From lp at 3dside.eu  Tue Jan  2 03:13:36 2018
From: lp at 3dside.eu (lolo)
Date: Tue, 2 Jan 2018 01:13:36 -0700 (MST)
Subject: [ITK] [ITK-users] add tag to nrrd header
Message-ID: <1514880816260-0.post@n7.nabble.com>

Hi all,

Happy new year. It seems I'm the first post of the year. Very glad :-)

I can't find any possibility to add a field (custom or not) into a nrrd
header. The NrrdImageIO doesn't allow it (or I missed it).
Is someone know how to do that?

Thanks,
Laurent



--
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!
________________________________
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From blowekamp at mail.nih.gov  Tue Jan  2 09:21:46 2018
From: blowekamp at mail.nih.gov (Lowekamp, Bradley (NIH/NLM/LHC) [C])
Date: Tue, 2 Jan 2018 14:21:46 +0000
Subject: [ITK] [ITK-users]   add tag to nrrd header
In-Reply-To: <1514880816260-0.post@n7.nabble.com>
References: <1514880816260-0.post@n7.nabble.com>
Message-ID: <70B43C7E-153F-4D97-A7BD-B46B93834711@mail.nih.gov>

Happy new year to you too!

Please repost your questions to: discourse.itk.org


Thanks,
Brad

p.s. I?m looking at the writer now to determine how the meta-data dictionary is handled.

On 1/2/18, 3:14 AM, "lolo" <lp at 3dside.eu> wrote:

    Hi all,
    
    Happy new year. It seems I'm the first post of the year. Very glad :-)
    
    I can't find any possibility to add a field (custom or not) into a nrrd
    header. The NrrdImageIO doesn't allow it (or I missed it).
    Is someone know how to do that?
    
    Thanks,
    Laurent
    
    
    
    --
    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
    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
    

The ITK community is transitioning from this mailing list to discourse.itk.org. Please join us there!
________________________________
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From francois.budin at kitware.com  Tue Jan  2 16:48:50 2018
From: francois.budin at kitware.com (Francois Budin)
Date: Tue, 2 Jan 2018 16:48:50 -0500
Subject: [ITK] [ITK-users]  add tag to nrrd header
In-Reply-To: <70B43C7E-153F-4D97-A7BD-B46B93834711@mail.nih.gov>
References: <1514880816260-0.post@n7.nabble.com>
 <70B43C7E-153F-4D97-A7BD-B46B93834711@mail.nih.gov>
Message-ID: <CAHwLD2Xv0tM2Ud0zF8-QTrDXYj_=rqh45ZRazJNjY8oxz2pwWA@mail.gmail.com>

Hello,

As Brad said, we are now using the discourse.itk.org forum for questions
and answers relative to ITK. I posted an answer to your question here:
https://discourse.itk.org/t/how-to-write-a-custom-tag-to-an-image-nrrd-or-other-header/565

Hope this helps,
Francois

On Tue, Jan 2, 2018 at 9:21 AM, Lowekamp, Bradley (NIH/NLM/LHC) [C] <
blowekamp at mail.nih.gov> wrote:

> Happy new year to you too!
>
> Please repost your questions to: discourse.itk.org
>
>
> Thanks,
> Brad
>
> p.s. I?m looking at the writer now to determine how the meta-data
> dictionary is handled.
>
> On 1/2/18, 3:14 AM, "lolo" <lp at 3dside.eu> wrote:
>
>     Hi all,
>
>     Happy new year. It seems I'm the first post of the year. Very glad :-)
>
>     I can't find any possibility to add a field (custom or not) into a nrrd
>     header. The NrrdImageIO doesn't allow it (or I missed it).
>     Is someone know how to do that?
>
>     Thanks,
>     Laurent
>
>
>
>     --
>     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
>     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
>
>
> 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
>
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From konradwerys at gmail.com  Fri Jan  5 06:34:09 2018
From: konradwerys at gmail.com (Konrad Werys)
Date: Fri, 5 Jan 2018 11:34:09 +0000
Subject: [ITK] Color lookup table from dicom metadata
Message-ID: <CAGK3DzUWmCwO8=Tqmo-FY8O4QTeLEC6+aijEaRsC8+3fGY-K4A@mail.gmail.com>

Hi,

I need help in getting the Palette Color Lookup Table Data from dicom using
ITK and preferably GDCM.

I want an array of values of PaletteColorLookupTableData from dicom (tags
0028,1201 0028,1202 0028,1203 for red, green, blue, see
http://dicom.nema.org/medical/dicom/2016a/output/chtml/
part03/sect_C.7.9.html). The fields are OW type and are described by
Palette Color Lookup Table Descriptor (tags 0028,1101 0028,1102 0028,1103
 for red, green, blue) each with 3 pieces of information: how many entries
are in the field/what is the first value mapped/how many bits per entry (
http://dicom.nema.org/medical/dicom/2016a/output/chtml/part03/sect_C.7.6.3.
html#sect_C.7.6.3.1.5).

In dicom files I am working with, Red Palette Color Lookup Table
Descriptor 0028,1101 field equals to 4096/0/16, I can also correctly read
the Red Palette Color Lookup Table Data 0028,1201 in matlab and it has 4096
entries.

I am reading Red Palette Color Lookup Table Data 0028,1201 as in the itk
example https://itk.org/Doxygen/html/Examples_2IO_
2DicomImageReadPrintTags_8cxx-example.html
The length of the result string is 10924. The only explanation of this
length that I can think of is that the dicom field is of OW type (just like
pixel data), and the BitsAllocated 0028,0100 field is 16
and BitsStored 0028,0101 is 12. So 10924*12/16 = 8193 which is close to the
number of bytes I would expect. But when I try to decode the values this
way I am getting completely different numbers than the numbers from matlab.

How can I get a nice array of values from Palette Color Lookup Table Data?

All help will be appreciated.
Kind regards,

-- 
Konrad Werys
http://mrkonrad.github.io <http://mrkonrad.github.io/MRKonrad/>
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From dzenanz at gmail.com  Fri Jan  5 09:56:45 2018
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Fri, 5 Jan 2018 09:56:45 -0500
Subject: [ITK] Color lookup table from dicom metadata
In-Reply-To: <CAGK3DzUWmCwO8=Tqmo-FY8O4QTeLEC6+aijEaRsC8+3fGY-K4A@mail.gmail.com>
References: <CAGK3DzUWmCwO8=Tqmo-FY8O4QTeLEC6+aijEaRsC8+3fGY-K4A@mail.gmail.com>
Message-ID: <CAPf2UMR7aiOmift7uoQFWzrocRWTZe+myQtSJWhaHBVwoQ2qCQ@mail.gmail.com>

Hi Konrad,

the binary values in meta-data dictionary are encoded using base64 scheme.
Once you fetch them from the dictionary, you should decode them. Here
<https://stackoverflow.com/questions/43328520/base64-decoding-in-itk-4-7-for-dicom>
is a similar question.

