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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>
External Email - Use Caution
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:
External Email - Use CautionThanks 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
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:
External Email - Use CautionDear 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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)
External Email - Use Caution
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:
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edumailto:freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edumailto:freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics:
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>
External Email - Use Caution
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:
External Email - Use CautionThanks 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
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:
External Email - Use CautionDear 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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ece ulug -
Mcnorgan, Christopher