Dear Freesurfers,
Using FreeSurfer 4.5.0, I am trying to map a binary *.nii roi-mask (defined in ${LABEL}) that has been outlined on the icbm-152 template in mni space to the inflated surface model of fsaverage.
The approach below gives me a solution that looks very trustworthy, however, I'd like to verify with the experts whether it is 100% accurate.
These are the commands I am using:
# to map the label to the fsaverage target mri_label2vol --seg ${LABEL} --temp fsaverage/mri/orig.mgz --reg ${FREESURFER_HOME}/average/mni152.register.dat --invertmtrx -fillthresh 0.5 --o ${LABEL%.nii}_fsa.nii
# to intersect it with the wm surface, and then map it to the sphere (note that identity.dat has been generate prior to running the command). mri_vol2surf --src ${LABEL%.nii}_fsa.nii --reg identity.dat --hemi lh --surf white --interp nearest --surfreg sphere.reg --icoorder 7 --out ${LABEL%.nii}_fsasurf_lh.mgh
# to convert the mgh to ascii mris_convert -c ${LABEL%.nii}_fsasurf_lh.mgh fsaverage/surf/lh.white {LABEL%.nii}_fsasurf_lh.asc
Many thanks, Boris