-parc fs_2005 unrecongized

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.

Hi Aaron,

The issue is in your docker run call; specifically this line:
bids/example \
You’re executing the BIDS Apps example container, rather than the MRtrix3_connectome container. This is why the -parc option is unrecognised. You can also tell from the fact that the script is simply running bet on the input T1; the MRtrix3_connectome container no longer uses this command (and it certainly was never the first & only step).

I’ve put a bit of effort into the script over the last couple of weeks so I hope it works out OK (use the 0.1.1 version if you can). Though I feel I should clarify straight out of the gate that this container is not officially “a part of MRtrix3”, but a solo derivative project thereof.


Thanks so much! I am new to this, and I have run several apps and not made that obvious mistake. Thanks for pointing it out. I used the commands from the documentation.

Now the app begins to run but I hit this error:

[ERROR] Unable to locate valid diffusion gradient table for image ‘/bids_dataset/sub-01/dwi/sub-01_ses-test_dwi.nii.gz’

I guess the data that I am using does not have all of the required files?

Yes, processing can’t possibly continue if a diffusion gradient table is not available. The BIDS specification gives instructions regarding how and where this information needs to be provided.