Re: [Freesurfer] Surface based analysis using FA maps

2016-03-24 Thread Matt Glasser
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 diffusio

Re: [Freesurfer] Surface based analysis using FA maps

2016-03-23 Thread Alshikho, Mohamad J.
...@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

Re: [Freesurfer] Surface based analysis using FA maps

2016-03-23 Thread Matt Glasser
>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 >Subject: Re: [Freesurfer] Surface based an

Re: [Freesurfer] Surface based analysis using FA maps

2016-03-23 Thread Alshikho, Mohamad J.
urfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser Sent: Wednesday, March 23, 2016 8:49 PM To: Freesurfer support list 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

Re: [Freesurfer] Surface based analysis using FA maps

2016-03-23 Thread Matt Glasser
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,

Re: [Freesurfer] Surface based analysis using FA maps

2016-03-23 Thread Alshikho, Mohamad J.
March 23, 2016 8:04 PM To: Freesurfer support list 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

Re: [Freesurfer] Surface based analysis using FA maps

2016-03-23 Thread Matt Glasser
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

Re: [Freesurfer] Surface based analysis using FA maps

2016-03-22 Thread Douglas N Greve
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 i

[Freesurfer] Surface based analysis using FA maps

2016-03-22 Thread Alshikho, Mohamad J.
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 -

[Freesurfer] surface based analysis using FA maps

2016-03-19 Thread Alshikho, Mohamad J.
Hi Doug, 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