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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