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5ttgen hsvs: Multiple changes / fixes#3076

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Lestropie merged 1 commit intodevfrom
5ttgen_hsvs_fixes
Mar 12, 2025
Merged

5ttgen hsvs: Multiple changes / fixes#3076
Lestropie merged 1 commit intodevfrom
5ttgen_hsvs_fixes

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  • Fix progress bar for when FSL FAST is not used for the cerebellum, and the FreeSurfer segmentations of the cerebellar hemispheres are propagated to the 5TT image.
  • New option -freesurfer_lut, for manually specifying the location of the FreeSurfer lookup table file; this permits utilisation of the script without environment variable FREESURFER_HOME being set, or indeed even the FreeSurfer software being present (related to Docker: No third-party software embedding #3073).
  • Add missing citations to help page documentation.

- Fix progress bar for when FSL FAST is not used for the cerebellum, and the FreeSurfer segmentations of the cerebellar hemispheres are propagated to the 5TT image.
- New option -freesurfer_lut, for manually specifying the location of the FreeSurfer lookup table file; this permits utilisation of the script without environment variable FREESURFER_HOME being set, or indeed even the FreeSurfer software being present (related to #3073).
- Add missing citations to help page documentation.
@Lestropie Lestropie merged commit 604307b into dev Mar 12, 2025
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@Lestropie Lestropie deleted the 5ttgen_hsvs_fixes branch March 12, 2025 03:02
@Lestropie Lestropie restored the 5ttgen_hsvs_fixes branch August 26, 2025 07:51
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