Dear Enrico, I just tested. The thr0 works really well and can cleanly separate a mask into non-overlapping ROIs and those ROIs capture the whole brain! to be exact, what does thr0 mean? Thanks again! Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: [log in to unmask] On 5/28/14 1:34 PM, "Enrico Glerean" <[log in to unmask]<mailto:[log in to unmask]>> wrote: One option is to use the HO maxprob th0 file that comes with fsl. Alternatively, you load the probabilistic HO atlas e.g. in matlab, then each volume is a Roi. If you take the max over the 4th dimension you see for each voxel which roi is more probable. You can see how I did it here https://code.google.com/p/funpsy/source/browse/#svn%2Ftrunk%2Fatlases%253Fstate%253Dclosed and if you download the file HO_2mm_rois.mat you get a struct with Rois and for each Rois the voxel ids. Best Enrico -- Enrico Glerean (MSc.) PhD Candidate, Brain & Mind Laboratory http://becs.aalto.fi/bml/ BECS, Aalto University School of Science 00076 AALTO, FINLAND mobile: +358 40 1877599<tel:+358%2040%201877599> email: [log in to unmask]<mailto:[log in to unmask]> www: www.glerean.com<http://www.glerean.com/> On 28 May 2014, at 20:12, "Yang, Daniel" <[log in to unmask]<mailto:[log in to unmask]>> wrote: Dear all, Or, alternatively, how to completely divide the brain (cortical area) into non-overlapping ROIs per the Harvard-Oxford atlas? Best, Daniel On 5/28/14 12:56 PM, "Yang, Daniel" <[log in to unmask]<mailto:[log in to unmask]>> wrote: Dear all, I found that the 48 cortical ROIs in the Harvard-Oxford atlas tend to partially overlap each other, due to the nature of a probabilistic atlas. However, it is possible to generate non-overlapping ROIs out of this atlas. Is it okay to do threshold/probability >= 50? Best, Daniel