JE5DDDMw@mail.gmail.com>
 <86a1fc0e-2c66-0e5c-5941-c348f99658f0@dclunie.com>
Message-ID: <CALzTN-Rn2jp=GShvMkjZvS-w6NfLV3mNQi8_VJj0GyqnZOeUuA@mail.gmail.com>

Hi David,

Thanks for chiming in. Don't worry, email lives on :-).

Instructions on how to use Discourse as a mailing list can be found here:

  https://discourse.itk.org/t/using-discourse-as-a-mailing-list/32

Thanks,
Matt

On Thu, Feb 8, 2018 at 10:11 AM, David Clunie <dclunie at dclunie.com> wrote:
> That's a bummer ... now I won't be able to have all the mail
> to the list archived and indexed in a standard format along
> with all the other lists that I subscribe to, so that I can
> search everything at once, and instead it will be hidden on
> some inaccessible proprietary system with dubious longevity.
>
> Is there a way to have discourse.itk.org forward every message
> by email? I couldn't find one.
>
> David
>
> On 2/8/18 9:36 AM, D?enan Zuki? wrote:
>> Hi Ibraheem,
>>
>> we are moving away from a mailing list, and into a forum <https://discourse.itk.org/>. Could you repost your question there?
>>
>> Thanks,
>> D?enan
> The ITK community is transitioning from this mailing list to discourse.itk.org. Please join us there!
> ________________________________
> 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:
> https://itk.org/mailman/listinfo/insight-users
The ITK community is transitioning from this mailing list to discourse.itk.org. Please join us there!
________________________________
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:
https://itk.org/mailman/listinfo/insight-users

From bill.lorensen at gmail.com  Thu Feb  8 11:46:31 2018
From: bill.lorensen at gmail.com (Bill Lorensen)
Date: Thu, 8 Feb 2018 08:46:31 -0800
Subject: [ITK] [ITK-users] Forums suck, long live email,
 was Re: ResampleDICOM example and DCMTK
In-Reply-To: <CALzTN-Rn2jp=GShvMkjZvS-w6NfLV3mNQi8_VJj0GyqnZOeUuA@mail.gmail.com>
References: <95FBA78F-1DFC-4F33-9572-DA0DD9DE1E73@gmail.com>
 <1409515613801-7586158.post@n2.nabble.com>
 <CALzTN-TBe7P43_vCantDDGXXNT_H9oLhaZ6EXT6Fmfe5qWVuRQ@mail.gmail.com>
 <CALzTN-RHz0=MnvJDGHoRpDTwnRXR-uGp7qNfm67NLrjLKtpxQQ@mail.gmail.com>
 <1518086204763-0.post@n7.nabble.com>
 <CAPf2UMS9TGHq7Y0NtYxC6j0NwAcu_b_W4YjLE2ZoZ0JE5DDDMw@mail.gmail.com>
 <86a1fc0e-2c66-0e5c-5941-c348f99658f0@dclunie.com>
 <CALzTN-Rn2jp=GShvMkjZvS-w6NfLV3mNQi8_VJj0GyqnZOeUuA@mail.gmail.com>
Message-ID: <CADZJ4hN36ofpdZ3Kh7Sa2Va5Uj4wPJPkz_8XNjKbUTXkiPZqWw@mail.gmail.com>

David, I agree. I only use the email option for discourse.

On Feb 8, 2018 7:48 AM, "Matt McCormick" <matt.mccormick at kitware.com> wrote:

> Hi David,
>
> Thanks for chiming in. Don't worry, email lives on :-).
>
> Instructions on how to use Discourse as a mailing list can be found here:
>
>   https://discourse.itk.org/t/using-discourse-as-a-mailing-list/32
>
> Thanks,
> Matt
>
> On Thu, Feb 8, 2018 at 10:11 AM, David Clunie <dclunie at dclunie.com> wrote:
> > That's a bummer ... now I won't be able to have all the mail
> > to the list archived and indexed in a standard format along
> > with all the other lists that I subscribe to, so that I can
> > search everything at once, and instead it will be hidden on
> > some inaccessible proprietary system with dubious longevity.
> >
> > Is there a way to have discourse.itk.org forward every message
> > by email? I couldn't find one.
> >
> > David
> >
> > On 2/8/18 9:36 AM, D?enan Zuki? wrote:
> >> Hi Ibraheem,
> >>
> >> we are moving away from a mailing list, and into a forum <
> https://discourse.itk.org/>. Could you repost your question there?
> >>
> >> Thanks,
> >> D?enan
> > The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> > ________________________________
> > 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:
> > https://itk.org/mailman/listinfo/insight-users
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ________________________________
> 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:
> https://itk.org/mailman/listinfo/insight-users
>
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The ITK community is transitioning from this mailing list to discourse.itk.org. Please join us there!
________________________________
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:
https://itk.org/mailman/listinfo/insight-users

