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 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
