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. Is this 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