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Well, if you use nonlinear registration to MNI, you can generally use the same subcortical ROIs across subjects, however such ROIs will be more variable with regard to the anatomy than correctly hand drawn ones (not less). I would put an ROI in the white matter posterior to the LGN and one at the beginning of the calcarine where the optic radiation is a clear "C" shape in coronal section on the color FA map. Peace, Matt. -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Sean F Walsh Sent: Thursday, June 23, 2011 9:07 AM To: [log in to unmask] Subject: [FSL] Optic radiation tractography ROIs Dear FSLers, I would like to track the optic radiations in several subjects (about 80 brains) and would appreciate some advice as to which regions of interest to use. I would like to automate the process as much as possible to avoid introducing too much variability with regards to the region of interests, in particular the placement of the ROI near the lateral geniculate nucleus. Of course this approach would only be as good as any registration that goes with it. I was considering using the part of the thalamic atlas which features projections to the occipital lobe as a seed point. This ROI however seems to be larger on one side than the other. I am worried that apart from introducing a left/right bias that I may also miss out on some parts of the tract which go to nearby parts of the thalamus. I know that in the fdt tutorial there is a lateral geniculate nucleus mask. Was this hand-drawn or taken from an atlas? If so, which one? Also are there any atlases available which feature V1 in each hemisphere, as in the tutorial example? Any recommendations will be warmly received, Many thanks, Sean