Internal benchmarking/execution time for segmentation pipeline

[dkuegler]

This PR adds a simple timing option of the segmentation pipeline that runs automatically.

This is tested in the docker image. The general intention would be to include execution time monitoring and improvements between libraries and python versions.

There are a couple of open questions to answer:

• Should recon-surf.sh also switch over to logging execution times in a different file for clarity and standardization?
  • Not right now
• Should this option be "hidden" behind a flag or just always active?
  • Always active

[dkuegler]

--timeit and --timeit_log flags removed from run_fastsurfer.sh

[Copilot]

Pull request overview

This PR introduces infrastructure for measuring and logging execution time for the FastSurfer segmentation and surface pipelines, primarily via a new fs_time wrapper and a time_it helper, and wires this into run_fastsurfer.sh.

Changes:

• Extend run_fastsurfer.sh to define an execution-time log path (via FASTSURFER_EXECTIMELOG), ensure its directory exists, and wrap major segmentation and surface commands with a time_it helper so their runtimes are logged.
• Add a new time_it function and tighten error handling and batch-job management in recon_surf/functions.sh, including more consistent PIPESTATUS checks.
• Replace the local fs_time implementation with a more flexible version supporting additional flags (-a, --no-load, --debug) and improved formatting of timing output.

Reviewed changes

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

File	Description
run_fastsurfer.sh	Wires in execution-time logging: documents FASTSURFER_EXECTIMELOG, sets a default exec_time_log path, ensures its directory exists, and wraps key segmentation and surface commands with time_it, while slightly reformatting command arrays and improving surface failure messaging.
recon_surf/functions.sh	Introduces time_it to run commands under fs_time into a timing file, adjusts RunIt/run_it/run_it_cmdf and RunBatchJobs for clearer status handling and logging, and keeps timecmd detection in sync with the new fs_time interface.
recon_surf/fs_time	Reworks the fs_time helper with a new option parser, configurable load-logging behavior, and improved output formatting, aligning it with the new timing pipeline while maintaining compatibility with existing usage in the recon-surf tools.

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