automatic segmentation from T2 WIs

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automatic segmentation from T2 WIs

Tatjana Polgar
Hi Slicers,
I have 3D T2 CUBE and T2 FLAIR CUBE WI that I'd like to segment into GM, WM, CSF and skull without T1WI.
IS ARCTIC capable to segment such sequences? So far, I was only able to use ARCTIC and atlas-based EM segmenter for T1 segmentation.
Is there any other module than ARCTIC to be used for segmentation and volumetry in this situation?

I use unix ubuntu, 3D Slicer3.6.3.
Thanks for your advise on this matter!
Tatjana

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Re: automatic segmentation from T2 WIs

Kilian Pohl
You can parameterize  EMSegmenter so that it will segment your T2 and Flair scan.

look at the information at http://www.slicer.org/slicerWiki/index.php/Modules:EMSegmenter-3.6

and

http://www.slicer.org/slicerWiki/index.php/EMSegmenter-Tasks

The MRI-Human-Brain Atlas comes with a T2 image which you can use for this task

Kilian


On 1/23/2013 4:59 PM, Tatjana Polgar wrote:
Hi Slicers,
I have 3D T2 CUBE and T2 FLAIR CUBE WI that I'd like to segment into GM, WM, CSF and skull without T1WI.
IS ARCTIC capable to segment such sequences? So far, I was only able to use ARCTIC and atlas-based EM segmenter for T1 segmentation.
Is there any other module than ARCTIC to be used for segmentation and volumetry in this situation?

I use unix ubuntu, 3D Slicer3.6.3.
Thanks for your advise on this matter!
Tatjana


_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject


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[hidden email]
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AtlasCreator_Error message

Tatjana Polgar
Hi Slicers,
We were wondering if Hans Johnson or anyone else can help us with the below listed problem (see error message) in AtlasCreator.
Thanks in advance
Tatjana

 
 
Hi Kilian, Hi Tatjana,

the error comes from BRAINSFit - I think Hans Johnson might know.

AtlasCreator just calls BRAINSFit at this step. Frankly, I am not sure how this happens:

  what():  /extra/pieper/slicer3/nightly/Slicer3-lib/Insight/Code/IO/itkImageFileReader.txx:146:
 Could not create IO object for file /home/szatmary/Documents/nrrd/RESEARCH/Output/registered/iteration2/acTmpMeanImageZSn_xS.nrrd
  Tried to create one of the following:
    MGHImageIO
    MRMLIDImageIO
    Brains2MaskImageIO
    BioRadImageIO
    GDCMImageIO
    MetaImageIO
    PNGImageIO
    VTKImageIO
    GiplImageIO
    LSMImageIO
    AnalyzeImageIO
    NiftiImageIO
    StimulateImageIO
    JPEGImageIO
    TIFFImageIO
    NrrdImageIO
    BMPImageIO
    DICOMImageIO2
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.

ITK should be able to visualize the .nrrd file. Could you open it in Slicer directly to look if it is a valid NRRD file?

Cheers,
Daniel


On Sat, Jan 26, 2013 at 4:20 PM, Kilian Pohl <[hidden email]> wrote:
Hi Daniel,

Can you help ?

K
On 1/26/2013 2:08 PM, Tatjana Polgar wrote:
Hi Kilian,
In addition to my previously described difficulties I have failed to use the AtlasCreator module several times. I have a deadline on this project in few days and I'd greatly appreciate your advice based on the below error message.
Thanks
Tatjana

File: /extra/pieper/slicer3/nightly/Slicer3-lib/Insight/Code/IO/itkImageFileReader.txx
Line: 146
Description:  Could not create IO object for file /home/szatmary/Documents/nrrd/RESEARCH/Output/registered/iteration1/acTmpMeanImageKRUMpY.nrrd
  Tried to create one of the following:
    MGHImageIO
    MRMLIDImageIO
    Brains2MaskImageIO
    BioRadImageIO
    GDCMImageIO
    MetaImageIO
    PNGImageIO
    VTKImageIO
    GiplImageIO
    LSMImageIO
    AnalyzeImageIO
    NiftiImageIO
    StimulateImageIO
    JPEGImageIO
    TIFFImageIO
    NrrdImageIO
    BMPImageIO
    DICOMImageIO2
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.


