Python script to perform the spatially constrained parcellation of functional MRI data as described in Craddock et al., Human Brain Mapp., 33 (9) 2012
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DOI pyClusterROI

Copyright (C) 2010 R. Cameron Craddock (

This is the pyClusterROI python toolbox for the spatially constrained clustering of fMRI data.

For more information refer to:

Craddock, R. C.; James, G. A.; Holtzheimer, P. E.; Hu, X. P. & Mayberg, H. S. A whole brain fMRI atlas generated via spatially constrained spectral clustering Human Brain Mapping, 2012, 33, 1914-1928 doi: 10.1002/hbm.21333..

   author = {Craddock, R C and James, G A and Holtzheimer, P E and Hu, X P and
   Mayberg, H S},
   title = {{A whole brain fMRI atlas generated via spatially constrained
   spectral clustering}},
   journal = {Human Brain Mapping},
   year = {2012},
   volume = {33},
   pages = {1914--1928},
   number = {8},
   address = {Department of Neuroscience, Baylor College of Medicine, Houston,
       TX, United States},
   pmid = {21769991},

Documentation, updated source code and other information can be found at the NITRC web page: and on github at

This library requires NumPy, SciPy, and NiBabel.

Please refer to for detailed instructions on how to use the code. This script can be executed using test data.