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Running the Clustering Pipeline

wm_registermultisubject.py

Runs a multisubject unbiased group registration of tractography.
This is used to before clustering the atlas and is typically used on the control subject data.

wm_cluster_atlas.py

Runs clustering of tractography for multiple subjects to create an atlas. Clusters can be viewed in Slicer following this step.
This step analyzes a subset of fibers from each subject to determine common structures in the population.

wm_label_from_atlas.py

Labels tractography for single cases according to the multi-subject cluster representation created in step 2
This code registers the atlas to the subject for comparison.
This analyzes the full subject dataset.

Additional command: wm_cluster_subject.py

Clusters tractography from a single subject
This is not commonly used. It is generally used for experimenting with one subject.

In order to use any of the commands, “python” must be entered first
Commands can be entered from anywhere, but the entire path to the file must be used. In most cases, the required command is something like “python _path to script__ _path to input directory___ ____path to output directory___
The output file(s) will be created in the directory you specify. Generally, the directory will be created for you if it does not exist.
Clustering commands can be found in the bin directory of whitematteranalysis: whitematteranalysis/bin/
Getting the “Help” menu for any of the scripts: Enter “python” then space, then the full path to the script, followed by “-h”. This can be run from any directory.
Example: ``<1862> pnl-t55-8 /net/lmi-terastation-a/mnt/array1/share/pnl/Collaborators/jstamm/NFL_Clustering% python /projects/schiz/software/whitematteranalysis/whitematteranalysis/bin/wm_register_multisubject.py –h>