Hi!
I’m using the latest nightly build of Slicer on Linux, and I’m trying to learn how to do registration of one temporal bone CT onto another. When I try to use “General Registration (BRAINSfit)”, I’m getting “Status: Completed with errors” and the following message after choosing fixed/moving images as well as “Output image volume” in the Output settings, and then clicking on apply:
"General Registration (BRAINS) standard error:
terminate called after throwing an instance of 'itk::ImageFileReaderException'
what(): /work/Preview/Slicer-0-build/ITKv4/Modules/IO/ImageBase/include/itkImageFileReader.hxx:143:
Could not create IO object for reading file /tmp/Slicer-torquil/CEAHH_vtkMRMLScalarVolumeNodeB.nrrd
Tried to create one of the following:
BMPImageIO
BioRadImageIO
DCMTKImageIO
GDCMImageIO
GiplImageIO
JPEGImageIO
LSMImageIO
MGHImageIO
MINCImageIO
MRCImageIO
MetaImageIO
NiftiImageIO
NrrdImageIO
PNGImageIO
StimulateImageIO
TIFFImageIO
VTKImageIO
GE4ImageIO
GE5ImageIO
HDF5ImageIO
You probably failed to set a file suffix, or
set the suffix to an unsupported type."
As an alternative, I have installed the SlicerElastix module, but when I use that I get an empty error message:
"Error:"
It does not matter if I choose different Preset values.
In the log files ~/.xsession-errors I’m seeing the following at each click on Apply:
"Volume registration is started in working directory: /tmp/Slicer-torquil/Elastix/20181016_144358_133
Generic Warning: In /work/Preview/Slicer-0/Libs/MRML/Core/vtkDataFileFormatHelper.cxx, line 237
vtkDataFileFormatHelper::GetFileExtensionFromFormatString: please update deprecated extension-only format specifier to 'File format name (.ext)' format! Current format string: .mha
MetaImage: M_WriteElementsData: file stream is fail after write
Generic Warning: In /work/Preview/Slicer-0/Libs/MRML/Core/vtkDataFileFormatHelper.cxx, line 237
vtkDataFileFormatHelper::GetFileExtensionFromFormatString: please update deprecated extension-only format specifier to 'File format name (.ext)' format! Current format string: .mha
MetaImage: M_WriteElementsData: file stream is fail after write
Register volumes...
Register volumes using: /home/torquil/.config/NA-MIC/Extensions-27483/SlicerElastix/lib/Slicer-4.9/elastix: ['-f', u'/tmp/Slicer-torquil/Elastix/20181016_144358_133/input/fixed.mha', '-m', u'/tmp/Slicer-torquil/Elastix/20181016_144358_133/input/moving.mha', '-out', u'/tmp/Slicer-torquil/Elastix/20181016_144358_133/result-transform', '-p', '/home/torquil/.config/NA-MIC/Extensions-27483/SlicerElastix/lib/Slicer-4.9/qt-scripted-modules/Resources/RegistrationParameters/Parameters.Par0009.affine.txt', '-p', '/home/torquil/.config/NA-MIC/Extensions-27483/SlicerElastix/lib/Slicer-4.9/qt-scripted-modules/Resources/RegistrationParameters/Parameters.Par0009.elastic.txt']
elastix is started at Tue Oct 16 14:43:58 2018.
which elastix: /home/torquil/.config/NA-MIC/Extensions-27483/SlicerElastix/lib/Slicer-4.9/elastix
elastix runs at: lenovo-p51
Linux 4.18.0-2-amd64 (x64), #1 SMP Debian 4.18.10-2 (2018-10-07)
with 15830 MB memory, and 4 cores @ 3835 MHz.
-------------------------------------------------------------------------
Running elastix with parameter file 0: "/home/torquil/.config/NA-MIC/Extensions-27483/SlicerElastix/lib/Slicer-4.9/qt-scripted-modules/Resources/RegistrationParameters/Parameters.Par0009.affine.txt".
Current time: Tue Oct 16 14:43:58 2018.
Reading the elastix parameters from file ...
ERROR: could not read fixed image.
itk::ImageFileReaderException (0x361de80)
Location: "unknown"
File: /work/Preview/Slicer-0-build/ITKv4/Modules/IO/ImageBase/include/itkImageFileReader.hxx
Line: 143
Description: Could not create IO object for reading file /tmp/Slicer-torquil/Elastix/20181016_144358_133/input/fixed.mha
Tried to create one of the following:
BMPImageIO
BioRadImageIO
Bruker2dseqImageIO
DCMTKImageIO
GDCMImageIO
GE4ImageIO
GE5ImageIO
GiplImageIO
HDF5ImageIO
JPEGImageIO
LSMImageIO
MGHImageIO
MINCImageIO
MRCImageIO
MetaImageIO
NiftiImageIO
NrrdImageIO
PNGImageIO
StimulateImageIO
TIFFImageIO
VTKImageIO
MRMLIDImageIO
You probably failed to set a file suffix, or
set the suffix to an unsupported type.
Errors occurred!
vtkDebugLeaks has found no leaks.
Command 'elastix' returned non-zero exit status 1
Traceback (most recent call last):
File "/home/torquil/.config/NA-MIC/Extensions-27483/SlicerElastix/lib/Slicer-4.9/qt-scripted-modules/Elastix.py", line 327, in onApplyButton
movingVolumeMaskNode = self.movingVolumeMaskSelector.currentNode())
File "/home/torquil/.config/NA-MIC/Extensions-27483/SlicerElastix/lib/Slicer-4.9/qt-scripted-modules/Elastix.py", line 579, in registerVolumes
self.logProcessOutput(ep)
File "/home/torquil/.config/NA-MIC/Extensions-27483/SlicerElastix/lib/Slicer-4.9/qt-scripted-modules/Elastix.py", line 519, in logProcessOutput
raise subprocess.CalledProcessError(return_code, "elastix")
CalledProcessError: Command 'elastix' returned non-zero exit status 1"
I’m using the following version of elastix
$ elastix --version
elastix version: 4.800