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Hi Ayan, Would you be able to upload the parcellation file to Oxfile? I can take a look and help debug. https://oxfile.ox.ac.uk/oxfile/work/extBox?id=786585C3220E6F2207 Cheers, Taylor Hanayik Taylor Hanayik PhD Analysis Research Software Engineer FMRIB, John Radcliffe Hospital University of Oxford [log in to unmask]<mailto:[log in to unmask]> On 1 Oct 2019, at 15:11, Ayan Mandal <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hi all, I need to extract coordinates for each parcel in a parcellation and I'm wondering if there's a simple command that will do it or if I'll have to script something. On the fslstats help page I found an interesting preoption "-K" that does the following: preoption -K < indexMask > will generate seperate n submasks from indexMask, for indexvalues 1..n where n is the maximum index value in indexMask, and generate statistics for each submask I was hoping that this command would give me the centroids for each parcel: fslstats -K parcellation.nii.gz -c But this didn't work and returned: Note - thresholds are not inclusive ie lthresh<allowed<uthresh parcellation.nii.gz is a discrete map of values between 1 and 334, where values indicate inclusion of a voxel within "parcel 1" or "parcel 2", etc. Can fslstats be used directly on this map, or will I have to create masks for each parcel and run fslstats on them separately? Thanks, Ayan ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1