5ttgen freesurfer¶
Synopsis¶
5ttgen freesurfer [ options ] input output
- input: The input FreeSurfer parcellation image (any image containing ‘aseg’ in its name)
- output: The output 5TT image
Description¶
Generate the 5TT image based on a FreeSurfer parcellation 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
- -verbose Display additional information for every command invoked
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
- If using ‘fsl’ algorithm: Smith, S. M. Fast robust automated brain extraction. Human Brain Mapping, 2002, 17, 143-155
- If using ‘fsl’ algorithm: 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
- If using ‘fsl’ algorithm: 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
- If using ‘fsl’ algorithm: 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) 2008-2016 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/
MRtrix 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 www.mrtrix.org
5ttgen fsl¶
Synopsis¶
5ttgen fsl [ options ] input output
- input: The input T1-weighted image
- output: The output 5TT image
Description¶
Use FSL commands to generate the 5TT image based on a T1-weighted 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
- -verbose Display additional information for every command invoked
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
- If using ‘fsl’ algorithm: Smith, S. M. Fast robust automated brain extraction. Human Brain Mapping, 2002, 17, 143-155
- If using ‘fsl’ algorithm: 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
- If using ‘fsl’ algorithm: 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
- If using ‘fsl’ algorithm: 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) 2008-2016 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/
MRtrix 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 www.mrtrix.org
5ttgen¶
Synopsis¶
5ttgen [ options ] algorithm ...
- algorithm: Select the software / algorithm to be used to derive the 5TT image; additional details and options become available once an algorithm is nominated. Options are: freesurfer, fsl
Description¶
Generate a 5TT image suitable for ACT
Options¶
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
- -verbose Display additional information for every command invoked
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
- If using ‘fsl’ algorithm: Smith, S. M. Fast robust automated brain extraction. Human Brain Mapping, 2002, 17, 143-155
- If using ‘fsl’ algorithm: 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
- If using ‘fsl’ algorithm: 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
- If using ‘fsl’ algorithm: 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) 2008-2016 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/
MRtrix 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 www.mrtrix.org