Remove corpus callosum processing from surface pipeline

[dkuegler]

This PR changes where the corpus callosum is run. It is no longer run in the surface pipeline, but now only checked. The surface pipeline terminates with error if mri/aseg.auto.mgz, the aseg with CC inpainted, is missing.
The PR also includes some flag filtering and cleanup and minor documentation fixes.

Remove corpus callosum processing from recon-surf.sh
Make sure the corpus callosum_seg variable gets set in the main process not just the subshell.
Add Corpus Callosum Paper Reference to run_fastsurfer.sh help text.
Fix --norm_name help text in run_fastsurfer.sh
Add asegdkt and corpus callosum dependency of surface pipeline in README.md
Filter corpus callosum and other "unused" flags for long_prepare_template.sh

[Copilot]

Pull request overview

This PR moves corpus callosum (CC) processing out of the surface pipeline and makes the surface pipeline depend on segmentation outputs (specifically an aseg with CC inpainted). It also cleans up/filters some flags and updates user-facing documentation/help text accordingly.

Changes:

• Remove CC segmentation/inpainting execution from recon-surf.sh and instead require mri/aseg.auto.mgz to exist.
• Fix CC module execution flow in run_fastsurfer.sh so failures propagate correctly and callosum_seg updates aren’t lost due to subshell scope.
• Update CLI help/README and adjust flag filtering in long_prepare_template.sh.

Reviewed changes

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

File	Description
run_fastsurfer.sh	Help text updates + CC module control-flow fix to propagate exit codes and update callosum_seg in the main shell.
recon_surf/recon-surf.sh	Removes CC processing from surface pipeline and adds prerequisite check for aseg.auto.mgz.
recon_surf/long_prepare_template.sh	Filters/ignores additional flags to better interoperate with higher-level longitudinal wrappers.
README.md	Documentation updates to reflect correct flags and new surface prerequisites.

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