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 > > > > >

Hi Bruce,

That’s exactly what I needed, thank you!

Best, Panos

On 7/7/19, 10:18 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:

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 > > > > > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >