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It looks like your first answer, i.e. use of mri_annotation2label to extract
pial labels almost gets me there. I see that the pial and white labels have
exactly the same number and values for their indices. Does this mean I can use
the distance between the white and pial vertex with the same label as a
cortical thickness?
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Krieger, Donald N.
Sent: Thursday, February 11, 2021 1:16 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] cortical thickness values for each point in a ctx
label file
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Thanks for getting back so quickly, Doug.
Creating pial label files will enable me to write something which does what I
want.
What I want to do is generate a list of cortical thickness values, one for each
vertex in a ctx label file. The main question is whether something to do this
has already been implemented in freesurfer. If not, I will generate pial label
files and then for each vertex in a ctx label file, I will find the nearest
points in that ROI's pial and white label files and use the sum of the two
distances as the cortical thickness.
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Douglas N. Greve
Sent: Thursday, February 11, 2021 1:04 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] cortical thickness values for each point in a ctx
label file
Not sure what you mean as the pial files are surfaces not labels or
annotations. If you want to extract labels from the annotations you can use
mri_annotation2label
On 2/11/2021 12:55 PM, Krieger, Donald N. wrote:
External Email - Use Caution
Dear freesurfer group,
I wish to measure a cortical thickness value for each entry in a label file,
e.g. SubNo/wmparc/ctx-lh-lateraloccipital_1011.label .
Is there a function in the freesurfer distribution which includes this
capability?
Also, is there a function in the distribution that produces regional label
files from the surf/[lr]h.pial files?
Thanks - Don
[cid:image001.jpg@01D70079.6E02F790]
Don Krieger, Ph.D.
Research Scientist
Department of Neurological Surgery
University of Pittsburgh
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