Query regarding dMRIprep

Hi all,

I am looking to use dMRIprep to preprocess my diffusion MRI data. However, I seem to be facing a few issues with the code. I was wondering if anyone has faced this issue and could suggest some solutions for the same.

I am using Docker and the latest image (version 0.5.0) of dMRIprep. All the anatomical preprocessing proceeds fine. However, during the DWI data preprocessing, I encounter the following error:

Could not build path with entities {'subject': 'S1', 'direction': 'AP', 'suffix': 'valid', 'extension': 'svg', 'desc': 'eddy', 'datatype': 'figures'}.

The command I use is as follows:

sudo docker run -ti --rm -v $HOME/data/S1:/inputs \
-v $HOME/outputs/S1:/outputs \
-v $HOME/freesurfer:/freesurfer \
nipreps/dmriprep:latest /inputs /outputs participant \
--participant-label S1 --fs-license-file /freesurfer/license.txt --fs-no-reconall

I also tried using some of the older versions of the dmriprep image (versions 0.4.0 and 0.2.2). While I do not encounter the aforementioned error there, I find that dmriprep ends immediately after preprocessing the anatomical scans, with all the outputs, and does not proceed to preprocessing the DWI data.

I would be very grateful if someone could help me address these concerns. Please do let me know if you need further details.

Many thanks and regards,
Varsha

1 Like

I have experienced the same problem. I can’t figure out the solution at the moment, but have raised the issue in github at ValueError while building path · Issue #642 · nipreps/niworkflows · GitHub.

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