Hi Matt, I highly appreciate your input on this!! Actually my goal is to study the difference in FA values between groups within the cortex. I know that diffusivities ( MD, AD and RD) can be used to evaluate gray matter and many people claim that it is much better to use diffusivities to evaluate gray matter But my interest is specifically in FA within the gray matter.
For that reason I want to do surface based analysis to study the differences in FA between my study groups. I checked for the optimal ways to do it: 1. I found https://surfer.nmr.mgh.harvard.edu/fswiki/dt_recon 2. And I found https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/028109.html I ran the analysis using both methods. For the second method I replaced PET maps by FA maps and this was the reason for my question! If we can do the analysis that way using PET maps, why we can't do it using FA maps? I will be more than happy if you can suggest me an alternative approach to study FA on a surface. Best, Mohamad -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser Sent: Wednesday, March 23, 2016 8:04 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Surface based analysis using FA maps I too am puzzled as to why you would want to do this. In terms of getting improvement in the alignment across subjects TBSS is one way to approach this. Another would be to use the fiber orientations in the registration like these folks have done: http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Main.HomePage If you are interested in studying the properties of cortical grey matter there might be better modalities than FA. If you can provide more details on what you are trying to do, perhaps that would clarify how to go about it? Peace, Matt. On 3/22/16, 2:49 PM, "Douglas N Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of gr...@nmr.mgh.harvard.edu> wrote: >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 subject¹s 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 Š. --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 >> can¹t 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. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