Regards,
D?enan

On Fri, Jan 5, 2018 at 6:34 AM, Konrad Werys <konradwerys at gmail.com> wrote:

> Hi,
>
> I need help in getting the Palette Color Lookup Table Data from dicom
> using ITK and preferably GDCM.
>
> I want an array of values of PaletteColorLookupTableData from dicom (tags
> 0028,1201 0028,1202 0028,1203 for red, green, blue, see
> http://dicom.nema.org/medical/dicom/2016a/output/
> chtml/part03/sect_C.7.9.html). The fields are OW type and are described
> by Palette Color Lookup Table Descriptor (tags 0028,1101 0028,1102
> 0028,1103  for red, green, blue) each with 3 pieces of information: how
> many entries are in the field/what is the first value mapped/how many bits
> per entry (http://dicom.nema.org/medical/dicom/2016a/output/chtml/
> part03/sect_C.7.6.3.html#sect_C.7.6.3.1.5).
>
> In dicom files I am working with, Red Palette Color Lookup Table
> Descriptor 0028,1101 field equals to 4096/0/16, I can also correctly read
> the Red Palette Color Lookup Table Data 0028,1201 in matlab and it has 4096
> entries.
>
> I am reading Red Palette Color Lookup Table Data 0028,1201 as in the itk
> example https://itk.org/Doxygen/html/Examples_2IO_2DicomImag
> eReadPrintTags_8cxx-example.html
> The length of the result string is 10924. The only explanation of this
> length that I can think of is that the dicom field is of OW type (just like
> pixel data), and the BitsAllocated 0028,0100 field is 16
> and BitsStored 0028,0101 is 12. So 10924*12/16 = 8193 which is close to the
> number of bytes I would expect. But when I try to decode the values this
> way I am getting completely different numbers than the numbers from matlab.
>
> How can I get a nice array of values from Palette Color Lookup Table Data?
>
> All help will be appreciated.
> Kind regards,
>
> --
> Konrad Werys
> http://mrkonrad.github.io <http://mrkonrad.github.io/MRKonrad/>
>
> 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 konradwerys at gmail.com  Sun Jan  7 15:19:47 2018
From: konradwerys at gmail.com (Konrad Werys)
Date: Sun, 7 Jan 2018 20:19:47 +0000
Subject: [ITK] Color lookup table from dicom metadata
In-Reply-To: <CAPf2UMR7aiOmift7uoQFWzrocRWTZe+myQtSJWhaHBVwoQ2qCQ@mail.gmail.com>
References: <CAGK3DzUWmCwO8=Tqmo-FY8O4QTeLEC6+aijEaRsC8+3fGY-K4A@mail.gmail.com>
 <CAPf2UMR7aiOmift7uoQFWzrocRWTZe+myQtSJWhaHBVwoQ2qCQ@mail.gmail.com>
Message-ID: <CAGK3DzWixeJGz3k_63pw1npUw7zQRo0=QQf24AVUpbo4R5_DBw@mail.gmail.com>

Hi D?enan,

This is exactly the information I needed, thank you very much!

Kind regards,
Konrad




On 5 January 2018 at 14:56, D?enan Zuki? <dzenanz at gmail.com> wrote:

> Hi Konrad,
>
> the binary values in meta-data dictionary are encoded using base64 scheme.
> Once you fetch them from the dictionary, you should decode them. Here
> <https://stackoverflow.com/questions/43328520/base64-decoding-in-itk-4-7-for-dicom>
> is a similar question.
>
> Regards,
> D?enan
>
> On Fri, Jan 5, 2018 at 6:34 AM, Konrad Werys <konradwerys at gmail.com>
> wrote:
>
>> Hi,
>>
>> I need help in getting the Palette Color Lookup Table Data from dicom
>> using ITK and preferably GDCM.
>>
>> I want an array of values of PaletteColorLookupTableData from dicom (tags
>> 0028,1201 0028,1202 0028,1203 for red, green, blue, see
>> http://dicom.nema.org/medical/dicom/2016a/output/chtml/
>> part03/sect_C.7.9.html). The fields are OW type and are described by
>> Palette Color Lookup Table Descriptor (tags 0028,1101 0028,1102 0028,1103
>>  for red, green, blue) each with 3 pieces of information: how many entries
>> are in the field/what is the first value mapped/how many bits per entry (
>> http://dicom.nema.org/medical/dicom/2016a/output/chtml/part
>> 03/sect_C.7.6.3.html#sect_C.7.6.3.1.5).
>>
>> In dicom files I am working with, Red Palette Color Lookup Table
>> Descriptor 0028,1101 field equals to 4096/0/16, I can also correctly read
>> the Red Palette Color Lookup Table Data 0028,1201 in matlab and it has 4096
>> entries.
>>
>> I am reading Red Palette Color Lookup Table Data 0028,1201 as in the itk
>> example https://itk.org/Doxygen/html/Examples_2IO_2DicomImag
>> eReadPrintTags_8cxx-example.html
>> The length of the result string is 10924. The only explanation of this
>> length that I can think of is that the dicom field is of OW type (just like
>> pixel data), and the BitsAllocated 0028,0100 field is 16
>> and BitsStored 0028,0101 is 12. So 10924*12/16 = 8193 which is close to the
>> number of bytes I would expect. But when I try to decode the values this
>> way I am getting completely different numbers than the numbers from matlab.
>>
>> How can I get a nice array of values from Palette Color Lookup Table Data?
>>
>> All help will be appreciated.
>> Kind regards,
>>
>> --
>> Konrad Werys
>> http://mrkonrad.github.io <http://mrkonrad.github.io/MRKonrad/>
>>
>> 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
>>
>>
>


-- 
Konrad Werys
http://mrkonrad.github.io <http://mrkonrad.github.io/MRKonrad/>
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From dzenanz at gmail.com  Tue Jan  9 16:21:19 2018
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Tue, 9 Jan 2018 16:21:19 -0500
Subject: [ITK] [ITK-users] Dynamic link library runtime error
In-Reply-To: <CALD_EpLFUUEnAZ9GyQ3JPnNGUEpnG=QaAUdKxJw6m5BjT983Xg@mail.gmail.com>
References: <CALD_EpLFUUEnAZ9GyQ3JPnNGUEpnG=QaAUdKxJw6m5BjT983Xg@mail.gmail.com>
Message-ID: <CAPf2UMQs-MPKYHvSzqm45HQj39+Y+da8=MzKccMd_V9=4=dAvQ@mail.gmail.com>

Hi Fabian,

it most likely means there is a version mismatch between you application
and the DLL. Your application was compiled using a different version from
the one used to compile the DLLs. You can use dependency walker
<http://www.dependencywalker.com/> to see if your application is using the
DLL you expect. You can also try compiling ITK as static libraries, and
link your application to that - thus avoid a possibility of such an error.

