Optimization for long_fastsurfer, one view only for skull stripping #659
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…nclude. - parser_defaults.py: Allow empty or none for --cfg_ax, --cfg_sag, --cfg_cor. - run_prediction.py: If cgf_ax/sag/cor is none/empty, do not use that view - some formatting cleanup
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This PR optimizes fastsurfer so that the skull stripping needed for longitudinal registration only uses one fastsurfer view.
Currently, run_prediction cannot be configured to only run on one view. But if it could, long_prepare_template would likely only need one view to compute the brainmask. Maybe we can even deactivate aseg and asegdkt output to save up time and disk space. This would then speed up this initial step.
Step 1: Modify run_prediction so the user is able to "deselect" views that should not be included. Syntax (example)
--cfg_ax noneStep 2 (optional) Modify run_predicrion so the user is able to "deselect" certain outputs. Syntax: no
--aseg_namemeans no aseg, unsure about--asegdkt_segfilemaybe none.Step 3: Test how reliable different view predict the brainmask.
Step 4: implement the best view for
long_prepare_template.sh.Step 5: Test impact on longitudinal pipeline.