Try running recon-all on the mni152
On 3/18/2020 5:05 PM, Ryne Nichols wrote:
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All,
I'm having trouble getting good surface projections of SPM results. My SPM results come from SPM normalization -- which should be MNI152 space.
I'm confused because fsaverage says it is in MNI305 space.
I've tried a few commands, but the two that confuses me the most is:
mri_vol2surf --mov SPMT_001.nii --mni152reg --trgsubject fsaverage --hemi lh --out lh_spm.mgh --projfrac-max 0 1 .1
Also the similar command:
mri_vol2surf --mov SPMT_001.nii --reg $FREESURFER_HOME/average/mni152.register.dat --trgsubject fsaverage --hemi lh --out lh_spm.mgh --projfrac-max 0 1 .1
both give results in a wildly different place on the brain than they should be -- it flips the SPMT_001.nii in the Y direction.
If I do
mri_vol2surf --mov SPMT_001.nii --regheader fsaverage --hemi lh --out lh_spm.mgh --projfrac-max 0 1 .1
things are close, but nor exactly how they should be (it seems).
Finally, if i use a surface that's in MNI152 space (cvs_avg35_inMNI152) things look the way they should, e.g.:
mri_vol2surf --mov SPMT_001.nii --regheader cvs_avg35_inMNI152 --hemi lh --out lh_spm.mgh --projfrac-max 0 1 .1
thank you for any help you may provide!
-ryne
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