In a FreeSurfer parcellation image, replace the sub-cortical grey matter structure delineations using FSL FIRST
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
- -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
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 the path 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.
- -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.
- 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 (email@example.com)
Copyright: Copyright (c) 2008-2019 the MRtrix3 contributors.
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