After spmregister, you can run
mri_vol2vol --mov pet.nii --reg reg.dat --tal --talres 2 --talxfm talairach.xfm --nearest --no-save-reg --o pet.tal2mm.nii
# mask out the cortical structures
mri_mask pet.tal2mm.nii $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz pet.tal2mm.subc.nii
# Concatenate all subjects together
mri_concat s1/pet.tal2mm.subc.nii s2/pet.tal2mm.subc.nii ... --o all.pet.tal2mm.subc.nii --prune
# smooth
mri_fwhm --i all.pet.tal2mm.subc.nii --mask $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz --fwhm X --smooth-only --o all.pet.tal2mm.subc.smoothed.nii
mri_glmfit --y all.pet.tal2mm.subc.smoothed.nii --fsgd fsgd.txt--C 2gc0.mtx --glmdir subc.glmdir
On 10/19/2016 05:09 PM, John Anderson wrote:
Dear experts, I ran surface based analysis using PET maps. As the following: spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh mris_preproc --target fsaverage --hemi lh --iv subj1/ubject1_pet.nii subject1/pet/pet_2_T1_register.dat ..... --projfrac 0.5 --out lh.mgh mri_surf2surf --hemi lh --s fsaverage --fwhm 6 --cortex --sval lh.mgh --tval lh.sm6.mgh mri_glmfit--y lh.sm6.mgh--fsgd fsgd.txt--C 2gc0.mtx --surf fsaverage lh --cortex --glmdir lh.glmdir// then mri_glmfit-sim to correct for multiple comparison. I want to study the subcortical regions and map it on MNI305. How can I resume tha analysis for subcortical structures? Thank you for any help! Bests, John
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