[Freesurfer] Whole brain gray matter image

Hello FS Experts, I am trying to generate the whole brain gray matter image, I use aparc_aseg.mgz - wm.mgz for gray matter mask, then use this mask for gray matter. Is it correct? What is the difference between aseg.mgz and ribbon.mgz? Hope your help. Thanks. Aize

[Freesurfer] Cortical thickness in the template space

Hello, We try to look at the two group difference of cortical thickness, but I need the lh(or rh).thickness file, which reported in template space (FS average space), but after run recon-all -all, what I have is only lh.thickness, or rh.thickness, which is in subject's space. Would someone p

[Freesurfer] Distance between two points along cortical

Hello FS Experts, Suppose we have two points on the cortical surface (pial for example), we want to know the distance between these two point along cortical surface (not direct distance). Does FS report this kind of distance? Any suggestion will be very appreciated. Aize

Re: [Freesurfer] Distance between two points along cortical

nd --mpmArgs > startVertex:1,endVertex:3 > > Note, that this is *not* the geodesic, but is very close. The path is > constrained to run along the surface mesh, so will in general be > slightly longer than the geodesic. > > > On 4/1/11 12:28 , caoaize wrote: > >

Re: [Freesurfer] Cortical thickness in the template space

rent smoothing levels onto the fsaverage subject space. > > n. > > On Wed, 2011-03-09 at 05:46 +0800, caoaize wrote: > > > > Hello, > > > > We try to look at the two group difference of cortical thickness, but > > I need the lh(or rh).thickness file, wh

Re: [Freesurfer] Cortical thickness in the template space

u > To: caoa...@hotmail.com > CC: ni...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Cortical thickness in the template space > > Hi Aize, > > yes, that should do it. > > cheers, > Bruce > On Fri, 15 Apr 2011, caoaize wrote: >

[Freesurfer] Stats for HC and lobar volumes in template space

Hello, We are thinking about the hippocampal and lobar volumes in FS template space, do we have such stats? Thanks. Aize ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.ed

[Freesurfer] (no subject)

Hi, there, I have some problem for the hippocampus segmentation results. 1. My structural data are originally in par-rec file. I used r2agui to convert them into .nii format, then use recon-all -i to convert the .nii data into freesurfer .mgz format. Based on these operations, I run recon-all -

[Freesurfer] Hippocampus segmentation problem

Hi, there, I have some problem for the hippocampus segmentation results. 1. My structural data are originally in par-rec file. I used r2agui to convert them into .nii format, then use recon-all -i to convert the .nii data into freesurfer .mgz format. Based on these operations, I run recon-all -a

Re: [Freesurfer] (no subject)

re fimbria and alveus considered part of > > the hippocampus? > > > > As far as left/right switches go, do you have any fiducial markers (e.g. > > vitamin E tablets) in the images? > > > > cheers > > Bruce > > On Sat, 15 Aug 2009, caoaize wrote: >

Re: [Freesurfer] (no subject)

ICE is usually close to .9 for hippocampus. > What acquisitions are you using? > > cheers, > Bruce > On Sat, 15 Aug 2009, caoaize wrote: > > > > > Hi, Bruce, > > > > > > > > Our segmentation protocol is the same one as Freesurfer's auto

Re: [Freesurfer] (no subject)

> wow, I don't think I've ever seen a T1-weighted MR with gray matter this > dark. The gray/csf contrast is very low. What kind of sequence is it? > > On Tue, 18 Aug 2009, caoaize wrote: > > > > > Hi, Bruce, > > > > > > > > Here is the aseg

Re: [Freesurfer] (no subject)

e parameters? If not, we probably could suggest some better ones. > > cheers, > Bruce > > On Tue, 18 Aug 2009, caoaize > wrote: > > > > > Hello Bruce, > > > > > > > > The sequence we used is called Turbo field Echo, I need to check it ag

Re: [Freesurfer] (no subject)

f from the atlas, that should help. > > cheers > Bruce > > On Tue, 18 Aug 2009, caoaize wrote: > > > > > Hi, Bruce, > > > > Do you mean that we can not use freesurfer for hippocampus volume > > segmentation, if my data are with the same sc

[Freesurfer] Volumes of four major cortical lobes

Hi, Bruce, We want calculate the four major cortical lobe volumes, i.e. frontal, parietal, temporal, and occipital, to see the relationship between them and some ROIs. I did fully run recon-all, but not clear which file should be used and what cortical areas should be included in these four

[Freesurfer] Symmetry on four major cortex lobes on left and right hemisphere

Hello Bruce, Based on Freesurfer segmentation, we calculated the volumes of four major cortex lobes on left and right hemisphere seperately. Now I hope to find some reports illustrate the symmetry stuff using Freesurfer. Do you know where I can find it ? Thanks. Aize

[Freesurfer] Question about manually editing pial surface

Hello Freesurfer expert, I have a question on how to manually edit the pial surface. My structure data are fully processed using recon-all -all. Then I go back to look at the white/pial surface and sub-cortical boundaries. In some data, I found the gray matter is not included in the pial surfac

[Freesurfer] Freesurfer subcortical segmentation and FSL FIRST

Hello Freesurfer Experts, I have a very basic question about the difference between Freesurfer subcortical segmentation tool and FSL FIRSTsub-cortical segmentation tool. May someone give me a point? Thanks. Aize _