Structural connectome construction: Using labelconfig

The labelconfig step in Structural-connectome construction has proven to be a hurdle for many. It may be a ‘unique’ step in so far as that other software packages probably deal with this step implicitly, but in MRtrix we prefer things to be explicit and modular. So here I’ll go through an example to demonstrate exactly what this command does.

Worked example

For this example, let’s imagine that we’re going to generate a structural connectome for Bert, the quintessential FreeSurfer subject. Also, we’re going to generate the connectome based on the Desikan-Killiany atlas. The default FreeSurfer pipeline provides the volumetric image aparc+aseg.mgz; this is the file that will be used to define the nodes of our connectome.


Looking at the raw image itself, each node possesses a particular intensity, corresponding to a particular integer value. If we focus on the superior frontal gyrus in the right hemisphere, we can see that the image intensity is 2028 for this structure. This immediately presents a problem for constructing a connectome: if any streamline encountering this region were written to row/column 2028, our connectome would be enormous, and consist mostly of zeroes (as most numbers between 1 and 2028 do not correspond to any structure). Therefore, what we’d prefer is to map the unique integer index of this structure to a particular row/column index of the connectome; this should be done in such a way that all structures of interest have a unique integer value between 1 and N, where N is the number of nodes in the connectome.

Now looking at the file FreeSurferColorLUT.txt provided with FreeSurfer, we see the following:

2026    ctx-rh-rostralanteriorcingulate     80  20  140 0
2027    ctx-rh-rostralmiddlefrontal         75  50  125 0
2028    ctx-rh-superiorfrontal              20  220 160 0
2029    ctx-rh-superiorparietal             20  180 140 0
2030    ctx-rh-superiortemporal             140 220 220 0

This gives us a meaningful name for this structure based on the integer index. It also gives us some colour information, but let’s not worry about that for now.

Our goal then is to determine a new integer index for this structure, that will determine the row/column of our connectome matrix that this structure corresponds to. This is dealt with using a connectome configuration file. For this example, let’s imagine that we’re using the default MRtrix connectome configuration file for the FreeSurfer Desikan-Killiany atlas segmentation: this is provided at src/connectome/config/fs_default.txt. Examining this file in detail, we see the following:

74 ctx-rh-rostralanteriorcingulate
75 ctx-rh-rostralmiddlefrontal
76 ctx-rh-superiorfrontal
77 ctx-rh-superiorparietal
78 ctx-rh-superiortemporal

This file contains the same structure name as the FreeSurfer look-up table, but it is assigned a different integer index (76)! What’s going on?

The following is what the labelconfig command is actually going to do under the bonnet using this configuration file:

  1. Read the integer value at each voxel
  2. Convert the integer value into a string, based on the FreeSurfer look-up table file
  3. Find this string in the connectome configuration file
  4. Write the integer index stored in the connectome configuration file for this structure to the voxel in the output image

This is what the actual command call looks like:

labelconfig $FREESURFER_HOME/subjects/bert/mri/aparc+aseg.mgz ~/mrtrix3/src/connectome/config/fs_default.txt bert_parcels.mif -lut_freesurfer $FREESURFER_HOME/FreeSurferColorLUT.txt

And this is what the resulting image looks like:


The integer labels of the underlying grey matter parcels have been re-configured based on the contents of the configuration file (hence the name labelconfig). They now increase monotonically from 1 to the maximum index, with no ‘gaps’ (i.e. ununsed integer values) in between. Therefore, when you construct your connectome using tck2connectome, the connectome matrix will only be as big as it needs to be to store all of the node-node connectivity information.

Design rationale

Making this step of re-indexing parcels explicit in connectome construction has a few distinct advantages: * You can use parcellations from any software / atlas: just define an appropriate configuration file, and provide the structure look-up table file using one of the -lut_ options in labelconfig (should come with the software / atlas download). * tck2connectome can be ‘dumb and blind’: it reads the integer indices at either end of the streamline, and that’s the row/column of the connectome matrix that needs to be incremented. * You can have your grey matter parcels appear in any order in your matrices: just define a new config file. This is less likely to lead to heartache than re-ordering the rows and columns in e.g. Matlab. * You can remove structures from the connectome, or merge multiple structures into a single parcel, just by setting the node indices appropriately in the config file. * Looking at your matrices and need to find out what structure corresponds to a particular row/column? Just look at the config file!

Obviously if your parcellation image already has node indices that increase monotonically from 1, and you’re happy enough with the numerical order of the nodes, you don’t actually need to use labelconfig at all.

Custom design connectomes

Some notes for anybody that wishes to define their own configuration files (either for re-ordering nodes, changing selection of nodes, or using parcellations from alternative sources):

  • If you wish to omit nodes from your connectome (e.g. the cerebellar hemispheres), you may be better off making these nodes the largest indices in your connectome and then cropping them from the connectome retrospectively, rather than omitting them from the parcellation image entirely. If you were to do the latter, streamlines that would otherwise be assigned to your unwanted nodes may instead be erroneously assigned to the nearest node that is part of your connectome (exactly what happens here will depend on the streamline-node assignment mechanism used).
  • The command labelconfig is capable of reading in atlas look-up tables in a number of formats (see the command’s help page). If you have an atlas from a different source, where the look-up table does not conform to any of these formats, a parser will need to be added to the MRtrix code. Contact me directly if this is the case.