labelsgmfix¶
Synopsis¶
In a FreeSurfer parcellation image, replace the sub-cortical grey matter structure delineations using FSL FIRST
Usage¶
labelsgmfix parc t1 lut output [ options ]
- parc: The input FreeSurfer parcellation image
- t1: The T1 image to be provided to FIRST
- lut: The lookup table file that the parcellated image is based on
- output: The output parcellation image
Options¶
Options for the labelsgmfix script¶
- -premasked Indicate that brain masking has been applied to the T1 input image
- -sgm_amyg_hipp Consider the amygdalae and hippocampi as sub-cortical grey matter structures, and also replace their estimates with those from FIRST
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¶
- 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
- Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. The effects of SIFT on the reproducibility and biological accuracy of the structural connectome. NeuroImage, 2015, 104, 253-265
Author: Robert E. Smith (robert.smith@florey.edu.au)
Copyright: Copyright (c) 2008-2017 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 http://www.mrtrix.org/.