I am new to fmriprep and fmri. I am trying to run version 20.0.3 in a bare-metal installation. I was able to run it to completion several months ago during testing, but now fmriprep is exiting without running.
My command is as follows:
fmriprep BIDS/NIFTI/ BIDS/derivatives/ participant --participant-label A001 --notrack
And I get the following error:
Traceback (most recent call last):
File “/gs/gsfs0/users/yifeman/.local/bin/fmriprep”, line 11, in
File “/gs/gsfs0/users/yifeman/.local/lib/python3.6/site-packages/fmriprep/cli/run.py”, line 355, in main
bids_dir = Path(retval.get(‘bids_dir’))
File “/public/apps/anaconda/3-5.2.0/lib/python3.6/pathlib.py”, line 999, in new
self = cls._from_parts(args, init=False)
File “/public/apps/anaconda/3-5.2.0/lib/python3.6/pathlib.py”, line 656, in _from_parts
drv, root, parts = self._parse_args(args)
File “/public/apps/anaconda/3-5.2.0/lib/python3.6/pathlib.py”, line 640, in _parse_args
a = os.fspath(a)
TypeError: expected str, bytes or os.PathLike object, not NoneType
Is this is an issue with one of the external dependencies having the correct path? I’m running freesurfer 6.0 and the license.txt file is in $FREESURFER_HOME so I don’t think that is the issue. Any other suggestions would be greatly appreciated.