From jhlegarreta at vicomtech.org  Mon Feb 12 07:01:56 2018
From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta)
Date: Mon, 12 Feb 2018 13:01:56 +0100
Subject: [ITK] [vtkusers] ITK Noise removal filter on VTK file
In-Reply-To: <1297652463.3144475.1518434869006@mail.yahoo.com>
References: <1297652463.3144475.1518434869006.ref@mail.yahoo.com>
 <1297652463.3144475.1518434869006@mail.yahoo.com>
Message-ID: <CAAKhGh9y9oA=WOVXqs_m9qkijhs4Pca-eL4+YaW8sFdE7OhMUQ@mail.gmail.com>

Dear Majid,
if you are processing a 2D/3D (medical image) volumetric dataset, I'd say
that it'd be easier to just use ITK as a starting point. If you then need
visualization capabilities, then you'd need to use VTK as well.

For resampling, and reslicing purposes, you may want to have a look at
https://itk.org/Doxygen/html/classitk_1_1ResampleImageFilter.html

and the examples
https://itk.org/ITKExamples/src/Filtering/ImageGrid/ResampleAnImage/Documentation.html

For using VTK with medical datasets:
https://lorensen.github.io/VTKExamples/site/Cxx/#medical

For edge preserving noise removal, you can have a look at
https://itk.org/Doxygen/html/classitk_1_1AnisotropicDiffusionImageFilter.html

Edge preserving noise removal is described in Section 2.7.3. of the ITK
Software Guide:
https://itk.org/ItkSoftwareGuide.pdf

For storing your image, ITK tends to use metaimage format:
https://itk.org/Doxygen/html/classitk_1_1MetaImageIO.html

VTK can also write/read it.

HTH,
JON HAITZ


PS: ITK has transitioned to discourse.itk.org as a discussion forum. So if
your question is only about ITK, it would be advisable to post it there.

--


On 12 February 2018 at 12:27, Majid M. Sadeghi via vtkusers <
vtkusers at vtk.org> wrote:

> Dear All,
>
> I am using a vtkGDCMImageReader to import 3D DICOM images. Then I adjust
> the spacing and reslice. After that I can save it as both image
> data|(vtkXMLImageDataWriter) or polydata(vtkImageDataGeometryFilter).
>
> I want to apply edge preserving noise removal to the data either just
> after reading images, or after saving as .vtp files.
>
> I have setup ITK and scanned the ITK book, but I have no experience on it.
>
> Is there any link or example which can guide me on how to perform this?
> (what type of structure is common between ITK and VTK? Should I perform the
> filter after saving in VTK or before that? which filter do you suggest for
> the best speed and perfomance?)
>
> Thanks a lot.
>
>
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
>
> Please keep messages on-topic and check the VTK FAQ at:
> http://www.vtk.org/Wiki/VTK_FAQ
>
> Search the list archives at: http://markmail.org/search/?q=vtkusers
>
> Follow this link to subscribe/unsubscribe:
> https://vtk.org/mailman/listinfo/vtkusers
>
>
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From matt.mccormick at kitware.com  Mon Feb 12 07:27:32 2018
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Mon, 12 Feb 2018 07:27:32 -0500
Subject: [ITK] [ITK-users] ITK Noise removal filter on VTK file
In-Reply-To: <1745079269.3165284.1518435700616@mail.yahoo.com>
References: <1745079269.3165284.1518435700616.ref@mail.yahoo.com>
 <1745079269.3165284.1518435700616@mail.yahoo.com>
Message-ID: <CALzTN-QDKk8=RJfR=khc25-49M3H3MJb-ZEk79B_=9eizoNwSA@mail.gmail.com>

Hi Majid,

For the best DICOM image compatibility, use itk::DCMTKImageIO:

  https://github.com/InsightSoftwareConsortium/ITK/blob/8a2a15f41218c925c0a89119e09419d48f83eb22/Modules/IO/DCMTK/test/itkDCMTKSeriesReadImageWrite.cxx

This also supports reading in the DICOM image orientation into the
itk::Image. This information is not retained in vtkImageData.


Writing the image to disk can be avoided with ITKVtkGlue:

  https://itk.org/ITKExamples/src/Bridge/VtkGlue/ConvertAnitkImageTovtkImageData/Documentation.html

but again, be aware of the loss of the Direction information.


Both ITK and VTK support image volumes written in MetaImage, NRRD, or
VTK Legacy file format.