 /extra/pieper/slicer3/nightly/Slicer3/Applications/CLI/BRAINSTools/BRAINSCommonLib/itkIO.h 85
terminate called after throwing an instance of 'itk::ExceptionObject'
  what():  /extra/pieper/slicer3/nightly/Slicer3-lib/Insight/Code/IO/itkImageFileReader.txx:146:
 Could not create IO object for file /home/szatmary/Documents/nrrd/RESEARCH/Output/registered/iteration1/acTmpMeanImageKRUMpY.nrrd
  Tried to create one of the following:
    MGHImageIO
    MRMLIDImageIO
    Brains2MaskImageIO
    BioRadImageIO
    GDCMImageIO
    MetaImageIO
    PNGImageIO
    VTKImageIO
    GiplImageIO
    LSMImageIO
    AnalyzeImageIO
    NiftiImageIO
    StimulateImageIO
    JPEGImageIO
    TIFFImageIO
    NrrdImageIO
    BMPImageIO
    DICOMImageIO2
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.

Aborted

Launch /gabi/szatmary/SLICER/Slicer3-3.6.4-beta-2012-04-25-linux-x86_64/lib/Slicer3/Plugins/BRAINSFit returned with error: child process exited abnormally

[AtlasCreator 01/26/2013 14:00:24] Registration Job with id 3 failed in attempt 4. Relaunching..
Caught an exception:

itk::ImageFileReaderException (0x236c3d0)
Location: "void itk::ImageFileReader<TOutputImage, ConvertPixelTraits>::GenerateOutputInformation() [with TOutputImage = itk::Image<float, 4u>, ConvertPixelTraits = itk::DefaultConvertPixelTraits<float>]"
File: /extra/pieper/slicer3/nightly/Slicer3-lib/Insight/Code/IO/itkImageFileReader.txx
Line: 146
Description:  Could not create IO object for file /home/szatmary/Documents/nrrd/RESEARCH/Output/registered/iteration1/acTmpMeanImageKRUMpY.nrrd
  Tried to create one of the following:
    MGHImageIO
    MRMLIDImageIO
    Brains2MaskImageIO
    BioRadImageIO
    GDCMImageIO
    MetaImageIO
    PNGImageIO
    VTKImageIO
    GiplImageIO
    LSMImageIO
    AnalyzeImageIO
    NiftiImageIO
    StimulateImageIO
    JPEGImageIO
    TIFFImageIO
    NrrdImageIO
    BMPImageIO
    DICOMImageIO2
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.


 /extra/pieper/slicer3/nightly/Slicer3/Applications/CLI/BRAINSTools/BRAINSCommonLib/itkIO.h 85
terminate called after throwing an instance of 'itk::ExceptionObject'
  what():  /extra/pieper/slicer3/nightly/Slicer3-lib/Insight/Code/IO/itkImageFileReader.txx:146:
 Could not create IO object for file /home/szatmary/Documents/nrrd/RESEARCH/Output/registered/iteration1/acTmpMeanImageKRUMpY.nrrd
  Tried to create one of the following:
    MGHImageIO
    MRMLIDImageIO
    Brains2MaskImageIO
    BioRadImageIO
    GDCMImageIO
    MetaImageIO
    PNGImageIO
    VTKImageIO
    GiplImageIO
    LSMImageIO
    AnalyzeImageIO
    NiftiImageIO
    StimulateImageIO
    JPEGImageIO
    TIFFImageIO
    NrrdImageIO
    BMPImageIO
    DICOMImageIO2
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.

