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poldracklab / pydeface

defacing utility for MRI images
MIT License
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defacing fails if environment variable FSLOUTPUTTYPE != NIFTI_GZ #3

Open wtriplett opened 8 years ago

wtriplett commented 8 years ago

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