Integrate into bids tree #30
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Made the code work for my data.
Adds stable parallel/serial processing and BIDS-App style inputs.
Updated the CLI display block
- Changed and moved print statements in deface.py - Removed chunksize arument from parallel processing - Pulled keys in generate_mappings.py function when acqtime is present
- Update shutil.move() to use absolute paths - Update the afni refacer cmd to use only one core, OMP_NUM_THREADS=1
Trying the pathlib Path.rename() function
Finally fixed the little shutil.move command
Broke a variable name during the last merge, fixed here
Hefty bunch of mini-edits to the README for this branch.
Wonderful additions! Co-authored-by: Arshitha Basavaraj <[email protected]>
Accepting per suggestion. Co-authored-by: Arshitha Basavaraj <[email protected]>
Accepting more per previous suggestion. Co-authored-by: Arshitha Basavaraj <[email protected]>
- change participant_label and session_id to default to None - add accompanying flow control logic for using None as the default
BIDS App preparation and serial/parallel behavior
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@ericearl The branch protections I've configured for the repo requires at least one reviewer's approval. This PR is only merging |
ericearl
reviewed
Apr 26, 2023
README.md
Outdated
| - **Other/Secondary Scans:** All scans *except* the primary scan are grouped together and referred to as "other" or | ||
| "secondary" scans for a given session. | ||
| - **Mapping File:** A JSON file that assigns/maps a primary scan (or `primary_t1`) to all other scans within a session. | ||
| Please find an example file [here](FILLINTHEBLANK). |
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@Arshitha Remember to FILLINTHEBLANK here.
ericearl
reviewed
Apr 26, 2023
| 2. Deface primary scans | ||
| with [@afni_refacer_run](https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/refacer/refacer_run.html) program | ||
| developed by the AFNI Team. | ||
| 3. To deface remaining scans in the session, register them to the primary scan (using FSL `flirt` command) and then use | ||
| the primary scan's defacemask to generate a defaced image (using `fslmaths` command). | ||
| 4. Visually inspect defaced scans with [VisualQC](https://raamana.github.io/visualqc) deface tool or any other preferred | ||
| tool. | ||
| 5. Correct/fix defaced scans that failed visual inspection. See [here]() for more info on types of failures. | ||
| 5. Correct/fix defaced scans that failed visual inspection. See [here](FILLINTHEBLANK) for more info on types of failures. |
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@ericearl This blank will be filled out in the upcoming PR. I'm putting together a google doc to put down types of failures and their fixes before updating the README.
ericearl
requested changes
Apr 26, 2023
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Merging changes from
eric-testingbranch to main with this PR