Right but what do you think FA, MD, AD, RD, etc are telling you neurobiologically in the grey matter?
Matt. On 3/23/16, 7:18 PM, "Alshikho, Mohamad J." <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of malshi...@mgh.harvard.edu> wrote: >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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