Aborted

Launch /gabi/szatmary/SLICER/Slicer3-3.6.4-beta-2012-04-25-linux-x86_64/lib/Slicer3/Plugins/BRAINSFit returned with error: child process exited abnormally

[AtlasCreator 01/26/2013 14:00:27] Registration Job with id 4 failed in attempt 4. Relaunching..
Caught an exception:

itk::ImageFileReaderException (0xf6a3d0)
Location: "void itk::ImageFileReader<TOutputImage, ConvertPixelTraits>::GenerateOutputInformation() [with TOutputImage = itk::Image<float, 4u>, ConvertPixelTraits = itk::DefaultConvertPixelTraits<float>]"
File: /extra/pieper/slicer3/nightly/Slicer3-lib/Insight/Code/IO/itkImageFileReader.txx
Line: 146
Description:  Could not create IO object for file /home/szatmary/Documents/nrrd/RESEARCH/Output/registered/iteration1/acTmpMeanImageKRUMpY.nrrd
  Tried to create one of the following:
    MGHImageIO
    MRMLIDImageIO
    Brains2MaskImageIO
    BioRadImageIO
    GDCMImageIO
    MetaImageIO
    PNGImageIO
    VTKImageIO
    GiplImageIO
    LSMImageIO
    AnalyzeImageIO
    NiftiImageIO
    StimulateImageIO
    JPEGImageIO
    TIFFImageIO
    NrrdImageIO
    BMPImageIO
    DICOMImageIO2
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.


 /extra/pieper/slicer3/nightly/Slicer3/Applications/CLI/BRAINSTools/BRAINSCommonLib/itkIO.h 85
terminate called after throwing an instance of 'itk::ExceptionObject'
  what():  /extra/pieper/slicer3/nightly/Slicer3-lib/Insight/Code/IO/itkImageFileReader.txx:146:
 Could not create IO object for file /home/szatmary/Documents/nrrd/RESEARCH/Output/registered/iteration1/acTmpMeanImageKRUMpY.nrrd
  Tried to create one of the following:
    MGHImageIO
    MRMLIDImageIO
    Brains2MaskImageIO
    BioRadImageIO
    GDCMImageIO
    MetaImageIO
    PNGImageIO
    VTKImageIO
    GiplImageIO
    LSMImageIO
    AnalyzeImageIO
    NiftiImageIO
    StimulateImageIO
    JPEGImageIO
    TIFFImageIO
    NrrdImageIO
    BMPImageIO
    DICOMImageIO2
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.

Aborted

Launch /gabi/szatmary/SLICER/Slicer3-3.6.4-beta-2012-04-25-linux-x86_64/lib/Slicer3/Plugins/BRAINSFit returned with error: child process exited abnormally

[AtlasCreator 01/26/2013 14:00:38] Registration Job with id 5 failed in attempt 4. Relaunching..
Caught an exception:

itk::ImageFileReaderException (0x15863d0)
Location: "void itk::ImageFileReader<TOutputImage, ConvertPixelTraits>::GenerateOutputInformation() [with TOutputImage = itk::Image<float, 4u>, ConvertPixelTraits = itk::DefaultConvertPixelTraits<float>]"
File: /extra/pieper/slicer3/nightly/Slicer3-lib/Insight/Code/IO/itkImageFileReader.txx
Line: 146
Description:  Could not create IO object for file /home/szatmary/Documents/nrrd/RESEARCH/Output/registered/iteration1/acTmpMeanImageKRUMpY.nrrd
  Tried to create one of the following:
    MGHImageIO
    MRMLIDImageIO
    Brains2MaskImageIO
    BioRadImageIO
    GDCMImageIO
    MetaImageIO
    PNGImageIO
    VTKImageIO
    GiplImageIO
    LSMImageIO
    AnalyzeImageIO
    NiftiImageIO
    StimulateImageIO
    JPEGImageIO
    TIFFImageIO
    NrrdImageIO
    BMPImageIO
    DICOMImageIO2
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.


 /extra/pieper/slicer3/nightly/Slicer3/Applications/CLI/BRAINSTools/BRAINSCommonLib/itkIO.h 85
terminate called after throwing an instance of 'itk::ExceptionObject'
  what():  /extra/pieper/slicer3/nightly/Slicer3-lib/Insight/Code/IO/itkImageFileReader.txx:146:
 Could not create IO object for file /home/szatmary/Documents/nrrd/RESEARCH/Output/registered/iteration1/acTmpMeanImageKRUMpY.nrrd
  Tried to create one of the following:
    MGHImageIO
    MRMLIDImageIO
    Brains2MaskImageIO
    BioRadImageIO
    GDCMImageIO
    MetaImageIO
    PNGImageIO
    VTKImageIO
    GiplImageIO
    LSMImageIO
    AnalyzeImageIO
    NiftiImageIO
    StimulateImageIO
    JPEGImageIO
    TIFFImageIO
    NrrdImageIO
    BMPImageIO
    DICOMImageIO2
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.

