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Running the Clustering Pipeline

Brief Outline of Steps

wm_registermultisubject.py

• Runs a multisubject unbiased group registration of tractography.
• This is used to create 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.

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.

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.

Help

• 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

  ***Check “help” to make sure all necessary information is included The output file will be created for you unless you directly indicate the specific output file Cluster software can be found found in the Bin directory whitematteranalysis: /projects/schiz/software/whitematteranalysis/whitematteranalysis/bin/

Getting the “Help” menu for any of the scripts Enter “python” the 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