I don't know of a reference where someone has done this (though I would be surprised if it is not out there), so just be aware of this if you try to publish. The commands look correct, however, you may or may not want to sample in the middle of the cortical ribbon (--projfrac 0.5). Since this is a DTI analysis, wouldn't you want to sample in the WM? Doing that is a little tricky, but you can use something like --projabs -1 to sample 1mm *away* from the ribbon into the WM.
On 03/22/2016 11:08 AM, Alshikho, Mohamad J. wrote:
Dear FS experts,
I would like to run surface based analysis using FA maps. I am not exactly sure that what I am doing is totally right specially step 2 . I used the following commands:
1.I registered the FA maps to T1 using the command: bbregister --s bert --mov dtifit_FA.nii --bold --init-fsl --reg reg.dat
2.I concatenated the subject’s FA maps using the command : mris_preproc –target fsaverage –hemi lh –iv .bert1/dtifit_FA.nii reg.dat –iv bert2/dtifit_FA.nii reg.dat …. --projfrac 0.5 --out lh.FA.mgz
3.Then smoothing mri_surf2surf --hemi lh --s fsaverage --fwhm 5 --cortex --sval lh.FA.mgz --tval lh.FA_5mm.mgz
4.Then GLM analysis using mri_glmfit
5.Correction for multiple comparison mri_glmfit-sim
Kindly, are these steps correct? I used the previous steps to do surface based analysis using PET images and it worked very well. While for the FA maps it seems that there is something wrong and I can’t figure out what it is!
I highly appreciate any input on this!
Best,
Mohamad
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