Minor bugfixes and docfixes#805
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Pull request overview
This PR adjusts run_fastsurfer.sh to restore intended module/argument behavior (notably around --no_biasfield) and updates user-facing documentation to match the updated behavior.
Changes:
- Update CLI/help + docs to clarify
--no_biasfieldbehavior, especially for HypVINN. - Fix a bash conditional so the asegdkt stats step only runs when
run_asegdkt_moduleis actually enabled. - Pass the preprocessed T2 path (
$norm_name_t2) into HypVINN even when--no_biasfieldis used.
Reviewed changes
Copilot reviewed 3 out of 3 changed files in this pull request and generated 1 comment.
| File | Description |
|---|---|
run_fastsurfer.sh |
Fixes a truthy-string bash bug and corrects HypVINN --t2 argument wiring; updates CLI help text. |
doc/scripts/RUN_FASTSURFER.md |
Updates --no_biasfield documentation to reflect HypVINN behavior. |
README.md |
Updates HypVINN module description regarding stats and biasfield recommendation. |
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dkuegler
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Still needs a couple smaller changes
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@dkuegler: Please have a quick look at 7fd07fd and 5bc53ba - these are one line changes. I think I restored the intended behaviour, but it would be good if you could double check