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
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