On 11/04/2016 07:25 AM, Alshikho, Mohamad J. wrote: > > 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 èthat means the surface based analysis is running in the > middle area between white and pial > > ·if it is zero èthe surface based analysis is running close to white > matter > > ·if it is +1 èthat means the surface based analysis is running close > to the pial > > ·if it is -1 èthat means the surface based analysis is running deep in > the white matter > > Kindly: > > 1.Is this correct? > Yes > > 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? > In principle, yes, but often what happens is that when you follow the normal vector into the white matter that far, you end up in GM or CSF and not WM. > > 3.What is the difference between the flag "*_projfrac_*" and the flag > "*_projdis_*" > projdist will project an absolute distance (in mm). projfrac will project a fraction of the thickness (as you describe above) > > 4.If I replace the PET maps in the previous pipeline by diffusion > maps? Is it keep valid for diffusion data? > I guess it depends on what you mean by "valid". As I mention above, it will not necessarily sample WM, and that probably invalidates it somewhat > > Many Thank! > > Mohamad > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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