A state-of-the-art edge preserving filter is the anisotropic diffusion
lattice basis reduction filter in ITK. For more information, see the
Insight Journal article:

  http://www.insight-journal.org/browse/publication/953

and instructions on how to install the Python package or enable its
module in ITK's build here:

  https://github.com/InsightSoftwareConsortium/ITKAnisotropicDiffusionLBR


Hope this helps,
Matt

On Mon, Feb 12, 2018 at 6:41 AM, Majid M. Sadeghi via Insight-users
<insight-users at itk.org> wrote:
> Dear All,
>
> I am using a vtkGDCMImageReader to import 3D DICOM images. Then I adjust the
> spacing and reslice. After that I can save it as both image
> data|(vtkXMLImageDataWriter) or polydata(vtkImageDataGeometryFilter).
>
> I want to apply edge preserving noise removal to the data either just after
> reading images, or after saving as .vtp files.
>
> I have setup ITK and scanned the ITK book, but I have no experience on it.
>
> Is there any link or example which can guide me on how to perform this?
> (what type of structure is common between ITK and VTK? Should I perform the
> filter after saving in VTK or before that? which filter do you suggest for
> the best speed and perfomance?)
>
> Thanks a lot.
>
>
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ________________________________
> 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:
> https://itk.org/mailman/listinfo/insight-users
>
The ITK community is transitioning from this mailing list to discourse.itk.org. Please join us there!
________________________________
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:
https://itk.org/mailman/listinfo/insight-users

From majid.msadeghi at yahoo.com  Mon Feb 12 07:58:05 2018
From: majid.msadeghi at yahoo.com (Majid M. Sadeghi)
Date: Mon, 12 Feb 2018 12:58:05 +0000 (UTC)
Subject: [ITK] [vtkusers] ITK Noise removal filter on VTK file
In-Reply-To: <CAAKhGh9y9oA=WOVXqs_m9qkijhs4Pca-eL4+YaW8sFdE7OhMUQ@mail.gmail.com>
References: <1297652463.3144475.1518434869006.ref@mail.yahoo.com>
 <1297652463.3144475.1518434869006@mail.yahoo.com>
 <CAAKhGh9y9oA=WOVXqs_m9qkijhs4Pca-eL4+YaW8sFdE7OhMUQ@mail.gmail.com>
Message-ID: <1739662613.3219458.1518440285948@mail.yahoo.com>

Thakn you so much for the great help.?
 

    On Monday, February 12, 2018 2:02 PM, Jon Haitz Legarreta <jhlegarreta at vicomtech.org> wrote:
 

 Dear Majid,if you are processing a 2D/3D (medical image) volumetric dataset, I'd say that it'd be easier to just use ITK as a starting point. If you then need visualization capabilities, then you'd need to use VTK as well.
For resampling, and reslicing purposes, you may want to have a look athttps://itk.org/Doxygen/html/classitk_1_1ResampleImageFilter.html

and the exampleshttps://itk.org/ITKExamples/src/Filtering/ImageGrid/ResampleAnImage/Documentation.html

For using VTK with medical datasets:https://lorensen.github.io/VTKExamples/site/Cxx/#medical

For edge preserving noise removal, you can have a look athttps://itk.org/Doxygen/html/classitk_1_1AnisotropicDiffusionImageFilter.html

Edge preserving noise removal is described in Section 2.7.3. of the ITK Software Guide:https://itk.org/ItkSoftwareGuide.pdf

For storing your image, ITK tends to use metaimage format:https://itk.org/Doxygen/html/classitk_1_1MetaImageIO.html

VTK can also write/read it.
HTH,JON HAITZ

PS: ITK has transitioned to discourse.itk.org as a discussion forum. So if your question is only about ITK, it would be advisable to post it there.
--


On 12 February 2018 at 12:27, Majid M. Sadeghi via vtkusers <vtkusers at vtk.org> wrote:

Dear All,
I am using a vtkGDCMImageReader to import 3D DICOM images. Then I adjust the spacing and reslice. After that I can save it as both image data|(vtkXMLImageDataWriter) or polydata( vtkImageDataGeometryFilter).
I want to apply edge preserving noise removal to the data either just after reading images, or after saving as .vtp files.
I have setup ITK and scanned the ITK book, but I have no experience on it. 

Is there any link or example which can guide me on how to perform this? (what type of structure is common between ITK and VTK? Should I perform the filter after saving in VTK or before that? which filter do you suggest for the best speed and perfomance?)
Thanks a lot.



