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Added info about consequences of using -white_stem in 5ttgen hsvs #3042

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Feb 6, 2025
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Added info about consequences of using -white_stem in 5ttgen hsvs #3042

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2 changes: 1 addition & 1 deletion docs/reference/commands/5ttgen.rst
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Expand Up @@ -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
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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2 changes: 1 addition & 1 deletion lib/mrtrix3/_5ttgen/hsvs.py
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Expand Up @@ -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)
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