Update documentation for 5ttgen msmt addition

docs/reference/commands/5ttgen.rst

@@ -15,7 +15,7 @@ Usage
 
     5ttgen algorithm [ options ] ...
 
--  *algorithm*: Select the algorithm to be used; additional details and options become available once an algorithm is nominated. Options are: freesurfer, fsl, gif, hsvs
+-  *algorithm*: Select the algorithm to be used; additional details and options become available once an algorithm is nominated. Options are: freesurfer, fsl, gif, hsvs, msmt
 
 Description
 -----------
@@ -476,3 +476,101 @@ See the Mozilla Public License v. 2.0 for more details.
 
 For more details, see http://www.mrtrix.org/.
 
+.. _5ttgen_msmt:
+
+5ttgen msmt
+===========
+
+Synopsis
+--------
+
+Generate a 5TT image from ODF images
+
+Usage
+-----
+
+::
+
+    5ttgen msmt odf_wm odf_gm odf_csf output [ options ]
+
+-  *odf_wm*: The input white matter ODF
+-  *odf_gm*: The input grey matter ODF
+-  *odf_csf*: The input cerebrospinal fluid ODF
+-  *output*: The output 5TT image
+
+Description
+-----------
+
+If the user does not manually provide a brain mask using the -mask option, the command will automatically determine a mask for the output 5TT image; this is necessary to conform to the expectations of the 5TT format. This mask will be computed based on where the sum of the ODFs exceeds 50% of what is expected from a voxel that contains a DWI signal that exactly matches one of the response functions.
+
+Options
+-------
+
+Options specific to the 'msmt' algorithm
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+- **-mask image** An input binary brain mask image
+
+Options common to all 5ttgen algorithms
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+- **-nocrop** Do NOT crop the resulting 5TT image to reduce its size (keep the same dimensions as the input image)
+
+- **-sgm_amyg_hipp** Represent the amygdalae and hippocampi as sub-cortical grey matter in the 5TT image
+
+Additional standard options for Python scripts
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+- **-nocleanup** do not delete intermediate files during script execution, and do not delete scratch directory at script completion.
+
+- **-scratch /path/to/scratch/** manually specify an existing directory in which to generate the scratch directory.
+
+- **-continue ScratchDir LastFile** continue the script from a previous execution; must provide the scratch directory path, and the name of the last successfully-generated file.
+
+Standard options
+^^^^^^^^^^^^^^^^
+
+- **-info** display information messages.
+
+- **-quiet** do not display information messages or progress status. Alternatively, this can be achieved by setting the MRTRIX_QUIET environment variable to a non-empty string.
+
+- **-debug** display debugging messages.
+
+- **-force** force overwrite of output files.
+
+- **-nthreads number** use this number of threads in multi-threaded applications (set to 0 to disable multi-threading).
+
+- **-config key value**  *(multiple uses permitted)* temporarily set the value of an MRtrix config file entry.
+
+- **-help** display this information page and exit.
+
+- **-version** display version information and exit.
+
+References
+^^^^^^^^^^
+
+* Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. Anatomically-constrained tractography: Improved diffusion MRI streamlines tractography through effective use of anatomical information. NeuroImage, 2012, 62, 1924-1938
+
+Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch, M.; Christiaens, D.; Jeurissen, B.; Yeh, C.-H. & Connelly, A. MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. NeuroImage, 2019, 202, 116137
+
+--------------
+
+
+
+**Author:** Arkiev D'Souza ([email protected]) & Robert E. Smith ([email protected])
+
+**Copyright:** Copyright (c) 2008-2024 the MRtrix3 contributors.
+
+This Source Code Form is subject to the terms of the Mozilla Public
+License, v. 2.0. If a copy of the MPL was not distributed with this
+file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
+Covered Software is provided under this License on an "as is"
+basis, without warranty of any kind, either expressed, implied, or
+statutory, including, without limitation, warranties that the
+Covered Software is free of defects, merchantable, fit for a
+particular purpose or non-infringing.
+See the Mozilla Public License v. 2.0 for more details.
+
+For more details, see http://www.mrtrix.org/.
+