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Hi, You can use fslmeants with the --showall command (and the -i and -m to specify your intensity image and the appropriate VOI mask). This will give you an output that contains three rows with values for the x, y and z coordinates respectively, and then the row containing your intensities. If you do not need the coordinates then you can simply use "tail -2" to give you the required values (as there is a blank line at the very end that needs to be ignored). All the best, Mark On 19 Aug 2010, at 10:18, Moran Artzi wrote: > Hi, > Flowing FAST segmentation I got 3 VOIs. > I want to extract the value of the voxels in each cluster to a text > file in order to scatter-plot them > > The fslmaths -M option gives the entire cluster mean value. > How can I get it's voxels values? > > Thanks > Moran > >