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psych-214-fall-2016 / project-red

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file names issues #61

Open jbpoline opened 7 years ago

jbpoline commented 7 years ago

hi,

running run_anat_preprocess.py from ~/code/psych214/project-red/code/fmri_utils/anat_preproc

git[master] $ python run_anat_preprocess.py Running Anatomical Preprocessing: MNI Reorient, Skull Strip, Deoblique.

running MNI reorientation for sub-10225 running MNI reorientation for sub-10227 running MNI reorientation for sub-10292 running MNI reorientation for sub-10193 running MNI reorientation for sub-10249 running MNI reorientation for sub-10271 running MNI reorientation for sub-10299 Traceback (most recent call last): File "run_anat_preprocess.py", line 107, in MNI_reorient(input_file, output_file) File "/home/jb/code/psych214/project-red/code/fmri_utils/anat_preproc/MNI_reorient.py", line 28, in MNI_reorient MNI.inputs.in_file = structural_nifti_file File "/home/jb/virtualenvs/red/lib/python3.5/site-packages/nipype/interfaces/traits_extension.py", line 80, in validate self.error(object, name, value) File "/home/jb/virtualenvs/red/lib/python3.5/site-packages/traits/trait_handlers.py", line 173, in error value ) traits.trait_errors.TraitError: The 'in_file' trait of a Reorient2StdInputSpec instance must be an existing file name, but a value of '../../../data/ds000030/sub-10299/anat/sub-10299_T1w.nii.gz' <class 'str'> was specified.

is there something specific to be done for subject 10299 ?