Aborted

Launch /gabi/szatmary/SLICER/Slicer3-3.6.4-beta-2012-04-25-linux-x86_64/lib/Slicer3/Plugins/BRAINSFit returned with error: child process exited abnormally

[AtlasCreator 01/26/2013 14:00:49] Waiting for Registration to complete.. (0/5 done)
[AtlasCreator 01/26/2013 14:00:50] -------------------------------------------------------
[AtlasCreator 01/26/2013 14:00:50] -------------------------------------------------------
[AtlasCreator 01/26/2013 14:00:50] FAILURE: Registration Job with id 1 failed 4 times! Let's continue without it..
[AtlasCreator 01/26/2013 14:00:50] FAILURE: File /home/szatmary/Documents/nrrd/RESEARCH/Output/registered/iteration1/case4.nrrd will NOT be considered during the next steps..
[AtlasCreator 01/26/2013 14:00:50] -------------------------------------------------------
[AtlasCreator 01/26/2013 14:00:50] -------------------------------------------------------
[AtlasCreator 01/26/2013 14:00:50] -------------------------------------------------------
[AtlasCreator 01/26/2013 14:00:50] -------------------------------------------------------
[AtlasCreator 01/26/2013 14:00:50] FAILURE: Registration Job with id 2 failed 4 times! Let's continue without it..
[AtlasCreator 01/26/2013 14:00:50] FAILURE: File /home/szatmary/Documents/nrrd/RESEARCH/Output/registered/iteration1/case6.nrrd will NOT be considered during the next steps..
[AtlasCreator 01/26/2013 14:00:50] -------------------------------------------------------
[AtlasCreator 01/26/2013 14:00:50] -------------------------------------------------------
[AtlasCreator 01/26/2013 14:00:50] -------------------------------------------------------
[AtlasCreator 01/26/2013 14:00:50] -------------------------------------------------------
[AtlasCreator 01/26/2013 14:00:50] FAILURE: Registration Job with id 3 failed 4 times! Let's continue without it..
[AtlasCreator 01/26/2013 14:00:50] FAILURE: File /home/szatmary/Documents/nrrd/RESEARCH/Output/registered/iteration1/case1.nrrd will NOT be considered during the next steps..
[AtlasCreator 01/26/2013 14:00:50] -------------------------------------------------------
[AtlasCreator 01/26/2013 14:00:50] -------------------------------------------------------
[AtlasCreator 01/26/2013 14:00:50] -------------------------------------------------------
[AtlasCreator 01/26/2013 14:00:50] -------------------------------------------------------
[AtlasCreator 01/26/2013 14:00:50] FAILURE: Registration Job with id 4 failed 4 times! Let's continue without it..
[AtlasCreator 01/26/2013 14:00:50] FAILURE: File /home/szatmary/Documents/nrrd/RESEARCH/Output/registered/iteration1/case5.nrrd will NOT be considered during the next steps..
[AtlasCreator 01/26/2013 14:00:50] -------------------------------------------------------
[AtlasCreator 01/26/2013 14:00:50] -------------------------------------------------------
[AtlasCreator 01/26/2013 14:00:50] -------------------------------------------------------
[AtlasCreator 01/26/2013 14:00:50] -------------------------------------------------------
[AtlasCreator 01/26/2013 14:00:50] FAILURE: Registration Job with id 5 failed 4 times! Let's continue without it..
[AtlasCreator 01/26/2013 14:00:50] FAILURE: File /home/szatmary/Documents/nrrd/RESEARCH/Output/registered/iteration1/case2.nrrd will NOT be considered during the next steps..
[AtlasCreator 01/26/2013 14:00:50] -------------------------------------------------------
[AtlasCreator 01/26/2013 14:00:50] -------------------------------------------------------
[AtlasCreator 01/26/2013 14:00:50] Starting iteration 2...
[AtlasCreator 01/26/2013 14:00:50] Empty filePathsList for ComputeMeanImage() command. Aborting..
[AtlasCreator 01/26/2013 14:00:50] Found 3D Slicer launcher at /home/szatmary/SLICER/Slicer3-3.6.4-beta-2012-04-25-linux-x86_64/Slicer3
   Background level guess :
   first place: 0 (46.1522%)
   second place: 2 (10.7749%)
   Guessed background level: 0
Caught an exception:

