Topography scripts

To set paths:

setpaths;

Clustering

embedding.py

To create cluster results based on individual connectivity matrices:

embedding.py -s <subject> -f <output filebasename>

where input is a connectivity matrix saved as a .mat file.

Paths through cluster results:

DoFindPaths.m

[clus, randpath] = DoFindPaths(n);

where `n` is the number of permutations,
and a config file is loaded in the script.

Then set config file for path order as in:

config/config_my18_path.m

And finally, to run permutation test on path order:

randPath = pathsPermute(clus, n);

find_similar_paths.py

To find most common paths through a cluster map.

Distance maps

Calculating distance from DMN on the group-level

[distDMN] = loadDistDMN_group(hemi);

New peaks can also be derived from clus.peaks(find(clus.edgeNet == 13))

[dist, zone] = distExactGeodesic(clus.peaks(find(clus.edgeNet == 13)), '32', 'L', 'zones', '1');

where XX = DMN network from cluster results

Comparing to myelin maps

DoMyelin();

Calculating distance from DMN on the individual-level

[distances, zones, surfi_164] = loadDistDMN_individual(sub, hemi);