Fix: Correct FastSurfer-CC error code handling and documentation formatting

[dkuegler]

Summary

This PR fixes the error code handling in the FastSurfer-CC (CorpusCallosum) module and corrects documentation formatting issues.

Changes Made

1. Error Code Handling (fastsurfer_cc.py)

• Fixed the error code return value in the main() function
• The function now correctly returns 0 on success or an error message string on failure
• Properly passed to sys.exit() to ensure correct process exit codes are communicated to the shell

2. Documentation Fixes

• Removed extra formatting characters ("===+") in FastSurfer-CC documentation
• Added proper heading to the argument parser's self-documentation

Motivation

Proper error code handling is critical for:

• Automated workflows and script pipelines that depend on exit codes
• CI/CD integration and error detection
• Correct reporting of pipeline failures to calling processes

The documentation fixes improve clarity and prevent build/documentation generation issues.

Files Modified

• CorpusCallosum/fastsurfer_cc.py - Error code handling in main function
• CorpusCallosum/README.md - Documentation formatting

Breaking Changes

None - this is a bug fix that corrects existing behavior.

Testing Recommendations

1. Test FastSurfer-CC with valid inputs and verify exit code is 0
2. Test FastSurfer-CC with invalid inputs (missing files, bad parameters) and verify non-zero exit code
3. Verify error messages are properly displayed
4. Check that documentation builds without warnings
5. Run existing test suite to ensure no regressions

Related Issues

Related to error handling improvements and documentation quality

Type

• Feature
• Bug Fix
• Documentation
• Code Quality/Refactoring

[Copilot]

Pull request overview

This PR aims to improve error code handling in the FastSurfer-CC (CorpusCallosum) module and includes several code quality improvements across multiple files. The primary goal is to align the error handling with the established pattern in the codebase where main functions return exit codes or error messages rather than calling sys.exit() directly.

Changes:

• Modified fastsurfer_cc.py main() function to return Literal[0] | str and wrapped the call with sys.exit() at the call site
• Renamed variable io_futures to futures throughout the file for improved clarity
• Added timing wrapper ${wrap[@]} to a command in run_fastsurfer.sh for consistent execution time logging
• Updated recon_surf/functions.sh to use ${BASH_SOURCE[0]} instead of $0 for proper path resolution in sourced scripts
• Enhanced documentation formatting in doc/scripts/fastsurfer_cc.rst with proper backticks and section headings

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 3 comments.

File	Description
CorpusCallosum/fastsurfer_cc.py	Updated return type from None to Literal[0] | str, renamed io_futures to futures, added error handling for failed futures, and wrapped main() call with sys.exit()
run_fastsurfer.sh	Added timing wrapper to reduce_to_aseg.py command (line 1012) and improved array append syntax (line 1278)
recon_surf/functions.sh	Changed from $0 to ${BASH_SOURCE[0]} for proper directory resolution in sourced scripts
doc/scripts/fastsurfer_cc.rst	Added command-line interface heading, changed start-line to skip title, and improved flag formatting with backticks

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.