itk::ImageFileReaderException (0xe213d0)
Location: "void itk::ImageFileReader<TOutputImage, ConvertPixelTraits>::GenerateOutputInformation() [with TOutputImage = itk::Image<float, 4u>, ConvertPixelTraits = itk::DefaultConvertPixelTraits<float>]"
File: /extra/pieper/slicer3/nightly/Slicer3-lib/Insight/Code/IO/itkImageFileReader.txx
Line: 146
Description:  Could not create IO object for file /home/szatmary/Documents/nrrd/RESEARCH/Output/registered/iteration2/acTmpMeanImageZSn_xS.nrrd
  Tried to create one of the following:
    MGHImageIO
    MRMLIDImageIO
    Brains2MaskImageIO
    BioRadImageIO
    GDCMImageIO
    MetaImageIO
    PNGImageIO
    VTKImageIO
    GiplImageIO
    LSMImageIO
    AnalyzeImageIO
    NiftiImageIO
    StimulateImageIO
    JPEGImageIO
    TIFFImageIO
    NrrdImageIO
    BMPImageIO
    DICOMImageIO2
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.


 /extra/pieper/slicer3/nightly/Slicer3/Applications/CLI/BRAINSTools/BRAINSCommonLib/itkIO.h 85
terminate called after throwing an instance of 'itk::ExceptionObject'
  what():  /extra/pieper/slicer3/nightly/Slicer3-lib/Insight/Code/IO/itkImageFileReader.txx:146:
 Could not create IO object for file /home/szatmary/Documents/nrrd/RESEARCH/Output/registered/iteration2/acTmpMeanImageZSn_xS.nrrd
  Tried to create one of the following:
    MGHImageIO
    MRMLIDImageIO
    Brains2MaskImageIO
    BioRadImageIO
    GDCMImageIO
    MetaImageIO
    PNGImageIO
    VTKImageIO
    GiplImageIO
    LSMImageIO
    AnalyzeImageIO
    NiftiImageIO
    StimulateImageIO
    JPEGImageIO
    TIFFImageIO
    NrrdImageIO
    BMPImageIO
    DICOMImageIO2
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.

Aborted

Launch /gabi/szatmary/SLICER/Slicer3-3.6.4-beta-2012-04-25-linux-x86_64/lib/Slicer3/Plugins/BRAINSFit returned with error: child process exited abnormally

   Background level guess :
   first place: 0 (46.1617%)
   second place: 2 (7.83306%)
   Guessed background level: 0
Caught an exception:

itk::ImageFileReaderException (0x23963d0)
Location: "void itk::ImageFileReader<TOutputImage, ConvertPixelTraits>::GenerateOutputInformation() [with TOutputImage = itk::Image<float, 4u>, ConvertPixelTraits = itk::DefaultConvertPixelTraits<float>]"
File: /extra/pieper/slicer3/nightly/Slicer3-lib/Insight/Code/IO/itkImageFileReader.txx
Line: 146
Description:  Could not create IO object for file /home/szatmary/Documents/nrrd/RESEARCH/Output/registered/iteration2/acTmpMeanImageZSn_xS.nrrd
  Tried to create one of the following:
    MGHImageIO
    MRMLIDImageIO
    Brains2MaskImageIO
    BioRadImageIO
    GDCMImageIO
    MetaImageIO
    PNGImageIO
    VTKImageIO
    GiplImageIO
    LSMImageIO
    AnalyzeImageIO
    NiftiImageIO
    StimulateImageIO
    JPEGImageIO
    TIFFImageIO
    NrrdImageIO
    BMPImageIO
    DICOMImageIO2
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.


