DWI preprocessing #13
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Could you rebase or merge master? |
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Could you also remove those XML files - I think they were added by accident. |
chrisgorgo
suggested changes
Mar 23, 2017
run.py
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| dwiname = "Diffusion" + "_dir-" + dirnum + "_" + session + "_corr" | ||
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| diracqs = [x for x in acqs if dirnum in x] | ||
| if "AP" or "PA" in diracqs: |
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You need to use the metadata in the sidecar JSON file instead of file names - we cannot rely on those. You can easily access it via get_metadata method from pybids.
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It's a good starting point! Let me know if you have any questions. |
chrisgorgo
reviewed
Apr 14, 2017
run.py
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| print('\n', cmd, '\n') | ||
| # run(cmd, cwd=args["path"], env={"OMP_NUM_THREADS": str(args["n_cpus"])}) | ||
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| def run_task_fmri_analysis(**args): |
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Let's leave this for another PR.
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The task FMRI processing that is.
chrisgorgo
reviewed
Apr 14, 2017
run.py
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| subject=subject_label, type='dwi', | ||
| extensions=["nii.gz", "nii"])) | ||
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| for session in numruns: |
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why not call it "run" instead of "session"? it would be less confusing
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Implementation of HCP minimal preprocessing pipeline's diffusion preprocessing.
Supports multiple runs (i.e. run-01, run-02) and directions (i.e. dir98, dir99). Requires both phase encodings (i.e. LR and RL or AP and PA).
Example BIDS compatible naming scheme:
sub-01_acq-dir98AP_run-01_dwi.bval
sub-01_acq-dir98AP_run-01_dwi.bvec
sub-01_acq-dir98AP_run-01_dwi.nii.gz
sub-01_acq-dir98AP_run-01_dwi.json
sub-01_acq-dir98AP_run-01_sbref.nii.gz
sub-01_acq-dir98AP_run-01_sbref.json
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etc.
Perhaps in the future, the naming scheme could be similar to this.