MRtrix3_connectome
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bids-apps
Generate subject connectomes from raw BIDS data & perform inter-subject connection density normalisation, using the MRtrix3 software package.
Currently, the code does the following: 1. Generate pseudo-T1w image from b=0 2. Generate pseudo-b=0 from T1w 3. Register between DWI-pseudo-T1w and T1w 4. Register between T1w-pseudo-b=0 and DWI b=0...
Had to address #123 due to it precluding processing of data in my own lab. Results in increment to version `0.6.0` as the incorporation of `dwicat` will result in a...
Need to be able to support data for which execution otherwise fails with [this error](https://github.com/bids-apps/MRtrix3_connectome/blob/0.5.3/mrtrix3_connectome.py#L1097-L1099). 1. Wait until denoising and Gibbs ringing removal have been completed 2. Define the average...
I have run the docker by the command with preproc mode. And I noticed that it generated a scratch folder. How can I store it or find it? I need...
relates to https://github.com/bids-apps/maintenance-tools/issues/7
`python2` is currently installed during container construction in order to execute `fslinstaller.py`. It appears as though this script has since been updated for Python3 compatibility.
Hi @Remi-Gau, Just bundling these together so that they all go to `master` in a single merge commit, there's a clean visible diff across the lot, and any relevant discussions...
As discussed here: https://github.com/BIDS-Apps/MRtrix3_connectome/issues/81
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...
The Docker file does not seem to contain any kind of CUDA installation. Is there any kind of future plan to extend this app with GPU support? `mrtrix3_connectome.py: [WARNING] CUDA...
