Unhandled Python exception

[granitz]

I'm running the following command: docker run -i --rm \ -v ~/data/:/bids_dataset \ -v ~/out:/output \ bids/mrtrix3_connectome \ /bids_dataset /output preproc --session_label store --participant_label x --skip-bids-validator -d

This yields the following error:

mrtrix3_connectome.py: [ERROR] Unhandled Python exception: mrtrix3_connectome.py: [ERROR] TypeError: endswith first arg must be str, unicode, or tuple, not list mrtrix3_connectome.py: [ERROR] Traceback: mrtrix3_connectome.py: [ERROR] /mrtrix3_connectome.py:4154 (in execute()) mrtrix3_connectome.py: [ERROR] output_app_path) mrtrix3_connectome.py: [ERROR] /mrtrix3_connectome.py:1130 (in run_preproc()) mrtrix3_connectome.py: [ERROR] for i in in_dwi_image_list): mrtrix3_connectome.py: [ERROR] /mrtrix3_connectome.py:1130 (in ()) mrtrix3_connectome.py: [ERROR] for i in in_dwi_image_list): mrtrix3_connectome.py: Scratch directory retained; location:

I Can't figure out what's causing this error.

[Lestropie]

That looks like the same error as was reported in #117, and is hopefully addressed by #118. However @lizannea reported that the proposed change in #118 did not resolve the error. I probably need to generate a dataset locally that replicates the exception and figure out why my fix didn't work; however I have higher priorities that I need to get to right now.

As a hack fix, you could:

• If you want the images in fmap/ to be used in DWI processing, make the contents of IntendedFor in the fmap/ JSONs just a string rather than a list, and specify just one of the input DWI paths in that string.
• If you don't want the images in fmap/ to be used in DWI processing, just delete them from the BIDS dataset.