Regards,
D?enan

On Tue, Jan 9, 2018 at 2:46 PM, Fabian Torres <fabian.trobles at gmail.com>
wrote:

> Hi all
>
> I'm trying to compile vtk5.10 and ITK 4.4 in visual studio 2013 in order
> to build an application using qt 4.8.7.
> I have already done this using visual studio 2008 and the libraries and my
> application works fine.
>
> The problem I have is that after some strugle I have already compiled the
> libraries (ITK and VTK) in visual studio 2013.
> Now I have compiled my application with the new libraries but when I run
> it I get a Runtime error I do not understand.
>
> The procedure entry point
> ?End at MetaDictionary@itk@@QAE?AV?$_Tree_iterator at V?...
> ....
> ...@@XZ could not be located in the dynamic link library ITKCommon-4.4.dll
>
> What does this mean?
>
> Thanks
>
>
>
> --
> Fabi?n Torres Robles
> Maestr?a en Ciencias en Ingenier?a Electr?nica
> Ingenier?a en Sistemas Electr?nicos
> Tel. 58081280, 0445534661338
> E-mail fabian.trobles at gmail.com, dae.wong at gmail.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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________________________________
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Kitware offers ITK Training Courses, for more information visit:
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From bakkari.abdelkhalek at hotmail.fr  Tue Jan 23 17:06:48 2018
From: bakkari.abdelkhalek at hotmail.fr (Abdelkhalek Bakkari)
Date: Tue, 23 Jan 2018 22:06:48 +0000
Subject: [ITK] [ITK-users] Binary Contour with outliers
Message-ID: <VI1PR0902MB204626FE4AA567C81EF064A983E30@VI1PR0902MB2046.eurprd09.prod.outlook.com>

Hi !

I applied the binary contour filter slice by slice to my binary mask. But the result for the Axial plane is not satisfied at all since it contains some outliers.
Please, find attached my binary contour result.
Is there any method to remove the outliers from the contour ?

Thank you in advance.
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________________________________
Powered by www.kitware.com

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

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From matt.mccormick at kitware.com  Tue Jan 23 17:18:44 2018
From: matt.mccormick at kitware.com (Matt McCormick)
Date: Tue, 23 Jan 2018 17:18:44 -0500
Subject: [ITK] [ITK-users] Binary Contour with outliers
In-Reply-To: <VI1PR0902MB204626FE4AA567C81EF064A983E30@VI1PR0902MB2046.eurprd09.prod.outlook.com>
References: <VI1PR0902MB204626FE4AA567C81EF064A983E30@VI1PR0902MB2046.eurprd09.prod.outlook.com>
Message-ID: <CALzTN-S+bVME+129y8UOxj8RwhW8fePB9aV+WTLBsTepc+bfjg@mail.gmail.com>

Hi,

By running OpeningByReconstructionImageFilter:

  https://itk.org/Doxygen/html/classitk_1_1OpeningByReconstructionImageFilter.html

before the binary contour, the smaller objects can be removed.

HTH,
Matt

On Tue, Jan 23, 2018 at 5:06 PM, Abdelkhalek Bakkari
<bakkari.abdelkhalek at hotmail.fr> wrote:
> Hi !
>
> I applied the binary contour filter slice by slice to my binary mask. But
> the result for the Axial plane is not satisfied at all since it contains
> some outliers.
> Please, find attached my binary contour result.
> Is there any method to remove the outliers from the contour ?
>
> Thank you in advance.
>
> 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:
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From Jared.Becksfort at STJUDE.ORG  Thu Jan 25 18:56:15 2018
From: Jared.Becksfort at STJUDE.ORG (Becksfort, Jared)
Date: Thu, 25 Jan 2018 23:56:15 +0000
Subject: [ITK] [ITK-users] Binary Contour with outliers
In-Reply-To: <CALzTN-S+bVME+129y8UOxj8RwhW8fePB9aV+WTLBsTepc+bfjg@mail.gmail.com>
References: <VI1PR0902MB204626FE4AA567C81EF064A983E30@VI1PR0902MB2046.eurprd09.prod.outlook.com>
 <CALzTN-S+bVME+129y8UOxj8RwhW8fePB9aV+WTLBsTepc+bfjg@mail.gmail.com>
Message-ID: <DB342095-7F03-4667-BBE2-F04EF9E940EB@stjude.org>

Hello,

I am having some difficulty overlaying boolean masks onto Nifti images. The code below is basically what is shown here (which does work for me when I use the images on the page):. https://itk.org/ITKExamples/src/Filtering/ImageFusion/OverlayLabelMapOnTopOfAnImage/Documentation.html

The differences that I can see are that I am using 3 dimensions and Nifti float input rather than 2D images of the same pixel and file types (8-bit PNG) in the example.

Can someone please tell me what I have done wrong?  The output image is garbled beyond recognition.

