# labelconvert¶

## Synopsis¶

Convert a connectome node image from one lookup table to another

## Usage¶

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

## Description¶

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.

## Example usages¶

• 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.

## Options¶

• -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.

### Standard options¶

• -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).
• -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.

### References¶

Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch, M.; Christiaens, D.; Jeurissen, B.; Yeh, C.-H. & Connelly, A. MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. NeuroImage, 2019, 202, 116137

Author: Robert E. Smith (robert.smith@florey.edu.au)