Do you have a question about the image?
On 11/04/2016 11:09 AM, Alshikho, Mohamad J. wrote:
Thank you Doug! Kindly in the attached figure are the "projfrac" values for #4 and #5 correct for at which level the analysis will be carried out.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Friday, November 4, 2016 10:29 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc
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
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