surface based analyses using PET - Freesurfer

27 Feb 2013


      Dear FreeSurfers,
I would like to perform surface based analyses using PET but I am not sure
I am doing things correctly. For each subject, I have reconstructed the
3DT1 MRI using recon-all –all.
Then I have coregistered the PETs with the anatomical using:
Bbregister  --s name  --mov pet.nii  --bold  --init-fsl  --reg
pet_2_T1_register.dat
Registration worked very well.
Now I  am trying to process the PET in order to do a surface based analysis
of the PET signal.
I was thinking of running:
1)      mris_preproc --target fsaverage --hemi lh  --iv
subject1/pet/subject1_pet.nii
 subject1/pet/pet_2_T1_register.dat  --iv  subject2/pet/subject2_pet.nii
subject2/pet/pet_2_T1_register.dat  --iv
subject3/pet/subject3_pet.nii  subject3/pet/pet_2_T1_register.dat
(…)  --projfrac 0.5  --out  lh.pet.mgh
I am not sure this is the right command line. I am especially concerned
with the registration file I should use. Here I used the PET àMRI
registration file. Is this the right one to use. Or should I use a
registration file from native space to fsaverage space. If so, how do I do
that?
2)      mri_surf2surf --hemi lh --s fsaverage --fwhm 10 --cortex
--sval  lh.pet.mgh
--tval lh.pet.sm10.mgh
Any advice on the fwhm I should use for smoothing the data to the surface?
3)      mri_glmfit  --y  lh.fmz.sm10.mgh  --fsgd  fsgd.txt  --C X.mtx  --surf
 fsaverage lh  --cortex  --glmdir lh.pet-age.glmdir
Can you please tell me if I got it right, especially regarding the
registration file I should use with mris_preproc?
Thank you so much,
Leorah Freeman, MD, MSc