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
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
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
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:
> >
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
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:
>
Hello,
We are thinking about the hippocampal and lobar volumes in FS template space,
do we have such stats? Thanks.
Aize ___
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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 -
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 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:
>
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
> 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
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
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
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
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
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
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
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