Hi Don

This is more Doug's domain than mine, but won't mri_label2label do the trick?

Cheers Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Krieger, Donald N. Sent: Thursday, December 2, 2021 8:38 AM To: 'freesurfer@nmr.mgh.harvard.edu' freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] howto create a .label files with dilated content

External Email - Use Caution Hi everyone,

I'm reposting this from November 29 as it hasn't gotten a reply and it hasn't shown up in the archive either so maybe it got lost in the sauce.

I wish to use the "-dilate n" capability of mri_extract_label, mris_label or other tool to dilate a ctx region and end up with an ascii list of xyz coordinates for the expanded points. mri_extract_label appears to only be capable of writing output to .mgz files and I do not find a tool for extracting labels from a .mgz into an ascii .label file. Your direction would be welcome.

Thanks - Don

[cid:image001.jpg@01D7E763.4AFBE640] Don Krieger, Ph.D. Research Scientist Department of Neurological Surgery University of Pittsburgh

Are you trying to dilate in 3D? If so, the mri_binarize will do it. Or are you trying to dilate along the surface?

On 12/2/2021 10:44 AM, Krieger, Donald N. wrote:

External Email - Use Caution

Thanks for posting back, Bruce.

Mri_label2label –projabs N does work but only dilates normal to a surface.

What I’m trying to do is the following.

For cortical region X, I want to identify the sub-volume of each adjacent cortical region which is adjacent to region X. The idea is to dilate region X, say 5 mm, and then use sort and uniq to identify the xyz coordinates in the dilated X which are coincident with xyz coordinates in each adjacent region. It doesn’t matter if the dilated region X has lots of points in common with region X and I can see a brute force way to do what I want and can write it and contribute it to you if it would be helpful. I was just looking for a freesurfer tool or tool combination which does it. I think the idea of adjacent subregions is a useful one.

*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Fischl, Bruce *Sent:* Thursday, December 2, 2021 10:00 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] howto create a .label files with dilated content

Hi Don

This is more Doug’s domain than mine, but won’t mri_label2label do the trick?

Cheers

Bruce

*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Krieger, Donald N. *Sent:* Thursday, December 2, 2021 8:38 AM *To:* 'freesurfer@nmr.mgh.harvard.edu' freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] howto create a .label files with dilated content

*        External Email - Use Caution *

Hi everyone,

I’m reposting this from November 29 as it hasn’t gotten a reply and it hasn’t shown up in the archive either so maybe it got lost in the sauce.

I wish to use the “-dilate n” capability of mri_extract_label, mris_label or other tool to dilate a ctx region and end up with an ascii list of xyz coordinates for the expanded points.

mri_extract_label appears to only be capable of writing output to .mgz files and I do not find a tool for extracting labels from a .mgz into an ascii .label file.

Your direction would be welcome.

Thanks -  Don

Don Krieger, Ph.D.

Research Scientist

Department of Neurological Surgery

University of Pittsburgh

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