[Freesurfer] Ynt: Desikan Atlas in volume space (ece ulug)

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Doctor i opened annotation file by read_annotation.m, but then i looked your page, firstly thanks for your work!

'vertex_key.m' file is worked but not exactly I wanted, get.Seg.Coords.m file doesn't work and i think an example can be helpful. (for every m file)

Best,

Ece

________________________________ Gönderen: Mcnorgan, Christopher cpmcnorg@buffalo.edu adına freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Gönderildi: 6 Kasım 2018 Salı 20:05 Kime: Freesurfer Mailing List Konu: Re: [Freesurfer] Desikan Atlas in volume space (ece ulug)

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Hi Ece,

I believe you will find a walkthrough of the steps to do exactly what you want done on my lab wiki:

http://ccnlab.psy.buffalo.edu/wiki/index.php/Annotation_Coordinates

Hope this helps, Chris

/********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/

On Nov 6, 2018, at 12:00 PM, freesurfer-request@nmr.mgh.harvard.edumailto:freesurfer-request@nmr.mgh.harvard.edu wrote:

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1. Ynt: Ynt: ?lt: Desikan Atlas in volume space (ece ulug)

From: ece ulug <eceulug77@hotmail.commailto:eceulug77@hotmail.com> Subject: [Freesurfer] Ynt: Ynt: İlt: Desikan Atlas in volume space Date: November 6, 2018 at 6:37:17 AM EST To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>

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Exactly. I cannot find in this file but i found lh.aparc.label and lh.aparc.annot files in freesurfer/subjects/fsaverage/label. Actually i told in my previous message. I need coordinates for generate caudalanteriorcingulate mask in coordinate system.

________________________________ Gönderen: Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> adına freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> Gönderildi: 6 Kasım 2018 Salı 00:45 Kime: Freesurfer support list Konu: Re: [Freesurfer] Ynt: İlt: Desikan Atlas in volume space

I don't think there is an lh.aparc.label file - I don't know what it would be if it existed.

Maybe we can take a step back and you can let us know what you are trying to achieve?

On Mon, 5 Nov 2018, ece ulug wrote:

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Thanks for your reply doctor. Actually I want to access Desikan K. Atlas coordinates as x, y, z. (each regions. for example caudalanteriorcingulate).

In that case, one expert said that ; the closest to what you want is probably $FREESURFER_HOME/subjects/fsaverage/surf/lh.aparc.label. You can open it with a text editor. Then you should cross-check with $FREESURFER_HOME/subjects/fsaverage/surf/lh.aparc.annot for the actual labels of those vertices. The .annot file can be opened in Matlab with the read_annotation command from FreeSurfer.

What do you recommend? Ece

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Gönderen: Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> adına freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> Gönderildi: 5 Kasım 2018 Pazartesi 20:18 Kime: Freesurfer support list Konu: Re: [Freesurfer] İlt: Desikan Atlas in volume space Hi Ece

for a given subject the Desikan parcellation is sampled into the volume alread in the file aparc+aseg.mgz in the subject's mri dir. Is that what you are looking for?

cheers Bruce

On Mon, 5 Nov 2018, ece ulug wrote:

...

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Dear Experts,

I am very beginner in Freesurfer, and I want to use 'read_annotation' function but i don't know what is the next step. I added the Matlab screenshoot.

Additionally; 'read_curv' function don't work in Matlab. I added it.

Thanks in advance

Ece

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