______________________________ _________________
Powered by www.kitware.com

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

Please keep messages on-topic and check the VTK FAQ at: http://www.vtk.org/Wiki/VTK_ FAQ

Search the list archives at: http://markmail.org/search/?q= vtkusers

Follow this link to subscribe/unsubscribe:
https://vtk.org/mailman/ listinfo/vtkusers





   
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From dzenanz at gmail.com  Tue Feb 13 15:16:43 2018
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Tue, 13 Feb 2018 15:16:43 -0500
Subject: [ITK] [ITK-users] [vtkusers] Convert vtkImageData to an
 itk::Image
In-Reply-To: <271213644.174330.1518539517781@mail.yahoo.com>
References: <271213644.174330.1518539517781.ref@mail.yahoo.com>
 <271213644.174330.1518539517781@mail.yahoo.com>
Message-ID: <CAPf2UMSn7m1e-QaUOiupUYh7U-yJK0a_9PaMft2pXT5U+Nxe7A@mail.gmail.com>

Hi Majid,

maybe you need to invoke reslice->Update(); before importing its output
into ITK?

Regards,
D?enan

On Tue, Feb 13, 2018 at 11:31 AM, Majid M. Sadeghi via vtkusers <
vtkusers at vtk.org> wrote:

> Dear All,
>
> I read some DICOM data using vtkGDCMImageReader, then I change the
> sapacing and reslice them. Next I want to change that vtk image to itk
> image to be able to apply noise removal. But as soon as the code reaches
> the "filter_toitkimage->Update();" line the program just exits without
> saying anything (actually it says:The program '[14040]
> QtGuiApplication2.exe' has exited with code 3 (0x3).).
>
> Here is the code:
>
> vtkSmartPointer<vtkGDCMImageReader> reader = vtkSmartPointer<
> vtkGDCMImageReader>::New();
>     reader->SetFileNames(vtkfiles);
>     reader->Update();
>
>     vtkSmartPointer<vtkImageChangeInformation> changer = vtkSmartPointer<
> vtkImageChangeInformation>::New();
>     changer->SetOutputSpacing(pixlespacing, pixlespacing,
> ippzspacing);//@majidnow
>     changer->SetInputConnection(reader->GetOutputPort());
>
>     vtkSmartPointer<vtkImageReslice> reslice = vtkSmartPointer<
> vtkImageReslice>::New();
>     reslice->SetInputConnection(changer->GetOutputPort());
>
>     //to change VTK image to ITK image
>     const unsigned int Dimension = 3;
>
>     using PixelType = double;
>     using ImageType = itk::Image< PixelType, Dimension >;
>
>     using FilterType = itk::VTKImageToImageFilter< ImageType >;
>     FilterType::Pointer filter_toitkimage = FilterType::New();
>     filter_toitkimage->SetInput(reslice->GetOutput());
>
>     try
>     {
>         filter_toitkimage->Update();
>     }
>     catch (itk::ExceptionObject & error)
>     {
>         std::cerr << "Error: " << error << std::endl;
>         //return EXIT_FAILURE;
>     }
>
>
> Any idea why this happens?
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
>
> Please keep messages on-topic and check the VTK FAQ at:
> http://www.vtk.org/Wiki/VTK_FAQ
>
> Search the list archives at: http://markmail.org/search/?q=vtkusers
>
> Follow this link to subscribe/unsubscribe:
> https://vtk.org/mailman/listinfo/vtkusers
>
>
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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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Follow this link to subscribe/unsubscribe:
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From julien.jomier at kitware.com  Wed Feb 14 02:32:57 2018
From: julien.jomier at kitware.com (Julien Jomier)
Date: Wed, 14 Feb 2018 08:32:57 +0100
Subject: [ITK] [ITK-users] [ANN] CMake Training Course in France - March 12
Message-ID: <e3c06bb6-c4af-a83c-819d-d70b2d033389@kitware.com>

Kitware will be holding a CMake training course on March 12, 2018 in 
Lyon, France. This one-day course will cover the best practice for 
CMake, CTest, CPack and CDash.

Please visit our website for more information and registration details:

     https://training.kitware.fr/browse/170

Note that the course will be taught in English. If you have any
questions, please contact us at training at kitware.fr or email me directly.

We are looking forward to seeing you in Lyon,
Julien
-- 
Kitware SAS
26 rue Louis Gu?rin
69100 Villeurbanne, France
http://www.kitware.eu
The ITK community is transitioning from this mailing list to discourse.itk.org. Please join us there!
________________________________
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 sean at rogue-research.com  Wed Feb 14 17:14:01 2018
From: sean at rogue-research.com (Sean McBride)
Date: Wed, 14 Feb 2018 17:14:01 -0500
Subject: [ITK] [ITK-users] Forums suck, long live email,
 was Re: ResampleDICOM example and DCMTK
In-Reply-To: <CALzTN-Rn2jp=GShvMkjZvS-w6NfLV3mNQi8_VJj0GyqnZOeUuA@mail.gmail.com>
References: <95FBA78F-1DFC-4F33-9572-DA0DD9DE1E73@gmail.com>
 <1409515613801-7586158.post@n2.nabble.com>
 <CALzTN-TBe7P43_vCantDDGXXNT_H9oLhaZ6EXT6Fmfe5qWVuRQ@mail.gmail.com>
 <CALzTN-RHz0=MnvJDGHoRpDTwnRXR-uGp7qNfm67NLrjLKtpxQQ@mail.gmail.com>
 <1518086204763-0.post@n7.nabble.com>
 <CAPf2UMS9TGHq7Y0NtYxC6j0NwAcu_b_W4YjLE2ZoZ0JE5DDDMw@mail.gmail.com>
 <86a1fc0e-2c66-0e5c-5941-c348f99658f0@dclunie.com>
 <CALzTN-Rn2jp=GShvMkjZvS-w6NfLV3mNQi8_VJj0GyqnZOeUuA@mail.gmail.com>
Message-ID: <20180214221401.1996920570@mail.rogue-research.com>

On Thu, 8 Feb 2018 10:47:55 -0500, Matt McCormick said:

>Thanks for chiming in. Don't worry, email lives on :-).
>
>Instructions on how to use Discourse as a mailing list can be found here:
>
>  https://discourse.itk.org/t/using-discourse-as-a-mailing-list/32

Alas, in my opinion anyway, using Discourse as a mailing list is a very subpar experience.

- it changes the 'from' address, making off-list replies impossible
- replying to the 'from' address bounces, making 'reply all' broken
- there's no 'List-Post' header, so it's hard to start new threads
- it sends html email
- the text-only part of the email renders quotations poorly
- quoted text in replies get removed, making inline replies impossible/broken
- it does something weird with emoji characters, changing them to strings like ":ok_hand:"
- it discards email signatures

Cheers,

Sean


The ITK community is transitioning from this mailing list to discourse.itk.org. Please join us there!
________________________________
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:
https://itk.org/mailman/listinfo/insight-users

From matt.mccormick at kitware.com  Wed Feb 14 18:48:26 2018
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Wed, 14 Feb 2018 18:48:26 -0500
Subject: [ITK] [ITK-users]   Forums suck, long live email,
 was Re: ResampleDICOM example and DCMTK
In-Reply-To: <CAH6Pt5p+jnzA-Nm0fUGJTotf3rd5gEuup7JfuJvTAA-_2HxXrA@mail.gmail.com>
References: <95FBA78F-1DFC-4F33-9572-DA0DD9DE1E73@gmail.com>
 <1409515613801-7586158.post@n2.nabble.com>
 <CALzTN-TBe7P43_vCantDDGXXNT_H9oLhaZ6EXT6Fmfe5qWVuRQ@mail.gmail.com>
 <CALzTN-RHz0=MnvJDGHoRpDTwnRXR-uGp7qNfm67NLrjLKtpxQQ@mail.gmail.com>
 <1518086204763-0.post@n7.nabble.com>
 <CAPf2UMS9TGHq7Y0NtYxC6j0NwAcu_b_W4YjLE2ZoZ0JE5DDDMw@mail.gmail.com>
 <86a1fc0e-2c66-0e5c-5941-c348f99658f0@dclunie.com>
 <CALzTN-Rn2jp=GShvMkjZvS-w6NfLV3mNQi8_VJj0GyqnZOeUuA@mail.gmail.com>
 <20180214221401.1996920570@mail.rogue-research.com>
 <CAH6Pt5p+jnzA-Nm0fUGJTotf3rd5gEuup7JfuJvTAA-_2HxXrA@mail.gmail.com>
Message-ID: <CALzTN-Q=h_TuwXZ6BMDXt=L-1ydkwObQLEcB3ocmovji12h5iw@mail.gmail.com>

On Wed, Feb 14, 2018 at 5:47 PM, Matthew Brett <matthew.brett at gmail.com> wrote:
> On Wed, Feb 14, 2018 at 10:14 PM, Sean McBride <sean at rogue-research.com> wrote:
>> On Thu, 8 Feb 2018 10:47:55 -0500, Matt McCormick said:
>>
>>>Thanks for chiming in. Don't worry, email lives on :-).
>>>
>>>Instructions on how to use Discourse as a mailing list can be found here:
>>>
>>>  https://discourse.itk.org/t/using-discourse-as-a-mailing-list/32
>>
>> Alas, in my opinion anyway, using Discourse as a mailing list is a very subpar experience.

These statements are very deceiving.


>> - it changes the 'from' address, making off-list replies impossible

This means it does not expose your email address to all the spammers
on the internets!


>> - replying to the 'from' address bounces, making 'reply all' broken

Use "reply" instead of "reply all".


