>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
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html On Mon, Nov 28, 2011 at 4:17 PM, Yolanda Vives <yvi...@pic.es> wrote: > 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 <yeoye...@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 <yvi...@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 >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > The information in this e-mail is intended only for the person to whom >> > it is >> > addressed. If you believe this e-mail was sent to you in error and the >> > e-mail >> > contains patient information, please contact the Partners Compliance >> > HelpLine at >> > http://www.partners.org/complianceline . If the e-mail was sent to you >> > in >> > error >> > but does not contain patient information, please contact the sender and >> > properly >> > dispose of the e-mail. >> > >> > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
