It is probably just off the surface. Try playing around with the projection options (projfrac, projabs). This is an inevitable problem because "cortex" does not really mean anything in a volume-based group average.
doug
On 7/31/13 5:03 PM, Yune Lee wrote:
Hello freesurfer users --
I noticed an issue with registering MNI template to freesurfer surface, whereby a cluster located on the right hemisphere does not appear at all in the fsaverage rh.inflated template while the left cluster was clearly seen. Inline image 1 The map was generated in SPM8, which indeed does not use MNI152 template. However, as far as I'm concerned, it should be more or less similar to MNI 152 template, so I can rule out the possibility of using a different template image instead of MNI152.
Any way, I'd be grateful if you guys let me know any thoughts on this issue. -ysl
fyi) below is the command line that I used.
#for LH mri_vol2surf --mov rad4_regions.img --reg /usr/local/freesurfer/centos4_x86_64-stable-pub-v5.1.0/average/mni152.register.dat --trgsubject fsaverage --hemi lh --projfrac 0.5 --o rad4_lh.mgh
#for RH mri_vol2surf --mov rad4_regions.img --reg /usr/local/freesurfer/centos4_x86_64-stable-pub-v5.1.0/average/mni152.register.dat --trgsubject fsaverage --hemi rh --projfrac 0.5 --o rad4_rh.mgh
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