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Thank you. I loaded aseg and input the crs values. The aseg file gave an
intensity value of 54 and the label as right amygdala! So it seems like the
problem is not with the aseg file. Is there another possibility?
Sparsh
On Fri, Mar 8, 2019 at 3:00 AM
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You could load the aseg in freeview and navigate to the voxel (you can enter
the CRS at the bottom, no need to scroll there). Then you have its intensity
value, which you can check against FreeSurferColorLUT.txt.
Tim
--
Dr. Tim Schäfer
Postdoc Compu
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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. <
dgr...@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
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 poin
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
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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).
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
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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
Spa
