Dear FS experts,

 I ran surface based analysis using PET maps, and the pipeline reported, in FS list, by multiple colleagues as  the following:

· spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh

· mris_preproc --target fsaverage --hemi lh --iv subj1/ubject1_pet.nii subject1/pet/pet_2_T1_register.dat ..... --projfrac 0.5 --out lh.mgh

· mri_surf2surf --hemi lh --s fsaverage --fwhm 6 --cortex --sval lh.mgh --tval lh.sm6.mgh

· mri_glmfit--y lh.sm6.mgh--fsgd fsgd.txt--C 2gc0.mtx --surf fsaverage lh --cortex --glmdir lh.glmdir//

· then mri_glmfit-sim to correct for multiple comparison.

I wanted to know the correct usage of the flag “projfrac” in the command "mris_preproc":

My understanding is that this flag control running the surface based analysis far from the surface (i.e. close to the surface or deep in the white matter)

· If it is 0.5 è that means the surface based analysis is running in the middle area between white and pial 

· if it is zero è the surface based analysis is running close to white matter

· if it is +1 è that means the surface based analysis is running close to the pial

· if it is -1 è that means the surface based analysis is running deep in the white matter

Kindly:

1. Is this correct?

2. Can I  use values like -2 or -3 ... etc to run the analysis deep in the white matter. I aim to run surface based analysis on multiple layers of the brain deep from the pial to investigate how the PET signal is going to change between these layers? 

3. What is the difference between the flag "projfrac" and the flag "projdis"

4. If I replace the PET maps in the previous pipeline by diffusion maps? Is it keep valid for diffusion data?

Many Thank!

Mohamad