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docs(segment): added **kwargs in docstrings - #693

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AgarwalNilay wants to merge 2 commits into
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evi-hendrikx:docs/segment-docstrings
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docs(segment): added **kwargs in docstrings#693
AgarwalNilay wants to merge 2 commits into
gallantlab:mainfrom
evi-hendrikx:docs/segment-docstrings

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init_subject's **kwargs (forwarded to freesurfer.autorecon, plus the deprecated run_all alias) and cut_surface's **kwargs (forwarded to freesurfer.flatten or flatten_slim depending on flatten_with) were both undocumented. Adds indented **kwargs entries listing each forwarded argument individually.

…rface

init_subject's **kwargs (forwarded to freesurfer.autorecon, plus the
deprecated run_all alias) and cut_surface's **kwargs (forwarded to
freesurfer.flatten or flatten_slim depending on flatten_with) were
both undocumented. Adds indented **kwargs entries listing each
forwarded argument individually.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
@AgarwalNilay
AgarwalNilay force-pushed the docs/segment-docstrings branch from 32d433b to cf3169d Compare August 24, 2026 16:37
Comment thread cortex/segment.py Outdated
Comment thread cortex/segment.py
Comment thread cortex/segment.py Outdated
@sjshim sjshim self-assigned this Aug 31, 2026
Address review feedback: rather than restating forwarded kwargs in
init_subject/cut_surface (which duplicates docs across files and lets
them drift), point at the function that owns them and document each
parameter once, where it's actually defined:

- autorecon(): add parallel, n_cores (were documented nowhere).
- flatten_slim(): add n_iterations, do_flatten (were documented
  nowhere).
- init_subject/cut_surface: condense **kwargs to a pointer plus a hint
  at the useful ones.

save_every and slim_path already had docs in freesurfer.flatten() and
flatten_slim() respectively, so the pointers now resolve for every
forwarded kwarg.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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5 participants