.. _5ttgen:

5ttgen
======

Synopsis
--------

Generate a 5TT image suitable for ACT

Usage
--------

::

    5ttgen algorithm [ options ] ...

-  *algorithm*: Select the algorithm to be used to complete the script operation; additional details and options become available once an algorithm is nominated. Options are: freesurfer, fsl, gif

Description
-----------

5ttgen acts as a 'master' script for generating a five-tissue-type (5TT) segmented tissue image suitable for use in Anatomically-Constrained Tractography (ACT). A range of different algorithms are available for completing this task. When using this script, the name of the algorithm to be used must appear as the first argument on the command-line after '5ttgen'. The subsequent compulsory arguments and options available depend on the particular algorithm being invoked.

Each algorithm available also has its own help page, including necessary references; e.g. to see the help page of the 'fsl' algorithm, type '5ttgen fsl'.

Options
-------

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

Standard options
^^^^^^^^^^^^^^^^

- **-continue <TempDir> <LastFile>** Continue the script from a previous execution; must provide the temporary directory path, and the name of the last successfully-generated file

- **-force** Force overwrite of output files if pre-existing

- **-help** Display help information for the script

- **-nocleanup** Do not delete temporary files during script, or temporary directory at script completion

- **-nthreads number** Use this number of threads in MRtrix multi-threaded applications (0 disables multi-threading)

- **-tempdir /path/to/tmp/** Manually specify the path in which to generate the temporary directory

- **-quiet** Suppress all console output during script execution

- **-info** Display additional information and progress for every command invoked

- **-debug** Display additional debugging information over and above the output of -info

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

--------------



**Author:** Robert E. Smith (robert.smith@florey.edu.au)

**Copyright:** Copyright (c) 2008-2018 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/

MRtrix3 is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty
of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

For more details, see http://www.mrtrix.org/

.. _5ttgen_freesurfer:

5ttgen freesurfer
=================

Synopsis
--------

Generate the 5TT image based on a FreeSurfer parcellation image

Usage
--------

::

    5ttgen freesurfer input output [ options ]

-  *input*: The input FreeSurfer parcellation image (any image containing 'aseg' in its name)
-  *output*: The output 5TT image

Options
-------

Options specific to the 'freesurfer' algorithm
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

- **-lut** Manually provide path to the lookup table on which the input parcellation image is based (e.g. FreeSurferColorLUT.txt)

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

Standard options
^^^^^^^^^^^^^^^^

- **-continue <TempDir> <LastFile>** Continue the script from a previous execution; must provide the temporary directory path, and the name of the last successfully-generated file

- **-force** Force overwrite of output files if pre-existing

- **-help** Display help information for the script

- **-nocleanup** Do not delete temporary files during script, or temporary directory at script completion

- **-nthreads number** Use this number of threads in MRtrix multi-threaded applications (0 disables multi-threading)

- **-tempdir /path/to/tmp/** Manually specify the path in which to generate the temporary directory

- **-quiet** Suppress all console output during script execution

- **-info** Display additional information and progress for every command invoked

- **-debug** Display additional debugging information over and above the output of -info

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

--------------



**Author:** Robert E. Smith (robert.smith@florey.edu.au)

**Copyright:** Copyright (c) 2008-2018 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/

MRtrix3 is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty
of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

For more details, see http://www.mrtrix.org/

.. _5ttgen_fsl:

5ttgen fsl
==========

Synopsis
--------

Use FSL commands to generate the 5TT image based on a T1-weighted image

Usage
--------

::

    5ttgen fsl input output [ options ]

-  *input*: The input T1-weighted image
-  *output*: The output 5TT image

Options
-------

Options specific to the 'fsl' algorithm
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

- **-t2 <T2 image>** Provide a T2-weighted image in addition to the default T1-weighted image; this will be used as a second input to FSL FAST

- **-mask** Manually provide a brain mask, rather than deriving one in the script

- **-premasked** Indicate that brain masking has already been applied to the input 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

Standard options
^^^^^^^^^^^^^^^^

- **-continue <TempDir> <LastFile>** Continue the script from a previous execution; must provide the temporary directory path, and the name of the last successfully-generated file

- **-force** Force overwrite of output files if pre-existing

- **-help** Display help information for the script

- **-nocleanup** Do not delete temporary files during script, or temporary directory at script completion

- **-nthreads number** Use this number of threads in MRtrix multi-threaded applications (0 disables multi-threading)

- **-tempdir /path/to/tmp/** Manually specify the path in which to generate the temporary directory

- **-quiet** Suppress all console output during script execution

- **-info** Display additional information and progress for every command invoked

- **-debug** Display additional debugging information over and above the output of -info

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

* Smith, S. M. Fast robust automated brain extraction. Human Brain Mapping, 2002, 17, 143-155

* Zhang, Y.; Brady, M. & Smith, S. Segmentation of brain MR images through a hidden Markov random field model and the expectation-maximization algorithm. IEEE Transactions on Medical Imaging, 2001, 20, 45-57

* Patenaude, B.; Smith, S. M.; Kennedy, D. N. & Jenkinson, M. A Bayesian model of shape and appearance for subcortical brain segmentation. NeuroImage, 2011, 56, 907-922

* Smith, S. M.; Jenkinson, M.; Woolrich, M. W.; Beckmann, C. F.; Behrens, T. E.; Johansen-Berg, H.; Bannister, P. R.; De Luca, M.; Drobnjak, I.; Flitney, D. E.; Niazy, R. K.; Saunders, J.; Vickers, J.; Zhang, Y.; De Stefano, N.; Brady, J. M. & Matthews, P. M. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 2004, 23, S208-S219

--------------



**Author:** Robert E. Smith (robert.smith@florey.edu.au)

**Copyright:** Copyright (c) 2008-2018 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/

MRtrix3 is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty
of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

For more details, see http://www.mrtrix.org/

.. _5ttgen_gif:

5ttgen gif
==========

Synopsis
--------

Generate the 5TT image based on a Geodesic Information Flow (GIF) segmentation image

Usage
--------

::

    5ttgen gif input output [ options ]

-  *input*: The input Geodesic Information Flow (GIF) segmentation image
-  *output*: The output 5TT image

Options
-------

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

Standard options
^^^^^^^^^^^^^^^^

- **-continue <TempDir> <LastFile>** Continue the script from a previous execution; must provide the temporary directory path, and the name of the last successfully-generated file

- **-force** Force overwrite of output files if pre-existing

- **-help** Display help information for the script

- **-nocleanup** Do not delete temporary files during script, or temporary directory at script completion

- **-nthreads number** Use this number of threads in MRtrix multi-threaded applications (0 disables multi-threading)

- **-tempdir /path/to/tmp/** Manually specify the path in which to generate the temporary directory

- **-quiet** Suppress all console output during script execution

- **-info** Display additional information and progress for every command invoked

- **-debug** Display additional debugging information over and above the output of -info

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

--------------



**Author:** Matteo Mancini (m.mancini@ucl.ac.uk)

**Copyright:** Copyright (c) 2008-2018 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/

MRtrix3 is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty
of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

For more details, see http://www.mrtrix.org/

