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!