defacing fails if environment variable FSLOUTPUTTYPE != NIFTI_GZ
wtriplett opened this issue · 0 comments
wtriplett commented
Causes flirt interface to make output files based on FSLOUTPUTTYPE, but pydeface looks for .nii.gz
$ echo $FSLOUTPUTTYPE
NIFTI
$ pydeface.py sub-1700/anat/sub-1700_T1w.nii.gz test.nii
defacing sub-1700/anat/sub-1700_T1w.nii.gz
Traceback (most recent call last):
File "/work/03872/wtriplet/lonestar/anaconda/bin/pydeface.py", line 6, in <module>
exec(compile(open(__file__).read(), __file__, 'exec'))
File "/home1/03872/wtriplet/software/pydeface/scripts/pydeface.py", line 143, in <module>
main()
File "/home1/03872/wtriplet/software/pydeface/scripts/pydeface.py", line 127, in main
flirt.run()
File "/home1/03872/wtriplet/software/nipype/nipype/interfaces/base.py", line 1046, in run
outputs = self.aggregate_outputs(runtime)
File "/home1/03872/wtriplet/software/nipype/nipype/interfaces/fsl/preprocess.py", line 550, in aggregate_outputs
runtime=runtime, needed_outputs=needed_outputs)
File "/home1/03872/wtriplet/software/nipype/nipype/interfaces/base.py", line 1140, in aggregate_outputs
raise FileNotFoundError(msg)
nipype.utils.filemanip.FileNotFoundError: File/Directory '/tmp/tmpzLbhge.nii.gz' not found for FLIRT output 'out_file'.
Interface FLIRT failed to run.
$ ls /tmp/tmpzLbhge.nii
/tmp/tmpzLbhge.nii