Thanks,
Jared

const unsigned int Dimension = 3;

typedef float PixelType;
typedef unsigned char LabelType;

typedef itk::Image< PixelType, Dimension > ImageVolumeType;
typedef itk::Image< LabelType, Dimension > ContourVolumeType;

typedef itk::ImageFileReader<ContourVolumeType> ContourReaderType;
typedef itk::ImageFileReader< ImageVolumeType >  ReaderType;

ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName( infile1 );

ContourReaderType::Pointer labelReader = ContourReaderType::New();
labelReader->SetFileName(infile2);

typedef itk::LabelObject< LabelType, Dimension > LabelObjectType;
typedef itk::LabelMap< LabelObjectType > LabelMapType;

typedef itk::LabelImageToLabelMapFilter< ContourVolumeType, LabelMapType > ConverterType;
ConverterType::Pointer converter = ConverterType::New();
converter->SetInput( labelReader->GetOutput() );

typedef itk::LabelMapOverlayImageFilter< LabelMapType, ImageVolumeType > FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetInput( converter->GetOutput() );
filter->SetFeatureImage( reader->GetOutput() );
filter->SetOpacity(0.5);


typedef itk::ImageFileWriter< FilterType::OutputImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName(outfile);
writer->SetInput( filter->GetOutput() );
writer->Update();

On 1/23/18, 4:19 PM, "Insight-users on behalf of Matt McCormick" <insight-users-bounces at itk.org on behalf of matt.mccormick at kitware.com> wrote:

    Hi,

    By running OpeningByReconstructionImageFilter:

      https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fitk.org%2FDoxygen%2Fhtml%2Fclassitk_1_1OpeningByReconstructionImageFilter.html&data=01%7C01%7Cjared.becksfort%40stjude.org%7Ce86b42bd4f52460a362708d562af538f%7C22340fa892264871b677d3b3e377af72%7C0&sdata=qbR%2BtUIsnrSfh01yNV9w94GGa%2FdEA7uXrisa%2BpVyJ0k%3D&reserved=0

    before the binary contour, the smaller objects can be removed.

    HTH,
    Matt

    On Tue, Jan 23, 2018 at 5:06 PM, Abdelkhalek Bakkari
    <bakkari.abdelkhalek at hotmail.fr> wrote:
    > Hi !
    >
    > I applied the binary contour filter slice by slice to my binary mask. But
    > the result for the Axial plane is not satisfied at all since it contains
    > some outliers.
    > Please, find attached my binary contour result.
    > Is there any method to remove the outliers from the contour ?
    >
    > Thank you in advance.
    >
    > The ITK community is transitioning from this mailing list to
    > discourse.itk.org. Please join us there!
    > ________________________________
    > Powered by https://na01.safelinks.protection.outlook.com/?url=www.kitware.com&data=01%7C01%7Cjared.becksfort%40stjude.org%7Ce86b42bd4f52460a362708d562af538f%7C22340fa892264871b677d3b3e377af72%7C0&sdata=wGgpmJ1V9kHLAeehfcg2TDwAl2%2B146KjXnNcJwxCUUE%3D&reserved=0
    >
    > Visit other Kitware open-source projects at
    > https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.kitware.com%2Fopensource%2Fopensource.html&data=01%7C01%7Cjared.becksfort%40stjude.org%7Ce86b42bd4f52460a362708d562af538f%7C22340fa892264871b677d3b3e377af72%7C0&sdata=NV76hUF0Y4voqN%2BMyiz9V5VES8ByVlx6u8soSOw%2FUG0%3D&reserved=0
    >
    > Kitware offers ITK Training Courses, for more information visit:
    > https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.kitware.com%2Fproducts%2Fprotraining.php&data=01%7C01%7Cjared.becksfort%40stjude.org%7Ce86b42bd4f52460a362708d562af538f%7C22340fa892264871b677d3b3e377af72%7C0&sdata=3ZE7IOXhdYDA7yn8FEmJBbbqsRS22LsDgcLGsCOpMXI%3D&reserved=0
    >
    > Please keep messages on-topic and check the ITK FAQ at:
    > https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.itk.org%2FWiki%2FITK_FAQ&data=01%7C01%7Cjared.becksfort%40stjude.org%7Ce86b42bd4f52460a362708d562af538f%7C22340fa892264871b677d3b3e377af72%7C0&sdata=zmDoewconF3K2V%2FHEljYWpZjjkqEM3zMgZomfc5XR6A%3D&reserved=0
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    >
    The ITK community is transitioning from this mailing list to discourse.itk.org. Please join us there!
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From Jared.Becksfort at STJUDE.ORG  Thu Jan 25 18:57:04 2018
From: Jared.Becksfort at STJUDE.ORG (Becksfort, Jared)
Date: Thu, 25 Jan 2018 23:57:04 +0000
Subject: [ITK] [ITK-users] Overlay Woes
Message-ID: <F3BC7CCC-FFCC-40E0-91F0-62ED15A5EB9A@stjude.org>

 Hello,
   Sorry to send this again, but it had the wrong subject.

    I am having some difficulty overlaying boolean masks onto Nifti images. The code below is basically what is shown here (which does work for me when I use the images on the page):. https://itk.org/ITKExamples/src/Filtering/ImageFusion/OverlayLabelMapOnTopOfAnImage/Documentation.html

    The differences that I can see are that I am using 3 dimensions and Nifti float input rather than 2D images of the same pixel and file types (8-bit PNG) in the example.

    Can someone please tell me what I have done wrong?  The output image is garbled beyond recognition.

    Thanks,
    Jared

    const unsigned int Dimension = 3;

    typedef float PixelType;
    typedef unsigned char LabelType;

    typedef itk::Image< PixelType, Dimension > ImageVolumeType;
    typedef itk::Image< LabelType, Dimension > ContourVolumeType;

    typedef itk::ImageFileReader<ContourVolumeType> ContourReaderType;
    typedef itk::ImageFileReader< ImageVolumeType >  ReaderType;

    ReaderType::Pointer reader = ReaderType::New();
    reader->SetFileName( infile1 );

    ContourReaderType::Pointer labelReader = ContourReaderType::New();
    labelReader->SetFileName(infile2);

    typedef itk::LabelObject< LabelType, Dimension > LabelObjectType;
    typedef itk::LabelMap< LabelObjectType > LabelMapType;

    typedef itk::LabelImageToLabelMapFilter< ContourVolumeType, LabelMapType > ConverterType;
    ConverterType::Pointer converter = ConverterType::New();
    converter->SetInput( labelReader->GetOutput() );

    typedef itk::LabelMapOverlayImageFilter< LabelMapType, ImageVolumeType > FilterType;
    FilterType::Pointer filter = FilterType::New();
    filter->SetInput( converter->GetOutput() );
    filter->SetFeatureImage( reader->GetOutput() );
    filter->SetOpacity(0.5);


    typedef itk::ImageFileWriter< FilterType::OutputImageType > WriterType;
    WriterType::Pointer writer = WriterType::New();
    writer->SetFileName(outfile);
    writer->SetInput( filter->GetOutput() );
    writer->Update();




________________________________

Email Disclaimer: www.stjude.org/emaildisclaimer
Consultation Disclaimer: www.stjude.org/consultationdisclaimer
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
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From jhlegarreta at vicomtech.org  Fri Jan 26 03:04:09 2018
From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta)
Date: Fri, 26 Jan 2018 09:04:09 +0100
Subject: [ITK] [ITK-users] Binary Contour with outliers
In-Reply-To: <DB342095-7F03-4667-BBE2-F04EF9E940EB@stjude.org>
References: <VI1PR0902MB204626FE4AA567C81EF064A983E30@VI1PR0902MB2046.eurprd09.prod.outlook.com>
 <CALzTN-S+bVME+129y8UOxj8RwhW8fePB9aV+WTLBsTepc+bfjg@mail.gmail.com>
 <DB342095-7F03-4667-BBE2-F04EF9E940EB@stjude.org>
Message-ID: <CAAKhGh9CM7w2u0MJ6GJAYwJDnd1qmn+_3ZbwfZ1=1sZGt0BjdQ@mail.gmail.com>

Dear Jared,
thanks for your question !