 /extra/pieper/slicer3/nightly/Slicer3/Applications/CLI/BRAINSTools/BRAINSCommonLib/itkIO.h 85
terminate called after throwing an instance of 'itk::ExceptionObject'
  what():  /extra/pieper/slicer3/nightly/Slicer3-lib/Insight/Code/IO/itkImageFileReader.txx:146:
 Could not create IO object for file /home/szatmary/Documents/nrrd/RESEARCH/Output/registered/iteration2/acTmpMeanImageZSn_xS.nrrd
  Tried to create one of the following:
    MGHImageIO
    MRMLIDImageIO
    Brains2MaskImageIO
    BioRadImageIO
    GDCMImageIO
    MetaImageIO
    PNGImageIO
    VTKImageIO
    GiplImageIO
    LSMImageIO
    AnalyzeImageIO
    NiftiImageIO
    StimulateImageIO
    JPEGImageIO
    TIFFImageIO
    NrrdImageIO
    BMPImageIO
    DICOMImageIO2
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.

Aborted

Launch /gabi/szatmary/SLICER/Slicer3-3.6.4-beta-2012-04-25-linux-x86_64/lib/Slicer3/Plugins/BRAINSFit returned with error: child process exited abnormally

   Background level guess :
   first place: 0 (56.9911%)
   second place: 1 (13.1299%)
   Guessed background level: 0
Caught an exception:

itk::ImageFileReaderException (0x1adb3d0)
Location: "void itk::ImageFileReader<TOutputImage, ConvertPixelTraits>::GenerateOutputInformation() [with TOutputImage = itk::Image<float, 4u>, ConvertPixelTraits = itk::DefaultConvertPixelTraits<float>]"
File: /extra/pieper/slicer3/nightly/Slicer3-lib/Insight/Code/IO/itkImageFileReader.txx
Line: 146
Description:  Could not create IO object for file /home/szatmary/Documents/nrrd/RESEARCH/Output/registered/iteration2/acTmpMeanImageZSn_xS.nrrd
  Tried to create one of the following:
    MGHImageIO
    MRMLIDImageIO
    Brains2MaskImageIO
    BioRadImageIO
    GDCMImageIO
    MetaImageIO
    PNGImageIO
    VTKImageIO
    GiplImageIO
    LSMImageIO
    AnalyzeImageIO
    NiftiImageIO
    StimulateImageIO
    JPEGImageIO
    TIFFImageIO
    NrrdImageIO
    BMPImageIO
    DICOMImageIO2
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.


 /extra/pieper/slicer3/nightly/Slicer3/Applications/CLI/BRAINSTools/BRAINSCommonLib/itkIO.h 85
terminate called after throwing an instance of 'itk::ExceptionObject'
  what():  /extra/pieper/slicer3/nightly/Slicer3-lib/Insight/Code/IO/itkImageFileReader.txx:146:
 Could not create IO object for file /home/szatmary/Documents/nrrd/RESEARCH/Output/registered/iteration2/acTmpMeanImageZSn_xS.nrrd
  Tried to create one of the following:
    MGHImageIO
    MRMLIDImageIO
    Brains2MaskImageIO
    BioRadImageIO
    GDCMImageIO
    MetaImageIO
    PNGImageIO
    VTKImageIO
    GiplImageIO
    LSMImageIO
    AnalyzeImageIO
    NiftiImageIO
    StimulateImageIO
    JPEGImageIO
    TIFFImageIO
    NrrdImageIO
    BMPImageIO
    DICOMImageIO2
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.

Aborted

Launch /gabi/szatmary/SLICER/Slicer3-3.6.4-beta-2012-04-25-linux-x86_64/lib/Slicer3/Plugins/BRAINSFit returned with error: child process exited abnormally

