oh, I see. It would be pretty easy to do in matlab. Something like:
v = load_mgh('aseg.mgz'); vnew = zeros(size(v)) left_hippo_ind = find(v == 17); for i=1:length(left_hippo_ind) vnew(i) = i end
On Mon, 8 Jul 2019, Fotiadis, Panagiotis wrote:
Hi Bruce,
Thanks for your response! Within aseg, however, there is a group of voxels with intensity 17 (and therefore comprising the left hippocampus). I was mainly wondering whether there is a way to assign a different intensity value to each individual voxel in aseg (so that for instance if you had 40,000 voxels in aseg.mgz then you would assign each one with a different intensity value so that you would end up with 40,000 "ROIs" ). Hope this clarifies a little bit my semi-abstract question!
Thanks again, Panos
On 7/7/19, 9:30 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
Hi Panos
I'm not sure I understand. Isn't that already what the aseg is? E.g. voxel intensity 17 means left hippocampus?
Bruce On Sun, 7 Jul 2019, Fotiadis, Panagiotis wrote:
Hello,
I was wondering whether there is a way to assign a different intensity value on each voxel within a parcellation file (such as aseg.mgz). What I’m essentially trying to do is create a file (using the aseg.mgz file as a template) where each voxel represents a different ROI. I can think of a way to do that in Freeview for each individual voxel but I wasn’t sure whether there was a more efficient/automated way in either bash or matlab.
Let me know if the above doesn’t make any sense, and thanks in advance!
Best,
Panos
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