Cleanup 2024a

[robdahn]

Code cleanup, documentation, and maintenance (2024a): As CAT12 has become more or less mature it is time to document and clean up unused functions, uncommented code blocks and connected or outdated parameters. This issue should help to organise this process.

• [ ] SegmentBatch: estimate dependencies is quite slow
• [ ] affscale: Improve documentation and help. Add artificial test case?
• [ ] cat_vol_morph: Enhance documentation etc.
• [ ] cat_vol_sanlm2180: Failed update.
• [ ] cat_vol_sanlm2: Unknown status (20220816).
• [ ] cat_vol_report cleanup and comments:
• [ ] cat_vol_report update:
  • [ ] remove all uses of k-means thickness (only used for developers, not working as hoped)
  • [ ] add BIDS directory path if used (helpful for comparison) in first line as "/[../..path/]"
  • [ ] add number of used cores close to "Processing time (n/n-cores)" (multiple cores slow down processing), add also processor & RAM? (expert)
  • [ ] add processing data & time (YYYYMMDD-hhmm) in first line "Version" (helpful for comparison)
  • [ ] T1w or p0-based surface reconstruction setting behind SRP (expert)
• [ ] check (buggy) corrections of head classes (cat_vol_main[1639][_updateSPM], cat_main_LAS)
• [ ] BIDS handling: There are bugs in handling the paths