External Email - Use Caution I see. How may I check that?
Sparsh On Thu, Mar 7, 2019 at 6:42 PM Greve, Douglas N.,Ph.D. < [email protected]> wrote: > Is that point labeled as WM in the aseg? If so, then it is not a problem > with matlab:) > > On 3/7/19 5:58 PM, Sparsh Jain wrote: > > > > External Email - Use Caution > > > > Thanks a lot! It worked. > > While most of the labels were correct, the matlab script returned the > > wrong location for one point . The script returned the label 'right > > cerebral white matter' for a point that seems to lie in the middle of > > the right amygdala. I have attached the screenshots. I do not think > > that there is a white matter area close enough to confuse the script. > > Could you tell me why this may have occurred? > > When I write the line "crs = round(inv(aparcaseg.tkrvox2ras)*[tkr tka > > tks 1]')+1" , is there an error due to rounding in the conversion? > > > > I was planning to inflate a sphere around each electrode point and get > > the neighboring anatomical regions as well. > > > > Sparsh > > > > On Thu, Feb 21, 2019 at 12:51 PM Greve, Douglas N.,Ph.D. > > <[email protected] <mailto:[email protected]>> wrote: > > > > For a volume, I would do it differently. In matlab > > > > [segcodes segnames ] = read_fscolorlut(); % read in the seg lookup > > table > > > > aparcaseg = MRIread('aparc+aseg.mgz'); % Load in the volume > > crs = round(inv(aparcaseg.tkrvox2ras)*[tkr tka tks 1]')+1; % convert > > your tkreg coords to col, row, and slice > > c = crs(1); > > r = crs(2); > > s = crs(3); > > segno = aparcaseg.vol(r,c,s); % extract the segmentation number > > ind = find(segno == segcodes); % convert to the ne name of the > > segmentation > > segname = segnames(ind,:) > > > > > > On 2/20/19 9:58 AM, Sparsh Jain wrote: > > > > > > External Email - Use Caution > > > > > > Hi Doug, > > > > > > I tried what you suggested, but it did not work (see below for > > details > > > of what we tried). We have TkReg RAS coordinates (or vertex points) > > > for our electrode contacts; most contacts are _deep within the > > > brain_ (e.g., hippocampus and amygdala). We want to get a > > variable in > > > Matlab that will give us the anatomical labels as a function of the > > > TkReg RAS coordinates (or vertex points). How can we do this? > > > > > > Thanks! > > > > > > Sparsh > > > > > > _What I tried:_ I read the 'rh.aparc.2009a.annot' file in matlab > > using > > > read_annotation.m. That gave me 76 labels for right hemisphere, > > which > > > I believe correspond to the surface parcellations only. In > > freeview I > > > loaded the orig.mgz, aparc.a2009s+aseg.mgz, rh.pial and > > rh.inflated. I > > > then clicked on a cortical surface point to see if I can get the > > > corresponding vertex number or structure ID. On doing so, I found a > > > value in the Vertex row under rh.pial of freeview but this number > > > wasn't found in the matlab output (in the colortable.label or > > > colortable.table). I think I am looking in the wrong place to > > find the > > > vertex # on freeview. > > > > > > Also, I did not find a readable file for the segmentation data. I > > > tried to read the aparc.a2009s+aseg.mgz on Matlab but that > > didn't work. > > > Show quoted text > > > > > > On Thu, 7 Feb 2019, 16:10 Greve, Douglas N.,Ph.D. > > > <[email protected] <mailto:[email protected]> > > <mailto:[email protected] <mailto:[email protected]>> > wrote: > > > > > > First, you'll have to find the closest vertex for each point in > > > fsavarage. You can do this with by creating a label file > > then using > > > mri_label2label with the --paint option. > > > > > > To find the label associated with each vertex, it is probably > > > easiest > > > to use matlab using read_surf.m and read_annotation.m > > > > > > On 2/5/19 11:17 AM, Sparsh Jain wrote: > > > > > > > > External Email - Use Caution > > > > > > > > Good afternoon > > > > > > > > Is there is way to automatically extract the anatomical > > locations > > > > corresponding to a set of RAS coordinates using Freesurfer's > > > atlas? I > > > > have a set of 200 points and I am trying to get their > > anatomical > > > > labels automatically. > > > > > > > > Thank you > > > > Sparsh > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > [email protected] > > <mailto:[email protected]> > > > <mailto:[email protected] > > <mailto:[email protected]>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > [email protected] > > <mailto:[email protected]> > > <mailto:[email protected] > > <mailto:[email protected]>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > [email protected] > > <mailto:[email protected]> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > [email protected] <mailto: > [email protected]> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > [email protected] > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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