Your question seems to drift apart from the one that started this
thread or the subject of this thread.

In order to increase the chances of it getting answered, could please
post your question on a different thread?

Please, read our community discussion guidelines, especially the "Keep
tidy" section:
https://discourse.itk.org/guidelines

Also, providing a minimal, compilable code snippet (either through a
GitHub gist) or by attaching your own files reproducing the issue
(.cxx files, CMakeLists.txt, your own input data, etc.) would help.

Note that we are transitioning from this mailing list to discourse:
https://discourse.itk.org

So we'd be grateful if you could post your question there taking into
account the above.

Cheers,
JON HAITZ

--



On 26 January 2018 at 00:56, Becksfort, Jared
<Jared.Becksfort at stjude.org> wrote:
> Hello,
>
> I am having some difficulty overlaying boolean masks onto Nifti images. The code below is basically what is shown here (which does work for me when I use the images on the page):. https://itk.org/ITKExamples/src/Filtering/ImageFusion/OverlayLabelMapOnTopOfAnImage/Documentation.html
>
> The differences that I can see are that I am using 3 dimensions and Nifti float input rather than 2D images of the same pixel and file types (8-bit PNG) in the example.
>
> Can someone please tell me what I have done wrong?  The output image is garbled beyond recognition.
>
> Thanks,
> Jared
>
> const unsigned int Dimension = 3;
>
> typedef float PixelType;
> typedef unsigned char LabelType;
>
> typedef itk::Image< PixelType, Dimension > ImageVolumeType;
> typedef itk::Image< LabelType, Dimension > ContourVolumeType;
>
> typedef itk::ImageFileReader<ContourVolumeType> ContourReaderType;
> typedef itk::ImageFileReader< ImageVolumeType >  ReaderType;
>
> ReaderType::Pointer reader = ReaderType::New();
> reader->SetFileName( infile1 );
>
> ContourReaderType::Pointer labelReader = ContourReaderType::New();
> labelReader->SetFileName(infile2);
>
> typedef itk::LabelObject< LabelType, Dimension > LabelObjectType;
> typedef itk::LabelMap< LabelObjectType > LabelMapType;
>
> typedef itk::LabelImageToLabelMapFilter< ContourVolumeType, LabelMapType > ConverterType;
> ConverterType::Pointer converter = ConverterType::New();
> converter->SetInput( labelReader->GetOutput() );
>
> typedef itk::LabelMapOverlayImageFilter< LabelMapType, ImageVolumeType > FilterType;
> FilterType::Pointer filter = FilterType::New();
> filter->SetInput( converter->GetOutput() );
> filter->SetFeatureImage( reader->GetOutput() );
> filter->SetOpacity(0.5);
>
>
> typedef itk::ImageFileWriter< FilterType::OutputImageType > WriterType;
> WriterType::Pointer writer = WriterType::New();
> writer->SetFileName(outfile);
> writer->SetInput( filter->GetOutput() );
> writer->Update();
>
> On 1/23/18, 4:19 PM, "Insight-users on behalf of Matt McCormick" <insight-users-bounces at itk.org on behalf of matt.mccormick at kitware.com> wrote:
>
>     Hi,
>
>     By running OpeningByReconstructionImageFilter:
>
>       https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fitk.org%2FDoxygen%2Fhtml%2Fclassitk_1_1OpeningByReconstructionImageFilter.html&data=01%7C01%7Cjared.becksfort%40stjude.org%7Ce86b42bd4f52460a362708d562af538f%7C22340fa892264871b677d3b3e377af72%7C0&sdata=qbR%2BtUIsnrSfh01yNV9w94GGa%2FdEA7uXrisa%2BpVyJ0k%3D&reserved=0
>
>     before the binary contour, the smaller objects can be removed.
>
>     HTH,
>     Matt
>
>     On Tue, Jan 23, 2018 at 5:06 PM, Abdelkhalek Bakkari
>     <bakkari.abdelkhalek at hotmail.fr> wrote:
>     > Hi !
>     >
>     > I applied the binary contour filter slice by slice to my binary mask. But
>     > the result for the Axial plane is not satisfied at all since it contains
>     > some outliers.
>     > Please, find attached my binary contour result.
>     > Is there any method to remove the outliers from the contour ?
>     >
>     > Thank you in advance.
>     >
>     > The ITK community is transitioning from this mailing list to
>     > discourse.itk.org. Please join us there!
>     > ________________________________
>     > Powered by https://na01.safelinks.protection.outlook.com/?url=www.kitware.com&data=01%7C01%7Cjared.becksfort%40stjude.org%7Ce86b42bd4f52460a362708d562af538f%7C22340fa892264871b677d3b3e377af72%7C0&sdata=wGgpmJ1V9kHLAeehfcg2TDwAl2%2B146KjXnNcJwxCUUE%3D&reserved=0
>     >
>     > Visit other Kitware open-source projects at
>     > https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.kitware.com%2Fopensource%2Fopensource.html&data=01%7C01%7Cjared.becksfort%40stjude.org%7Ce86b42bd4f52460a362708d562af538f%7C22340fa892264871b677d3b3e377af72%7C0&sdata=NV76hUF0Y4voqN%2BMyiz9V5VES8ByVlx6u8soSOw%2FUG0%3D&reserved=0
>     >
>     > 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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>     > Follow this link to subscribe/unsubscribe:
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>     >
>     The ITK community is transitioning from this mailing list to discourse.itk.org. Please join us there!
>     ________________________________
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>
>
>
> ________________________________
>
> Email Disclaimer: www.stjude.org/emaildisclaimer
> Consultation Disclaimer: www.stjude.org/consultationdisclaimer
> 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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The ITK community is transitioning from this mailing list to discourse.itk.org. Please join us there!
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From norbert.lang at live.de  Fri Jan 26 08:03:32 2018
From: norbert.lang at live.de (Norbert Martin Lang)
Date: Fri, 26 Jan 2018 13:03:32 +0000
Subject: [ITK] Build Error MITK 2016.11: ITK targets not defined
Message-ID: <VI1PR04MB140687389501123FDF0CD6469BE00@VI1PR04MB1406.eurprd04.prod.outlook.com>

Hello,

I already posted this on the MITK mailing list but still got no answer.
So I will try it here.

