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