I use the ‘Histogram’ plugin to output the voxel counts of different intensity values within a roi mask. I just toggle and provide the ‘Source’ dataset, ‘Mask’ dataset and ‘Output’ filename in the plugin. The output numbers (values in bins and voxel counts) are slightly different from those using ‘3dhistog’ command line below:
3dhistog -mask eyeball.nii -prefix test T1_al.nii
Wonder whether I’ve missed some options in the command line so as to make the output the same as that from plugin.