Hi Thomas,
Thank you for your answer, I will try to project your parcellation in fsaverage space to BASGU space first.
Regards, Yolanda
2011/11/26 Thomas Yeo yeoyeo02@gmail.com
Hi Yolanda,
Just to understand what you are doing, you have run BASGU through recon-all and you are trying to project the surface parcellation into the anatomical volume of BASGU?
The annotation we are providing is actually in fsaverage space, so you need to first project the parcellation from fsaverage space to BASGU native surface space before running mris_annot_to_segmentation to project the parcellation into his/her anatomical volume.
To project the parcellation from freesurfer surface space to the subject's native surface space, I think you can use mri_surf2surf, although I am not sure if there's a more specific freesurfer function that is specialized for transferring annotation files.
--Thomas
On Thu, Nov 24, 2011 at 4:11 PM, Yolanda Vives yvives@pic.es wrote:
Dear Freesurfer experts,
I would like to use the Yeo_JNeurophysiol11_FreeSurfer parcellations
with my
dataset and I am not sure what I have to do. I have used the mris_annot_to_segmentation command but I have the following error:
mris_annot_to_segmentation BASGU lh inflated ./fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot ../Yeo_JNeurophysiol11_MNI152/Yeo2011_17Networks_ColorLUT.txt test reading /freesurfer/BASGU/surf/lh.inflated... reading colortable from annotation file... colortable with 18 entries read (originally MyColorLUT) mri_read(): couldn't determine type of file /freesurfer/BASGU/mri/T1 (null): could not read T1 for template volume
I have a T1.mgz file inside mri/. Where could be the problem? Is this command appropriate?
Thank you in advance, Yolanda
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From Doug:
yes, use mri_surf2surf to map from fsaverage to the individual, then use mri_aparc2aseg to map from the surface back into the volume doug
freesurfer@nmr.mgh.harvard.edu
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Thomas Yeo -
Yolanda Vives