>> - there's no 'List-Post' header, so it's hard to start new threads

See the link above on how to start a new thread.


>> - it sends html email

Yes, this is too bad. However, HTML email is simply a standard today
in all kinds of communication.


>> - the text-only part of the email renders quotations poorly

I am not sure how bad this is relative having content only limited to
plain text. In imaging, it is helpful to be able to share images.


>> - quoted text in replies get removed, making inline replies impossible/broken

It is still possible to quote replies.


>> - it does something weird with emoji characters, changing them to strings like ":ok_hand:"

Is this bad?


>> - it discards email signatures

This is a feature.


2 cents,
Matt
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From bakkari.abdelkhalek at hotmail.fr  Sat Feb 17 06:23:41 2018
From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari)
Date: Sat, 17 Feb 2018 11:23:41 +0000
Subject: [ITK] [ITK-users] Characterization degree  using ITK
Message-ID: <VI1PR0902MB2046F02EAE978CCB7E4E442683CA0@VI1PR0902MB2046.eurprd09.prod.outlook.com>

Dear All,


I am trying to compute the characterization degree for a statistical  features of an image using ITK .

This criterion is based on the report/ratio of the between classes (inter-class) variance by the intra-class variance, calculated in order to extract the best statistical features of an image.


Could you please, provide me any help.


Thank you in advance.



Kind regards,


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From mrguilfoyle at gmail.com  Sat Feb 17 10:28:59 2018
From: mrguilfoyle at gmail.com (Mathew Guilfoyle)
Date: Sat, 17 Feb 2018 15:28:59 +0000
Subject: [ITK] [ITK-users] SimpleITK R Wrapping of ChangeLabel and ChangeMap
Message-ID: <124D2356-CD65-4779-9BA5-56B2CB71682E@gmail.com>

I am struggling to find the correct way to specify a ChangeMap to supply to the ChangeLabel filter in the R wrapping of SimpleITK.

I can create the filter object but supplying a R list of (vector) pairs of from/to labels causes R to crash.  Looking through the SimpleITK docs the ChangeMap is specified as a std::map<double, double> structure and in the R SWIG file there is a DoubleDoubleMap() function specified which seems to be a mechanism to create the map in R.  However, despite trying various ways of using the DoubleDoubleMap I cannot get it to work.  I can create a DoubleDoubleMap object but then can't supplying the pairs of labels that define the map.  One Python example I came across uses the DoubleDoubleMap like this:

import SimpleITK as silk

changeLabel = sitk.ChangeLabelImageFilter()
changeMap  = sitk.DoubleDoubleMap()

changeMap[0] = 1
changeMap[1] = 2

etc..

Doing the equivalent indexing in R produces the error:

Error: evaluation nested too deeply: infinite recursion / options(expressions=)?
Error during wrapup: evaluation nested too deeply: infinite recursion / options(expressions=)?

Does anyone know how to correctly interact with the DoubleDoubleMap object and/or otherwise specify a change map in R?

Many thanks

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From richard.beare at gmail.com  Sat Feb 17 17:35:36 2018
From: richard.beare at gmail.com (Richard Beare)
Date: Sun, 18 Feb 2018 09:35:36 +1100
Subject: [ITK] [ITK-users] SimpleITK R Wrapping of ChangeLabel and
 ChangeMap
In-Reply-To: <124D2356-CD65-4779-9BA5-56B2CB71682E@gmail.com>
References: <124D2356-CD65-4779-9BA5-56B2CB71682E@gmail.com>
Message-ID: <CA+V7QS8Mu5-4yQN5Pt1oDJ=ZyEHftHmtv_7_1spYk0PDvMRWqA@mail.gmail.com>

I'm afraid this is one thing we haven't yet fixed up in the R bindings.
There aren't useful generators of std::map class bindings in SWIG/R at
present, so you just end up with the class pointers and no methods to
construct or manipulate them. It's on my list. My original plan was to use
named vectors for the common case changing labels, but there are certainly
going to be messy issues in converting keys to strings. However this
approach is probably most like the dictionary method used by python.

