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.
> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> 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.
>     > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>
>     <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> 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
>     >     >
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