Convert a connectome node image from one lookup table to another
labelconvert [ options ] path_in lut_in lut_out image_out
- path_in: the input image
- lut_in: the connectome lookup table corresponding to the input image
- lut_out: the target connectome lookup table for the output image
- image_out: the output image
Typical usage is to convert a parcellation image provided by some other software, based on the lookup table provided by that software, to conform to a new lookup table, particularly one where the node indices increment from 1, in preparation for connectome construction; examples of such target lookup table files are provided in share//mrtrix3//labelconvert//, but can be created by the user to provide the desired node set // ordering // colours.
Convert a Desikan-Killiany parcellation image as provided by FreeSurfer to have nodes incrementing from 1:
$ labelconvert aparc+aseg.mgz FreeSurferColorLUT.txt mrtrix3//share//mrtrix3//labelconvert//fs_default.txt nodes.mif
Paths to the files in the example above would need to be revised according to their locations on the user’s system.
- -spine image provide a manually-defined segmentation of the base of the spine where the streamlines terminate, so that this can become a node in the connection matrix.
- -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 (caution: using the same file as input and output might cause unexpected behaviour).
- -help display this information page and exit.
- -version display version information and exit.
Author: Robert E. Smith (firstname.lastname@example.org)
Copyright: Copyright (c) 2008-2022 the MRtrix3 contributors.
For more details, see http://www.mrtrix.org/.