On Sun, Feb 18, 2018 at 2:28 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com>
wrote:

> I am struggling to find the correct way to specify a ChangeMap to supply
> to the ChangeLabel filter in the R wrapping of SimpleITK.
>
> I can create the filter object but supplying a R list of (vector) pairs of
> from/to labels causes R to crash.  Looking through the SimpleITK docs the
> ChangeMap is specified as a std::map<double, double> structure and in the R
> SWIG file there is a DoubleDoubleMap() function specified which seems to be
> a mechanism to create the map in R.  However, despite trying various ways
> of using the DoubleDoubleMap I cannot get it to work.  I can create a
> DoubleDoubleMap object but then can't supplying the pairs of labels that
> define the map.  One Python example I came across uses the DoubleDoubleMap
> like this:
>
> import SimpleITK as silk
>
> changeLabel = sitk.ChangeLabelImageFilter()
> changeMap  = sitk.DoubleDoubleMap()
>
> changeMap[0] = 1
> changeMap[1] = 2
>
> etc..
>
> Doing the equivalent indexing in R produces the error:
>
> Error: evaluation nested too deeply: infinite recursion /
> options(expressions=)?
> Error during wrapup: evaluation nested too deeply: infinite recursion /
> options(expressions=)?
>
> Does anyone know how to correctly interact with the DoubleDoubleMap object
> and/or otherwise specify a change map in R?
>
> Many thanks
>
>
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ________________________________
> 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:
> https://itk.org/mailman/listinfo/insight-users
>
>
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From dzenanz at gmail.com  Mon Feb 19 11:11:30 2018
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Mon, 19 Feb 2018 11:11:30 -0500
Subject: [ITK] [ITK-users] Characterization degree using ITK
In-Reply-To: <VI1PR0902MB2046F02EAE978CCB7E4E442683CA0@VI1PR0902MB2046.eurprd09.prod.outlook.com>
References: <VI1PR0902MB2046F02EAE978CCB7E4E442683CA0@VI1PR0902MB2046.eurprd09.prod.outlook.com>
Message-ID: <CAPf2UMQkB4xR0PPDqL3=b8YBqtjaybf-oRmWsd4SkbQHkusExQ@mail.gmail.com>

Hi Abdelkhalek,

your question is general and kind of vague. Giving example image and better
describing the expected output would make it clearer.

Also, posting to discourse <https://discourse.itk.org/> would reach a more
active audience.

Regards,
D?enan

On Sat, Feb 17, 2018 at 6:23 AM, Abdelkhalek Bakkari <
bakkari.abdelkhalek at hotmail.fr> wrote:

> Dear All,
>
>
> I am trying to compute the characterization degree for a statistical
> features of an image using ITK .
>
> This criterion is based on the report/ratio of the between classes
> (inter-class) variance by the intra-class variance, calculated in order to
> extract the best statistical features of an image.
>
>
> Could you please, provide me any help.
>
>
> Thank you in advance.
>
>
>
> Kind regards,
>
>
>
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From g.lemaitre58 at gmail.com  Sun Feb 25 10:26:11 2018
From: g.lemaitre58 at gmail.com (=?UTF-8?Q?Guillaume_Lema=C3=AEtre?=)
Date: Sun, 25 Feb 2018 16:26:11 +0100
Subject: [ITK] [ITK-users] VNL matrix with the Python wrapper
Message-ID: <CACDxx9jXEJYLRDKfpuNNvE+0qeViyoPk7Vcmk1kRZ7VXo848Ag@mail.gmail.com>

Hi All,

I am using the python wrapper of itk to manipulate. I checked the quick
start guide (
http://itkpythonpackage.readthedocs.io/en/latest/Quick_start_guide.html#usage)
to go from numpy to vnl matrices and vice-versa. However, I got into
trouble when trying to use those utils with itk images. As a short example:

```python
>>> import numpy as np

>>> img = np.random.random((100, 100, 100))
>>> img_itk = itk.GetImageFromArray(img)

>>> vnl_matrix = img_itk.GetDirection().GetVnlMatrix()
>>> type(vnl_matrix)
vnl_matrix_fixedPython.vnl_matrix_fixedD_3_3

>>> itk.GetArrayFromVnlMatrix(vnl_matrix)

TypeError: in method 'itkPyVnlD__GetArrayViewFromVnlMatrix', argument 1 of
type 'vnl_matrixD *'
```

So what would the proper way of converting this matrix into a numpy array
or view.

Cheers,
-- 
Guillaume Lemaitre
INRIA Saclay - Parietal team
Center for Data Science Paris-Saclay
https://glemaitre.github.io/
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From dzenanz at gmail.com  Mon Feb 26 09:33:07 2018
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Mon, 26 Feb 2018 09:33:07 -0500
Subject: [ITK] [ITK-users] VNL matrix with the Python wrapper
In-Reply-To: <CACDxx9jXEJYLRDKfpuNNvE+0qeViyoPk7Vcmk1kRZ7VXo848Ag@mail.gmail.com>
References: <CACDxx9jXEJYLRDKfpuNNvE+0qeViyoPk7Vcmk1kRZ7VXo848Ag@mail.gmail.com>
Message-ID: <CAPf2UMR0jOXwTWO_2PgEoRv0za71Qe3FE=kuNFQrTheaQN5y6w@mail.gmail.com>

Hi Guillaume,

we have switched to discourse <https://discourse.itk.org/> forum for
discussion. Can you repost your question there?

