FIX pass freesurfer_subject_dir to get_surf() in cut_surface() (#591)

[mvdoc]

Summary

Fixes #591

• Pass freesurfer_subject_dir parameter to both freesurfer.get_surf() calls in cut_surface() function
• Add regression tests to verify the fix

Problem

The cut_surface() function in cortex/segment.py accepts a freesurfer_subject_dir parameter but was not passing it to the freesurfer.get_surf() calls on lines 189-190. This caused a KeyError when the SUBJECTS_DIR environment variable was not set.

Solution

Pass the freesurfer_subject_dir parameter to both get_surf() calls:

ipt, ipoly, inrm = freesurfer.get_surf(
    fs_subject, hemi, "inflated", freesurfer_subject_dir=freesurfer_subject_dir
)
fpt, fpoly, fnrm = freesurfer.get_surf(
    fs_subject, hemi, "fiducial", freesurfer_subject_dir=freesurfer_subject_dir
)

Test plan

• Added regression test verifying freesurfer_subject_dir is passed to get_surf() calls
• Added test for error handling when SUBJECTS_DIR is not set
• Added backward compatibility test when using SUBJECTS_DIR environment variable
• All new tests pass: pytest cortex/tests/test_segment.py -v
• Full test suite passes (except pre-existing unrelated failure)

🤖 Generated with Claude Code

[Copilot]

Pull request overview

This pull request fixes issue #591 where the cut_surface() function in cortex/segment.py was not passing the freesurfer_subject_dir parameter to internal freesurfer.get_surf() calls, causing a KeyError when the SUBJECTS_DIR environment variable was not set.

Changes:

• Fixed cut_surface() to pass freesurfer_subject_dir to both get_surf() calls for inflated and fiducial surfaces
• Added comprehensive regression tests to verify the fix and ensure backward compatibility
• Applied code formatting improvements throughout cortex/segment.py (quote style, line breaks, spacing)

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.

File	Description
cortex/segment.py	Fixed the bug by passing freesurfer_subject_dir to get_surf() calls on lines 205-210; also includes extensive formatting improvements throughout the entire file
cortex/tests/test_segment.py	New test file with comprehensive test coverage for the fix, including regression tests, error handling tests, and backward compatibility tests

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