Hello. I am trying to run the bids/mrtrix3_connectome app using the following commands:
docker run -i --rm \
-v /Users/ajacobson/Desktop/BIDSMRTRIX3/cfmridti:/bids_dataset \
-v /Users/ajacobson/Desktop/BIDSMRTRIX3/outputs:/outputs \
bids/example \
/bids_dataset /outputs participant --participant_label 01 -parc fs_2005
I am getting an error:
run.py: error: unrecognized arguments: -parc fs_2005
When I try to run it without this argument I get the following:
This dataset appears to be BIDS compatible.
Summary: Available Tasks: Available Modalities:
7 Files, 76.8MB T1w
1 - Subject dwi
1 - Session
bet /bids_dataset/sub-01/anat/sub-01_T1w.nii.gz /outputs/sub-01_brain.nii.gz
At that point nothing happens… I get no output and the process seems to stop.
I am noew to this app and would be very appreciative of any suggestions that anyone might have as to why -parc is not recognized, or why the command without -parc seems to do nothing.
Thanks so much.