From Kilian:

one more thing :

http://www.na-mic.org/Bug/view.php?id=2741
list two failing tests:

• http://slicer.cdash.org/testDetails.php?test=3128493&build=46902
  does not have nothing to do with http://www.na-mic.org/Bug/view.php?id=2569

and I am not sure that http://slicer.cdash.org/testDetails.php?test=3128494&build=46902
does with http://www.na-mic.org/Bug/view.php?id=2569

bc

TCL: Create file: C:/Users/kitware/AppData/Local/Temp/EMS10406a02864.mat
TCL: Executing "C:/D/N/Slicer-1-build/Slicer-build/lib/Slicer-4.2/cli-modules/Release/BRAINSFit" --fixedVolume "C:/Users/kitware/AppData/Local/Temp/EMS5212a02864_vtkMRMLScalarVolumeNode23.nrrd" --movingVolume "C:/D/N/Slicer-1-build/Slicer-build/share/Slicer-4.2/qt-loadable-modules/EMSegment/Tasks/MRI-Human-Brain/atlas_t1.nrrd" --outputVolume C:/Users/kitware/AppData/Local/Temp/EMS28308a02864.nrrd --outputTransform C:/Users/kitware/AppData/Local/Temp/EMS10406a02864.mat --initializeTransformMode useCenterOfHeadAlign --numberOfIterations 3 --numberOfSamples 100 --minimumStepLength 0.005 --translationScale 1000 --reproportionScale 1 --skewScale 1 --maskProcessingMode NOMASK --numberOfHistogramBins 40 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --costMetric MMI
TCL: child killed: unknown signal
TCL: Create file: C:/Users/kitware/AppData/Local/Temp/EMS23053a02864.nrrd
TCL: Create file: C:/Users/kitware/AppData/Local/Temp/EMS18611a02864.nrrd
TCL: Executing "C:/D/N/Slicer-1-build/Slicer-build/lib/Slicer-4.2/cli-modules/Release/BRAINSDemonWarp" -f "C:/Users/kitware/AppData/Local/Temp/EMS5212a02864_vtkMRMLScalarVolumeNode23.nrrd" -m "C:/D/N/Slicer-1-build/Slicer-build/share/Slicer-4.2/qt-loadable-modules/EMSegment/Tasks/MRI-Human-Brain/atlas_t1.nrrd" --initializeWithTransform C:/Users/kitware/AppData/Local/Temp/EMS10406a02864.mat --outputVolume C:/Users/kitware/AppData/Local/Temp/EMS18611a02864.nrrd --outputDeformationFieldVolume C:/Users/kitware/AppData/Local/Temp/EMS23053a02864.nrrd -i 40,20,10,5,2 -n 5 -e --numberOfMatchPoints 16 --numberOfHistogramBins 1024
Error executing tpycl_result = slicer.DQZXSAQl.PrintText('TCL: Long flag "--outputDeformationFieldVolume" is deprecated. Please use long flag "--outputDisplacementFieldVolume" instead. \nRead ITK transform from text file: C:/Users/kitware/AppData/Local/Temp/EMS10406a02864.mat\nCaught an ITK exception: \n\nitk::ExceptionObject (00000000009D8280)\nLocation: "class itk::SmartPointer<class itk::Transform<double,3,3> > cdecl itk::ReadTransformFromDisk(const class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> > &)" \nFile: ..........\BRAINSTools\BRAINSCommonLib\GenericTransformImage.cxx\nLine: 249\nDescription: itk::ERROR: Number of currentTransformList = 0FATAL ERROR: Failed to read transformC:/Users/kitware/AppData/Local/Temp/EMS10406a02864.mat\n\n c:\d\n\slicer-1-build\brainstools\brainscommonlib\ApplicationBase.hxx 53\nCaught an ITK exception: \n\nitk::ExceptionObject (00000000009D8700)\nLocation: "class itk::
SmartPointer<class itk::Transform<double,3,3> > cdecl itk::ReadTransformFromDisk(const class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> > &)" \nFile: ..........\BRAINSTools\BRAINSCommonLib\GenericTransformImage.cxx\nLine: 249\nDescription: itk::ERROR: Number of currentTransformList = 0FATAL ERROR: Failed to read transformC:/Users/kitware/AppData/Local/Temp/EMS10406a02864.mat\n\n c:\d\n\slicer-1-build\brainstools\brainsdemonwarp\BRAINSDemonWarpTemplates.h 554\n\nThis application has requested the Runtime to terminate it in an unusual way.\nPlease contact the application's support team for more information.')
(<type 'exceptions.SyntaxError'>, SyntaxError('invalid syntax', ('<string>', 1, 1567, '__tpycl_result = slicer.DQZXSAQl.PrintText(\'TCL: Long flag "--outputDeformationFieldVolume" is deprecated. Please use long flag "--outputDisplacementFieldVolume" instead. \nRead ITK transform from text file: C:/Users/kitware/AppData/Local/Temp/EMS10406a02864.mat\nCaught an ITK exception: \n\nitk::ExceptionObject (00000000009D8280)\nLocation: "class itk::SmartPointer<class itk::Transform<double,3,3> > cdecl itk::ReadTransformFromDisk(const class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> > &)" \nFile: ..\..\..\..\..\BRAINSTools\BRAINSCommonLib\GenericTransformImage.cxx\nLine: 249\nDescription: itk::ERROR: Number of currentTransformList = 0FATAL ERROR: Failed to read transformC:/Users/kitware/AppData/Local/Temp/EMS10406a02864.mat\n\n c:\d\n\slicer-1-build\brainstools\brainscommonlib\Applicati
onBase.hxx 53\nCaught an ITK exception: \n\nitk::ExceptionObject (00000000009D8700)\nLocation: "class itk::SmartPointer<class itk::Transform<double,3,3> > __cdecl itk::ReadTransformFromDisk(const class std::basic_string<char,struct std::char_traits<char>,class std::allocator<char> > &)" \nFile: ..\..\..\..\..\BRAINSTools\BRAINSCommonLib\GenericTransformImage.cxx\nLine: 249\nDescription: itk::ERROR: Number of currentTransformList = 0FATAL ERROR: Failed to read transformC:/Users/kitware/AppData/Local/Temp/EMS10406a02864.mat\n\n c:\d\n\slicer-1-build\brainstools\brainsdemonwarp\BRAINSDemonWarpTemplates.h 554\n\nThis application has requested the Runtime to terminate it in an unusual way.\nPlease contact the application\'s support team for more information.\')')), <traceback object at 0x00000000144F7C08>)

