The point is that more than tissue damage will cause changes to FA. Matt.
On 3/23/16, 9:17 PM, "Alshikho, Mohamad J." <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of malshi...@mgh.harvard.edu> wrote: >This is theoritically correct! >If we do DTI to study the liver. How these measures can explain the >tissue? It is not only white matter and gray matter! > >All DTI measures can explain how much space we have between the cells. >More space means low FA and high RD. The opposit correct as well. >Given that they share the same formula. If we accept RD as a marker for >gray matter integrity. We should accept FA a marker for gray matter >integrity. > >Yes I am looking for an optimal measure to evaluate tissue damage. > >Mohamad >________________________________________ >From: freesurfer-boun...@nmr.mgh.harvard.edu >[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Matt Glasser >[m...@ma-tea.com] >Sent: Wednesday, March 23, 2016 9:29 PM >To: Freesurfer support list >Subject: Re: [Freesurfer] Surface based analysis using FA maps > >FA or fractional anisotropy explains the fraction of the diffusion that is >along the long axis of the diffusion tensor. In so far as the diffusion >tensor is an accurate model of the underlying structural architecture, >what you say might be true (e.g. in the small number of white matter >regions with only one main fiber orientation). Most of white matter has >multiple fiber orientations and thus the diffusion tensor is not a great >model. In grey matter, the principle orientation of processes is radial >to the surface (e.g. radial fibers, major dendrites), but there are are >also tangential processes (e.g. Bands of Baillarger). To get a decrease >in FA, one could do a number of things: > >1) Decrease the strength of radial diffusion >2) Increase the strength of tangential diffusion >3) Decrease the strength of both radial and tangential diffusion > >Are you looking for a measure that shows tissue damage? > >Matt. > >On 3/23/16, 7:55 PM, "Alshikho, Mohamad J." ><freesurfer-boun...@nmr.mgh.harvard.edu on behalf of >malshi...@mgh.harvard.edu> wrote: > >>It can explain one thing "tissue integrity" >> >>It will tell us neurobiologically exactly what can tell us in tissues >>other than the brain such as liver, lung, heart, joints, .... etc >> >>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 8:49 PM >>To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >>Subject: Re: [Freesurfer] Surface based analysis using FA maps >> >>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/028 >>>109 >>>.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 >> >>_______________________________________________ >>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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