I tried to build MITK (v2016.11) from source with external VTK (v8.1.0)
and external ITK (v4.13.0) on Windows 10 with MVSC 15 2017 Win64. ITK,
VTK and Qt is built with the same compiler (and so on) and works fine
running standalone.

Additionaly i added the paths to the .dll's to the Windows system path
before.

So, the MITK build went fine (except for a few warnings) until it
searches for ITK (i suppose it doesnt reached VTK settings); it shows
following error:


>  CMake Error at
C:/VisLibs/ITK4/InsightToolkit-4.13.0-build/ITKTargets.cmake:37 (message):
>  Some (but not all) targets in this export set were already defined.
>  Targets Defined:
> gdcmCommon; gdcmDICT; gdcmDSED; gdcmIOD; gdcmMEXD; gdcmMSFF;
gdcmcharls; gdcmjpeg12; gdcmjpeg16; gdcmjpeg8; hdf5-static; hdf5_cpp-static
>
>  Targets not yet defined:
>  itkdouble-conversion; itksys; itkvcl; itkv3p_netlib; itktestlib;
itkvnl; itkvnl_algo; itknetlib; ITKVNLInstantiation; ITKCommon;
itkNetlibSlatec; ITKStatistics; ITKTransform; ITKLabelMap; ITKMesh;
itkzlib; ITKMetaIO; ITKSpatialObjects; ITKPath; ITKQuadEdgeMesh;
ITKIOImageBase; ITKOptimizers; ITKPolynomials; ITKBiasCorrection;
ITKBioCell; ITKDICOMParser; ITKEXPAT; ITKIOXML; ITKIOSpatialObjects;
ITKFEM; itkgdcmopenjp2; gdcmsocketxx; ITKznz; ITKniftiio; ITKgiftiio;
GTest::GTest; GTest::Main; ITKIOBMP; ITKIOBioRad; ITKIOBruker; ITKIOCSV;
ITKIOGDCM; ITKIOIPL; ITKIOGE; ITKIOGIPL; ITKIOHDF5; itkjpeg; ITKIOJPEG;
itktiff; ITKIOTIFF; ITKIOLSM; itkminc2 //[... and so on]
>
>Call Stack (most recent call first):
>  C:/VisLibs/ITK4/InsightToolkit-4.13.0-build/ITKConfig.cmake:64 (include)
>  CMakeLists.txt:758 (find_package)
>
>
>-- Configuring incomplete, errors occurred!
>See also
"C:/VisLibs/MITK2016/MITK-build/MITK-build/CMakeFiles/CMakeOutput.log".
>C:\Program Files (x86)\Microsoft Visual
Studio\2017\Community\Common7\IDE\VC\VCTargets\Microsoft.CppCommon.targets(171,5):
error MSB6006: "cmd.exe" exited with code 1.
>Done building project "MITK-Configure.vcxproj" -- FAILED.

So, somehow it cannot include all the ITK libraries. Path to
ITKConfig.cmake is well set as i see. Any ideas how to solve this? Is
this a problem related to the CMake files of MITK or should i apply some
additional configuration to the ITK build?

Thanks
Norbert

From Jared.Becksfort at STJUDE.ORG  Fri Jan 26 11:56:37 2018
From: Jared.Becksfort at STJUDE.ORG (Becksfort, Jared)
Date: Fri, 26 Jan 2018 16:56:37 +0000
Subject: [ITK] [ITK-users] Binary Contour with outliers
In-Reply-To: <CAAKhGh9CM7w2u0MJ6GJAYwJDnd1qmn+_3ZbwfZ1=1sZGt0BjdQ@mail.gmail.com>
References: <VI1PR0902MB204626FE4AA567C81EF064A983E30@VI1PR0902MB2046.eurprd09.prod.outlook.com>
 <CALzTN-S+bVME+129y8UOxj8RwhW8fePB9aV+WTLBsTepc+bfjg@mail.gmail.com>
 <DB342095-7F03-4667-BBE2-F04EF9E940EB@stjude.org>,
 <CAAKhGh9CM7w2u0MJ6GJAYwJDnd1qmn+_3ZbwfZ1=1sZGt0BjdQ@mail.gmail.com>
Message-ID: <MWHPR04MB11698FC2B51C7D6BE2B70AD792E00@MWHPR04MB1169.namprd04.prod.outlook.com>

Yes, sorry.  I sent another email with the proper format shortly thereafter.  Sorry for the noise.


Jared

________________________________
From: Jon Haitz Legarreta <jhlegarreta at vicomtech.org>
Sent: Friday, January 26, 2018 2:04:09 AM
To: Becksfort, Jared
Cc: ITK Users
Subject: Re: [ITK-users] Binary Contour with outliers

Dear Jared,
thanks for your question !

Your question seems to drift apart from the one that started this
thread or the subject of this thread.

In order to increase the chances of it getting answered, could please
post your question on a different thread?

Please, read our community discussion guidelines, especially the "Keep
tidy" section:
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdiscourse.itk.org%2Fguidelines&data=01%7C01%7CJared.Becksfort%40stjude.org%7C2070d2bf4b7944b95bb308d564937a1b%7C22340fa892264871b677d3b3e377af72%7C0&sdata=xPacI3N%2B2bxM6VjGt5o%2Be7JQjrd7fAtQS12nDxDmdWk%3D&reserved=0

Also, providing a minimal, compilable code snippet (either through a
GitHub gist) or by attaching your own files reproducing the issue
(.cxx files, CMakeLists.txt, your own input data, etc.) would help.

Note that we are transitioning from this mailing list to discourse:
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdiscourse.itk.org&data=01%7C01%7CJared.Becksfort%40stjude.org%7C2070d2bf4b7944b95bb308d564937a1b%7C22340fa892264871b677d3b3e377af72%7C0&sdata=Ml2KzsOGytZ5ylV9khEWD0rs3QA89TRY2W8IWdCO8tw%3D&reserved=0

So we'd be grateful if you could post your question there taking into
account the above.