while executing

"py_eval $pycmd"
(procedure "::tpycl::methodCaller" line 117)
invoked from within
"::tpycl::methodCaller DQZXSAQl slicer.DQZXSAQl $args"
(procedure "DQZXSAQl" line 1)
invoked from within
"$LOGIC PrintText "TCL: $errmsg""
("BRAINS" arm line 82)
invoked from within
"switch -exact "$selectedRegistrationPackage" {
"CMTK" {

            set affineType 1

            ## CMTK specific arguments

..."
(procedure "SkullStripper" line 48)

Something funky seems to happen with Brains tools

Kilian

From Jc:

The two test are failing because they timeout ... should we expect these test to take more than 15 min to run ?
Jc

From Kilian:
appears that brains tool takes very long under windows

From Kilian:
it might take 5 min max under linux

Regarding note http://www.na-mic.org/Bug/view.php?id=2741#c7140,

would be great if you could provide both datasets and the command line causing BRAINS module to fail. Then, we would create an issue and ask Hans to work on it.

Thanks

data with readme file on the running the brainsfit command are located in

https://dl.dropbox.com/u/3652483/bug_2741.tgz

Thanks Kilian. I created issue 0002780 assigned to Hans. We should head back from him shortly.

Test " EMSeg_MRML_DiffReadWriteNodes " still failing on windows 32/64, ubuntu and macosx.

Test "EMSegCL_Task_MRIHumanBrainFullParcellation_BRAINS_small" failing on windows 32/64

Test "EMSegCL_Task_MRIHumanBrainFullParcellation_BRAINS_small" still failing on windows. See http://trunk.cdash.org/testDetails.php?test=4488023&amp;build=155820

The error breaking the test is

invalid command name "vtkImageLabelPropagation"
invalid command name "vtkImageLabelPropagation"
while executing
"vtkImageLabelPropagation New"
(procedure "GeneratedVoronoi" line 6)
invoked from within
"GeneratedVoronoi [$outputVolumeNode GetImageData]"
(procedure "RegisterAtlas" line 265)
invoked from within
"RegisterAtlas $atlasAlignedFlag"
(procedure "::EMSegmenterPreProcessingTcl::Run" line 53)
invoked from within
"::EMSegmenterPreProcessingTcl::Run"
EMSEG: Preprocessing complete.
EMSEG: Start Segmentation.

The filter is not found when called in Tcl. I have not idea why. I checked the CMakeLocal files - the filter is compiled under windows

Fixed in r23640
See http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=23640