Comments (2)
richford
commented on August 21, 2024
List of potential commands:
dmripreprun the BIDS appdmriprep-data(non BIDS-app compliant command) takes in source, spits out local dir with downloaded filesdmriprep-testrun dmriprep with/without PA/AP filenames, with niter=1 for eddy correction
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richford
commented on August 21, 2024
Need two separate docker workflows (possibly necessetating two difference Dockerfiles). One for BIDS app only, the other for development. BIDS version should have dmriprep entrypoint. Dev version should include ipython and have bash entrypoint.
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Related Issues (20)
- Use `get_bval` and `get_bvec` to get bval/bvec files
- Cannot run dMRIPrep. Missing dependencies:antsAI (Interface: AI)
- dMRIprep 0.5.0: No folder output dir of dwi created HOT 5
- Archive this project? HOT 1
- add another postprocessing step to HBN study data -- rename AP/PA fmaps
- nibabel get_data vs get_fdata HOT 5
- ENH: Two pipelines HOT 4
- Cloudknot Freesurfer
- ENH: Optional preprocessing steps for denoising, unringing and upsampling HOT 3
- For `data.Study` object, maybe the `s3_prefix` input should default to None?
- regenerate neurodocker docker file with min version of Freesurfer
- Longitudinal pipeline
- make a CLI that would run docker with the dependencies in it HOT 1
- End-to-end testing
- Add a docker entry point
- Handle multiple runs in the same session
- Handle cases where field-map is collected with a different resolution than the dwi HOT 1
- Two phase encode directions, but no field maps
- Replace Freesurfer registration with DIPY-based registration
- Doesn't work with no field maps
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