Thanks,
D?enan

On Sun, Feb 25, 2018 at 10:26 AM, Guillaume Lema?tre <g.lemaitre58 at gmail.com
> wrote:

> Hi All,
>
> I am using the python wrapper of itk to manipulate. I checked the quick
> start guide (http://itkpythonpackage.readthedocs.io/en/latest/
> Quick_start_guide.html#usage) to go from numpy to vnl matrices and
> vice-versa. However, I got into trouble when trying to use those utils with
> itk images. As a short example:
>
> ```python
> >>> import numpy as np
>
> >>> img = np.random.random((100, 100, 100))
> >>> img_itk = itk.GetImageFromArray(img)
>
> >>> vnl_matrix = img_itk.GetDirection().GetVnlMatrix()
> >>> type(vnl_matrix)
> vnl_matrix_fixedPython.vnl_matrix_fixedD_3_3
>
> >>> itk.GetArrayFromVnlMatrix(vnl_matrix)
>
> TypeError: in method 'itkPyVnlD__GetArrayViewFromVnlMatrix', argument 1
> of type 'vnl_matrixD *'
> ```
>
> So what would the proper way of converting this matrix into a numpy array
> or view.
>
> Cheers,
> --
> Guillaume Lemaitre
> INRIA Saclay - Parietal team
> Center for Data Science Paris-Saclay
> https://glemaitre.github.io/
>
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ________________________________
> 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:
> https://itk.org/mailman/listinfo/insight-users
>
>
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From urban.simoncic at gmail.com  Mon Feb 26 18:46:20 2018
From: urban.simoncic at gmail.com (Urban Simoncic)
Date: Tue, 27 Feb 2018 00:46:20 +0100
Subject: [ITK] Manual creation of FEMObject
Message-ID: <af31ca89-477b-1228-3767-827cee4ba060@gmail.com>

Hi,

I am thinking of using ITK for simple FEM elasticity problems, where FEM 
models would be derived from the medical image. However, I don't want 
uniform mesh, so I will need to somehow create FEMObject myself. Is 
there any tool to create mesh from medical images, and any example that 
shows how to work with that?

Urban


From dzenanz at gmail.com  Tue Feb 27 08:27:06 2018
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Tue, 27 Feb 2018 08:27:06 -0500
Subject: [ITK] Manual creation of FEMObject
In-Reply-To: <af31ca89-477b-1228-3767-827cee4ba060@gmail.com>
References: <af31ca89-477b-1228-3767-827cee4ba060@gmail.com>
Message-ID: <CAPf2UMSH7KCzXJKgUqA7tYD3Y753==rguv5WXxTnKAuePYfbng@mail.gmail.com>

Hi Urban,

we have moved to discourse <http://discourse.itk.org/> forum. If you repost
your question there, it will reach greater active audience.

Regards,
D?enan

On Mon, Feb 26, 2018 at 6:46 PM, Urban Simoncic <urban.simoncic at gmail.com>
wrote:

> Hi,
>
> I am thinking of using ITK for simple FEM elasticity problems, where FEM
> models would be derived from the medical image. However, I don't want
> uniform mesh, so I will need to somehow create FEMObject myself. Is there
> any tool to create mesh from medical images, and any example that shows how
> to work with that?
>
> Urban
>
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ________________________________________
> Community mailing list
> Community at itk.org
> https://itk.org/mailman/listinfo/community
>
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From mageshwar.selvakumar at outlook.com  Wed Feb 28 10:34:19 2018
From: mageshwar.selvakumar at outlook.com (Mageshwar Selvakumar)
Date: Wed, 28 Feb 2018 15:34:19 +0000
Subject: [ITK] Query regarding implementation of
 itkGeometricJacobianDeterminantImageFilter.hxx
Message-ID: <VI1PR0901MB1245481027750846A08B8D078EC70@VI1PR0901MB1245.eurprd09.prod.outlook.com>

Dear ITK community members,

I want to have a deeper insight into the implementation of jacobian determinant in itkGeometricJacobianDeterminantImageFilter.hxx, but I'm unable to find some theory which explains on what basis this code is implemented. It would be nice if someone could refer some books or literature on jacobian implementation, especially the method used here, the connection between triangular area and tetrahedral volume computation and jacobian determinant. It would be of a great help to me, if someone can direct me towards it.

Thank you,


Kind regards

Mageshwar Selvakumar, M.Sc


Department of Pharmakologische Bildgebung und Bildanalyse

Friedrich Alexander Universit?t Erlangen N?rnberg


Office: Fahrstr. 17, 91054 Erlangen

Phone: + 49-9131-8522898

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