Fmriprep Sentry error

fmriprep
bids

#1

Hello,

Can someone please help me make sense of the error below. I am trying to run fmriprep v1.2.6-1 on my first test cases. The dataset is BIDS valid (checked on validator online and the dataset comes up as valid within the fmriprep test).

The command used in the Linux shell is:
fmriprep /m/shared/Suyash/testdata/tmp_BIDS/ /m/InProcess/3T/NABM/fMRI/fMRIprep_output/ participant --participant_label sub-188 -w /m/InProcess/3T/NABM/fMRI/work/ --ignore slicetiming --sloppy

The error is a sentry error that I can’t make sense of. Am I missing one of the dependencies for fmriprep or missing a flag in the command?

Traceback (most recent call last):
  File "/home/vhasfctersaa/projects/nabm/nabm/bin/fmriprep", line 11, in <module>
    load_entry_point('fmriprep==1.2.6.post1', 'console_scripts', 'fmriprep')()
  File "/home/vhasfctersaa/projects/nabm/nabm/lib64/python3.6/site-packages/fmriprep/cli/run.py", line 357, in main
    default_license = str(Path(os.getenv('FREESURFER_HOME')) / 'license.txt')
  File "/usr/lib64/python3.6/pathlib.py", line 999, in __new__
    self = cls._from_parts(args, init=False)
  File "/usr/lib64/python3.6/pathlib.py", line 656, in _from_parts
    drv, root, parts = self._parse_args(args)
  File "/usr/lib64/python3.6/pathlib.py", line 640, in _parse_args
    a = os.fspath(a)
TypeError: expected str, bytes or os.PathLike object, not NoneType
Sentry is attempting to send 1 pending error messages
Waiting up to 2.0 seconds
Press Ctrl-C to quit

Thanks for the help.


#2

Hi @atersakyan,

fMRIPrep is having trouble to find your freesurfer license file. Please, check this tutorial to learn more about how to get the file and make fMRIPrep aware of it.

It would be greatly helpful if you posted how you are running fMRIPrep (in particular, whether you are using containers or not).


#3

Thank you for the help.

We are running fMRIPrep in a python virtual environment due to Docker issues on our network, but we are working on moving to Docker.


#4

In that case, please define a FS_LICENSE environment variable, pointing to the license file.

However, the fact that the FREESURFER_HOME environment variable is not set makes me doubtful that your environment is correctly set up. Please make sure that all the external dependencies are correctly installed. For instance, not having FREESURFER_HOME set indicates that freesurfer is not available.