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Cleanup - Merge main1639 and main pipelines #15

@robdahn

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@robdahn

As the "enhanced" pipeline (cat_run/cat_main) was performing worse in normal data, a previous pipeline (r1639) was reactivated and currently used as default for T1 processing (cat_run1639/cat_main1639). However, both function should be merged, to keep the better results in standard T1 and at once to use the new backup functions, simpler structure and enhanced T2/PD processing.

  • Backup-functions: Integrate backup-funktion of the cat_run pipeline into cat_main*1639er sub-functions and finally remove the 1639er pipeline. Better to do this step by step ...
  • cat_vol_partvol1639 (minor changes, i.e. 1639 could be replaced by a newer version)
  • cat_main_clean_gwc1639 (medium changes, additional harder cleanups (new>1), multiple different calls)
  • cat_main_updateSPM1639 (many changes, +registration update, +inv skull-stripping)
  • cat_main_gintnorm1639 (major changes, -PD/T2 inversion)
  • cat_main1639
  • cat_run_job1639

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CleanupRemoving of old/unused/unfinished functionsenhancementNew feature or request

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