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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Thursday, February 11, 2021 1:04 PM To: 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@01D70078.13992C80] Don Krieger, Ph.D. Research Scientist Department of Neurological Surgery University of Pittsburgh

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yes, the pial and white surfaces have the same number of vertices and they have the same identities

On 2/11/2021 1:25 PM, Krieger, Donald N. wrote:

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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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

*        External Email - Use Caution *

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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@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

Don Krieger, Ph.D.

Research Scientist

Department of Neurological Surgery

University of Pittsburgh

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Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>

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