From 58da1477ffb24778b89300c9c4d05f9707adf61f Mon Sep 17 00:00:00 2001 From: NicDC Date: Sat, 23 Nov 2024 20:11:55 +1100 Subject: [PATCH] Added info about consequences of using -white_stem in 5ttgen hsvs Manual cherry-pick from ff6c6ddb77f50975ee988edf4f339450c43cc07f (#2330). --- docs/reference/commands/5ttgen.rst | 2 +- lib/mrtrix3/_5ttgen/hsvs.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/reference/commands/5ttgen.rst b/docs/reference/commands/5ttgen.rst index 664161daac..2bee738fa2 100644 --- a/docs/reference/commands/5ttgen.rst +++ b/docs/reference/commands/5ttgen.rst @@ -399,7 +399,7 @@ Options - **-thalami** Select method to be used for thalamic segmentation; options are: nuclei,first,aseg -- **-white_stem** Classify the brainstem as white matter +- **-white_stem** Classify the brainstem as white matter; streamlines will not be permitted to terminate within this region Options common to all 5ttgen algorithms ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ diff --git a/lib/mrtrix3/_5ttgen/hsvs.py b/lib/mrtrix3/_5ttgen/hsvs.py index 8b0407cabc..2fca45f3b8 100644 --- a/lib/mrtrix3/_5ttgen/hsvs.py +++ b/lib/mrtrix3/_5ttgen/hsvs.py @@ -43,7 +43,7 @@ def usage(base_parser, subparsers): #pylint: disable=unused-variable parser.add_argument('-template', help='Provide an image that will form the template for the generated 5TT image') parser.add_argument('-hippocampi', choices=HIPPOCAMPI_CHOICES, help='Select method to be used for hippocampi (& amygdalae) segmentation; options are: ' + ','.join(HIPPOCAMPI_CHOICES)) parser.add_argument('-thalami', choices=THALAMI_CHOICES, help='Select method to be used for thalamic segmentation; options are: ' + ','.join(THALAMI_CHOICES)) - parser.add_argument('-white_stem', action='store_true', help='Classify the brainstem as white matter') + parser.add_argument('-white_stem', action='store_true', help='Classify the brainstem as white matter; streamlines will not be permitted to terminate within this region') parser.add_citation('Smith, R.; Skoch, A.; Bajada, C.; Caspers, S.; Connelly, A. Hybrid Surface-Volume Segmentation for improved Anatomically-Constrained Tractography. In Proc OHBM 2020') parser.add_citation('Fischl, B. Freesurfer. NeuroImage, 2012, 62(2), 774-781', is_external=True) parser.add_citation('Iglesias, J.E.; Augustinack, J.C.; Nguyen, K.; Player, C.M.; Player, A.; Wright, M.; Roy, N.; Frosch, M.P.; Mc Kee, A.C.; Wald, L.L.; Fischl, B.; and Van Leemput, K. A computational atlas of the hippocampal formation using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation of in vivo MRI. NeuroImage, 2015, 115, 117-137', condition='If FreeSurfer hippocampal subfields module is utilised', is_external=True)