   Background level guess :
   first place: 0 (49.5556%)
   second place: 2 (11.4977%)
   Guessed background level: 0
Caught an exception:

itk::ImageFileReaderException (0x1a5e3d0)
Location: "void itk::ImageFileReader<TOutputImage, ConvertPixelTraits>::GenerateOutputInformation() [with TOutputImage = itk::Image<float, 4u>, ConvertPixelTraits = itk::DefaultConvertPixelTraits<float>]"
File: /extra/pieper/slicer3/nightly/Slicer3-lib/Insight/Code/IO/itkImageFileReader.txx
Line: 146
Description:  Could not create IO object for file /home/szatmary/Documents/nrrd/RESEARCH/Output/registered/iteration2/acTmpMeanImageZSn_xS.nrrd
  Tried to create one of the following:
    MGHImageIO
    MRMLIDImageIO
    Brains2MaskImageIO
    BioRadImageIO
    GDCMImageIO
    MetaImageIO
    PNGImageIO
    VTKImageIO
    GiplImageIO
    LSMImageIO
    AnalyzeImageIO
    NiftiImageIO
    StimulateImageIO
    JPEGImageIO
    TIFFImageIO
    NrrdImageIO
    BMPImageIO
    DICOMImageIO2
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.


 /extra/pieper/slicer3/nightly/Slicer3/Applications/CLI/BRAINSTools/BRAINSCommonLib/itkIO.h 85
terminate called after throwing an instance of 'itk::ExceptionObject'
  what():  /extra/pieper/slicer3/nightly/Slicer3-lib/Insight/Code/IO/itkImageFileReader.txx:146:
 Could not create IO object for file /home/szatmary/Documents/nrrd/RESEARCH/Output/registered/iteration2/acTmpMeanImageZSn_xS.nrrd
  Tried to create one of the following:
    MGHImageIO
    MRMLIDImageIO
    Brains2MaskImageIO
    BioRadImageIO
    GDCMImageIO
    MetaImageIO
    PNGImageIO
    VTKImageIO
    GiplImageIO
    LSMImageIO
    AnalyzeImageIO
    NiftiImageIO
    StimulateImageIO
    JPEGImageIO
    TIFFImageIO
    NrrdImageIO
    BMPImageIO
    DICOMImageIO2
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.


________________________________
From: Kilian Pohl <[hidden email]><mailto:[hidden email]>
To: Tatjana Polgar <[hidden email]><mailto:[hidden email]>
Sent: Saturday, January 26, 2013 12:13 PM
Subject: Re: Fw: [slicer-users] automatic segmentation from T2 WIs

On 1/26/2013 12:12 PM, Tatjana Polgar wrote:
Yes, Kilian! I do have nightly 4.2.0 on my linux. Does it have to be the latest version?
Yes it will have to be bc that is the easiest way for you to get the template . Does that make sense ? I will notify you when I have created the template for you

Kilian

Thanks
Tatjana

----- Forwarded Message -----
From: Kilian Pohl <[hidden email]><mailto:[hidden email]>
To: Tanya <[hidden email]><mailto:[hidden email]>
Sent: Saturday, January 26, 2013 9:43 AM
Subject: Re: [slicer-users] automatic segmentation from T2 WIs

will do - are you able to install the nightly version of Slicer ? If so then I can create a template for you, push it in slicer, and you can simply use it - does that sound good ?

Kilian


On 1/26/2013 10:25 AM, Tanya wrote:
Thank you Kilian!
Could you send me the link for the MRI-HumanBrain Atlas T2 data because I am not able to find it.
Thank you!
Tatjana

On Jan 23, 2013, at 7:43 PM, Kilian Pohl <[hidden email]<mailto:[hidden email]>> wrote:

You can parameterize  EMSegmenter so that it will segment your T2 and Flair scan.

look at the information at http://www.slicer.org/slicerWiki/index.php/Modules:EMSegmenter-3.6

and

http://www.slicer.org/slicerWiki/index.php/EMSegmenter-Tasks

The MRI-Human-Brain Atlas comes with a T2 image which you can use for this task

Kilian


On 1/23/2013 4:59 PM, Tatjana Polgar wrote:
Hi Slicers,
I have 3D T2 CUBE and T2 FLAIR CUBE WI that I'd like to segment into GM, WM, CSF and skull without T1WI.
IS ARCTIC capable to segment such sequences? So far, I was only able to use ARCTIC and atlas-based EM segmenter for T1 segmentation.
Is there any other module than ARCTIC to be used for segmentation and volumetry in this situation?

I use unix ubuntu, 3D Slicer3.6.3.
Thanks for your advise on this matter!
Tatjana



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