Hi freesurfer experts, I want to use a volume based MNI152 ROI in Freesurfer, when I check it over fsaverage with the following command the ROI is not in the correct position...:
tkmedit fsaverage T1.mgz -overlay ROI45.nii -overlay-reg $FREESURFER_HOME/average/mni152.register.dat And I have the same problem when I convert it to surface: cd $SUBJECTS_DIR/fsaverage/surf mri_vol2surf \ --mov ../../ROI2/ROI45.nii \ --reg $FREESURFER_HOME/average/mni152.register.dat \ --projdist-max 0 1 0.1 \ --interp nearest \ --hemi lh \ --out lh.fsaverage.ROI45.mgh \ --reshape - Is this a correct way of using it? Should I get proper results or I am missing anything? and, - Does it make sense creating a new fsaverage using the /spm8/canonical/avg152T1.nii, then applying the ROI which is already in 152 space, and referring the cortical thickness of all the subjects to this "new fsaverage"? (the functional analysis is being carried in SPM as well). Many thanks for your answers, Gari
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