Cheers,
JON HAITZ

--



On 26 January 2018 at 00:56, Becksfort, Jared
<Jared.Becksfort at stjude.org> wrote:
> Hello,
>
> I am having some difficulty overlaying boolean masks onto Nifti images. The code below is basically what is shown here (which does work for me when I use the images on the page):. https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fitk.org%2FITKExamples%2Fsrc%2FFiltering%2FImageFusion%2FOverlayLabelMapOnTopOfAnImage%2FDocumentation.html&data=01%7C01%7CJared.Becksfort%40stjude.org%7C2070d2bf4b7944b95bb308d564937a1b%7C22340fa892264871b677d3b3e377af72%7C0&sdata=j7IB4JaPUdTP%2BnMM4ez7Hb4aiuOQ%2Fk41WI2RCh%2FvQJA%3D&reserved=0
>
> The differences that I can see are that I am using 3 dimensions and Nifti float input rather than 2D images of the same pixel and file types (8-bit PNG) in the example.
>
> Can someone please tell me what I have done wrong?  The output image is garbled beyond recognition.
>
> Thanks,
> Jared
>
> const unsigned int Dimension = 3;
>
> typedef float PixelType;
> typedef unsigned char LabelType;
>
> typedef itk::Image< PixelType, Dimension > ImageVolumeType;
> typedef itk::Image< LabelType, Dimension > ContourVolumeType;
>
> typedef itk::ImageFileReader<ContourVolumeType> ContourReaderType;
> typedef itk::ImageFileReader< ImageVolumeType >  ReaderType;
>
> ReaderType::Pointer reader = ReaderType::New();
> reader->SetFileName( infile1 );
>
> ContourReaderType::Pointer labelReader = ContourReaderType::New();
> labelReader->SetFileName(infile2);
>
> typedef itk::LabelObject< LabelType, Dimension > LabelObjectType;
> typedef itk::LabelMap< LabelObjectType > LabelMapType;
>
> typedef itk::LabelImageToLabelMapFilter< ContourVolumeType, LabelMapType > ConverterType;
> ConverterType::Pointer converter = ConverterType::New();
> converter->SetInput( labelReader->GetOutput() );
>
> typedef itk::LabelMapOverlayImageFilter< LabelMapType, ImageVolumeType > FilterType;
> FilterType::Pointer filter = FilterType::New();
> filter->SetInput( converter->GetOutput() );
> filter->SetFeatureImage( reader->GetOutput() );
> filter->SetOpacity(0.5);
>
>
> typedef itk::ImageFileWriter< FilterType::OutputImageType > WriterType;
> WriterType::Pointer writer = WriterType::New();
> writer->SetFileName(outfile);
> writer->SetInput( filter->GetOutput() );
> writer->Update();
>
> On 1/23/18, 4:19 PM, "Insight-users on behalf of Matt McCormick" <insight-users-bounces at itk.org on behalf of matt.mccormick at kitware.com> wrote:
>
>     Hi,
>
>     By running OpeningByReconstructionImageFilter:
>
>       https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fitk.org%2FDoxygen%2Fhtml%2Fclassitk_1_1OpeningByReconstructionImageFilter.html&data=01%7C01%7Cjared.becksfort%40stjude.org%7Ce86b42bd4f52460a362708d562af538f%7C22340fa892264871b677d3b3e377af72%7C0&sdata=qbR%2BtUIsnrSfh01yNV9w94GGa%2FdEA7uXrisa%2BpVyJ0k%3D&reserved=0
>
>     before the binary contour, the smaller objects can be removed.
>
>     HTH,
>     Matt
>
>     On Tue, Jan 23, 2018 at 5:06 PM, Abdelkhalek Bakkari
>     <bakkari.abdelkhalek at hotmail.fr> wrote:
>     > Hi !
>     >
>     > I applied the binary contour filter slice by slice to my binary mask. But
>     > the result for the Axial plane is not satisfied at all since it contains
>     > some outliers.
>     > Please, find attached my binary contour result.
>     > Is there any method to remove the outliers from the contour ?
>     >
>     > Thank you in advance.
>     >
>     > The ITK community is transitioning from this mailing list to
>     > discourse.itk.org. Please join us there!
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>     > Please keep messages on-topic and check the ITK FAQ 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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>
>     Follow this link to subscribe/unsubscribe:
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>
>
>
> ________________________________
>
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>
> Please keep messages on-topic and check the ITK FAQ at:
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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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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  Fri Jan 26 13:26:32 2018
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Fri, 26 Jan 2018 13:26:32 -0500
Subject: [ITK] Build Error MITK 2016.11: ITK targets not defined
In-Reply-To: <VI1PR04MB140687389501123FDF0CD6469BE00@VI1PR04MB1406.eurprd04.prod.outlook.com>
References: <VI1PR04MB140687389501123FDF0CD6469BE00@VI1PR04MB1406.eurprd04.prod.outlook.com>
Message-ID: <CAPf2UMQywPBabBRiUjx+q+2o0LPByxg=W=V0mjFE6NZeE82jtw@mail.gmail.com>

Hi Norbert,

it is more likely to be due to MITK configuration. We have switched to
Discourse <https://discourse.itk.org/> forum. Reposting the question there
might yield more answers.

Regards,
D?enan

On Fri, Jan 26, 2018 at 8:03 AM, Norbert Martin Lang <norbert.lang at live.de>
wrote:

> Hello,
>
> I already posted this on the MITK mailing list but still got no answer.
> So I will try it here.
>
> I tried to build MITK (v2016.11) from source with external VTK (v8.1.0)
> and external ITK (v4.13.0) on Windows 10 with MVSC 15 2017 Win64. ITK,
> VTK and Qt is built with the same compiler (and so on) and works fine
> running standalone.
>
> Additionaly i added the paths to the .dll's to the Windows system path
> before.
>
> So, the MITK build went fine (except for a few warnings) until it
> searches for ITK (i suppose it doesnt reached VTK settings); it shows
> following error:
>
>
> >  CMake Error at
> C:/VisLibs/ITK4/InsightToolkit-4.13.0-build/ITKTargets.cmake:37 (message):
> >  Some (but not all) targets in this export set were already defined.
> >  Targets Defined:
> > gdcmCommon; gdcmDICT; gdcmDSED; gdcmIOD; gdcmMEXD; gdcmMSFF;
> gdcmcharls; gdcmjpeg12; gdcmjpeg16; gdcmjpeg8; hdf5-static; hdf5_cpp-static
> >
> >  Targets not yet defined:
> >  itkdouble-conversion; itksys; itkvcl; itkv3p_netlib; itktestlib;
> itkvnl; itkvnl_algo; itknetlib; ITKVNLInstantiation; ITKCommon;
> itkNetlibSlatec; ITKStatistics; ITKTransform; ITKLabelMap; ITKMesh;
> itkzlib; ITKMetaIO; ITKSpatialObjects; ITKPath; ITKQuadEdgeMesh;
> ITKIOImageBase; ITKOptimizers; ITKPolynomials; ITKBiasCorrection;
> ITKBioCell; ITKDICOMParser; ITKEXPAT; ITKIOXML; ITKIOSpatialObjects;
> ITKFEM; itkgdcmopenjp2; gdcmsocketxx; ITKznz; ITKniftiio; ITKgiftiio;
> GTest::GTest; GTest::Main; ITKIOBMP; ITKIOBioRad; ITKIOBruker; ITKIOCSV;
> ITKIOGDCM; ITKIOIPL; ITKIOGE; ITKIOGIPL; ITKIOHDF5; itkjpeg; ITKIOJPEG;
> itktiff; ITKIOTIFF; ITKIOLSM; itkminc2 //[... and so on]
> >
> >Call Stack (most recent call first):
> >  C:/VisLibs/ITK4/InsightToolkit-4.13.0-build/ITKConfig.cmake:64
> (include)
> >  CMakeLists.txt:758 (find_package)
> >
> >
> >-- Configuring incomplete, errors occurred!
> >See also
> "C:/VisLibs/MITK2016/MITK-build/MITK-build/CMakeFiles/CMakeOutput.log".
> >C:\Program Files (x86)\Microsoft Visual
> Studio\2017\Community\Common7\IDE\VC\VCTargets\Microsoft.
> CppCommon.targets(171,5):
> error MSB6006: "cmd.exe" exited with code 1.
> >Done building project "MITK-Configure.vcxproj" -- FAILED.
>
> So, somehow it cannot include all the ITK libraries. Path to
> ITKConfig.cmake is well set as i see. Any ideas how to solve this? Is
> this a problem related to the CMake files of MITK or should i apply some
> additional configuration to the ITK build?
>
> Thanks
> Norbert
> 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 gregthom992 at gmail.com  Wed Jan 31 12:08:24 2018
From: gregthom992 at gmail.com (G Tom)
Date: Wed, 31 Jan 2018 12:08:24 -0500
Subject: [ITK] [ITK-users] Extract Line/Intensity profile from image given
 start and stop points
Message-ID: <CAFh_-OOCZY4FRfRH-51K2OiZAa69+CduOOyrifTh0SLhw+8h6w@mail.gmail.com>

HI all

I am not sure if this is alread done before but I have 2D and 3D images and
I would like to extract a line/intensity profile through the image given a
start and and end point. The line need not be oriented parallel to any of
the major axis. Any ideas ?

I see the LineSpatialObject can define a line but how do I extract the line
from an image. Oh and one more thing, suppose I want to vary the radius of
the line , how can that be achieved.

Please let me now approaches and I will try them out.

Thanks
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From dzenanz at gmail.com  Wed Jan 31 12:38:14 2018
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 31 Jan 2018 12:38:14 -0500
Subject: [ITK] [ITK-users] Extract Line/Intensity profile from image
 given start and stop points
In-Reply-To: <CAFh_-OOCZY4FRfRH-51K2OiZAa69+CduOOyrifTh0SLhw+8h6w@mail.gmail.com>
References: <CAFh_-OOCZY4FRfRH-51K2OiZAa69+CduOOyrifTh0SLhw+8h6w@mail.gmail.com>
Message-ID: <CAPf2UMQ4DQhKm896u6amKA5vCJ_0c4mhB=9DbvXzOvYZ_M9h=w@mail.gmail.com>

Hi Tom,

does this <https://itk.org/Wiki/ITK/Examples/SimpleOperations/BresenhamLine>
example do what you want?

Regards,
D?enan

On Wed, Jan 31, 2018 at 12:08 PM, G Tom <gregthom992 at gmail.com> wrote:

> HI all
>
> I am not sure if this is alread done before but I have 2D and 3D images
> and I would like to extract a line/intensity profile through the image
> given a start and and end point. The line need not be oriented parallel to
> any of the major axis. Any ideas ?
>
> I see the LineSpatialObject can define a line but how do I extract the
> line from an image. Oh and one more thing, suppose I want to vary the
> radius of the line , how can that be achieved.
>
> Please let me now approaches and I will try them out.
>
> 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 gregthom992 at gmail.com  Wed Jan 31 16:23:52 2018
From: gregthom992 at gmail.com (gregthom992)
Date: Wed, 31 Jan 2018 14:23:52 -0700 (MST)
Subject: [ITK] [ITK-users] Extract Line/Intensity profile from image
 given start and stop points
In-Reply-To: <CAPf2UMQ4DQhKm896u6amKA5vCJ_0c4mhB=9DbvXzOvYZ_M9h=w@mail.gmail.com>
References: <CAFh_-OOCZY4FRfRH-51K2OiZAa69+CduOOyrifTh0SLhw+8h6w@mail.gmail.com>
 <CAPf2UMQ4DQhKm896u6amKA5vCJ_0c4mhB=9DbvXzOvYZ_M9h=w@mail.gmail.com>
Message-ID: <1517433832235-0.post@n7.nabble.com>

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



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From dzenanz at gmail.com  Wed Jan 31 18:01:41 2018
From: dzenanz at gmail.com (=?UTF-8?B?RMW+ZW5hbiBadWtpxIc=?=)
Date: Wed, 31 Jan 2018 18:01:41 -0500
Subject: [ITK] [ITK-users] Extract Line/Intensity profile from image
 given start and stop points
In-Reply-To: <1517433832235-0.post@n7.nabble.com>
References: <CAFh_-OOCZY4FRfRH-51K2OiZAa69+CduOOyrifTh0SLhw+8h6w@mail.gmail.com>
 <CAPf2UMQ4DQhKm896u6amKA5vCJ_0c4mhB=9DbvXzOvYZ_M9h=w@mail.gmail.com>
 <1517433832235-0.post@n7.nabble.com>
Message-ID: <CAPf2UMRLQWgZfV8k1N7Jmxb_ROmNphiz4Ugt-zcrNdfj40NmZg@mail.gmail.com>

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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