labelsgmfix [ options ] parc t1 lut output
  • 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


In a FreeSurfer parcellation image, replace the sub-cortical grey matter structure delineations using FSL FIRST


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
  • -verbose Display additional information for every command invoked


  • 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 (

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