Re: [Freesurfer] Extracting anatomical locations for a set of RAS coordinates

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I see. How may I check that?

Sparsh

On Thu, Mar 7, 2019 at 6:42 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> 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:

...

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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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