Hi Dr Greve,

I am using pet surfer to analyze suv images. I followed all the steps in wiki, I used the option mgx then I fed the images mgx.{ctxgm,subctxgm,gm} into surface based analysis for left and right hemispheres. I want to inquire about the sub cortical analysis.

1. I assume the analysis for sub cortical gray matter (i.e. using the images subctxgm) is volumetric. Correct?

2. Are the following steps correct for sub cortical gray matter analysis

mri_vol2vol --mov subctxgm.nii.gz --reg reg.dat --tal --talres 2 --talxfm talairach.xfm --nearest --no-save-reg --o subctxgm.tal2mm.nii.gz

mri_mask subctxgm.tal2mm.nii.gz $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz subctxgm.tal2mm_subc.nii.gz &

Concatenate all subjects together using mri_concat

smooth using mri_fwhm (what is the recommended smoothing for suv)?

Then Group analysis:

mri_glmfit --y all.suvr.tal2mm.subc.sm10.nii --fsgd fsgd.dat --C contrast.mtx --glmdir dir

mri_glmfit-sim --glmdir dir --grf 1.3 pos --cwpvalthresh 0.0166

for "mri_glmfit-sim" in subcortical structure is the flag grf correct or cache?

Thanks in advance!

John