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Describe the changes implemented in this pull request. If the changes fix a bug or resolves a feature request, be sure to link the issue. Please explain the issue and how the changes address the issue.
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Bugfix (non-breaking change which fixes an issue)
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Checklist
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Changes have been tested to ensure that fix is effective or that a feature works.
Changes pass the unit tests
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All PRs will undergo the unit testing before being reviewed. You may be requested to explain or make additional changes before the PR is accepted.
I was successfully able to run: ./scattr/scattr/run.py ~/graham/projects/ctb-akhanf/djay/synthstrip/ ~/graham/scratch/test-scattr participant --participant-label P003 --freesurfer_dir ~/graham/projects/ctb-akhanf/djay/fmriprep_all/sourcedata/freesurfer/ --dwi_dir ~/graham/projects/ctb-akhanf/mliu366/4_SNSX_7T/derivatives/prepdwi_v0.0.13/prepdwi/ --cores all --fs-license ~/graham/projects/ctb-akhanf/akhanf/opt/freesurfer/.license --show-failed-logs --use-conda --skip_thal_seg --bzero_thresh 50 --rerun-incomplete --filter-T1w desc=synthstrip --force-output --until tckgen --omit-from tckgen
Point to note though: I had to copy over zona_bb_subcortex dir to the output dir from when I ran the pipeline with the thalamic_segmentation rule before running the above pipeline.
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Proposed changes
Describe the changes implemented in this pull request. If the changes fix a bug or resolves a feature request, be sure to link the issue. Please explain the issue and how the changes address the issue.
Types of changes
What types of changes does your code introduce? Put an
xin the boxes that applyChecklist
Put an
xin the boxes that apply. You can also fill these out after creating the PR. If you are unsure about any of the choices, don't hesitate to ask!poe qualitytaskNotes
All PRs will undergo the unit testing before being reviewed. You may be requested to explain or make additional changes before the PR is accepted.