For mni152 space, you'll need to register your anatomical to the 152 brain. You can do this with the freesurfer mni152reg program (might only be in the new version). Then use mri_vol2vol specifying this reg and also making sure that you use nearest neighbor interpolation. One problem is that this does not rotate the directions, so it might not be useful to you.
doug
caoaize wrote:
Hi, Doug,
If I want to use the generated gray matter for VBM analysis, I need to put them into the same space (MNI, or Talariach). Do you know where or how I can get that ? Thanks.
Aize
Date: Tue, 1 Mar 2011 16:31:52 -0500 From: greve@nmr.mgh.harvard.edu To: caoaize@hotmail.com Subject: Re: [Freesurfer] Whole brain gray matter image
You'll probably have to go to 255 or so (255 is corpus callosum). Also, for aparc+aseg, everything above 1000 will be GM. doug
caoaize wrote:
I am saying just look through 1to 98, and remove the IDs that relate with WM,vent, etc. No need to look at the the ID more than 100,
right?
Thanks.
Aize
Date: Tue, 1 Mar 2011 15:42:28 -0500 From: greve@nmr.mgh.harvard.edu To: caoaize@hotmail.com Subject: Re: [Freesurfer] Whole brain gray matter image
No, that will give you both WM and GM.
caoaize wrote:
Hi, Doug,
Should I just check the IDs from 1 to 98 in
FreesurferColorLUT.txt?
Aize
Date: Wed, 9 Feb 2011 14:27:08 -0500 From: greve@nmr.mgh.harvard.edu To: caoaize@hotmail.com Subject: Re: [Freesurfer] Whole brain gray matter image
Yea, though I think I'd use aparc+aseg for this since the cortex boundaries in the aseg are not great. The easiest way to do it
is to use
mri_binarize with the --match option. You could list all of the
IDs that
correspond to gray matter structures, but it is probably easier
to list
all the stuff that you don't want (eg, cerebral and
cerebellar white
matter, CC, hypointensit ies, CSF, etc, (and 0)), then use the
--inv to
invert it.
doug
caoaize wrote: > I need both cortical and subcortical. As I understand, I can
extract
> them from aseg.mgz, right? ribbon.mgz gives some information
too, any
> idea? Thanks. > > Aize > > > Date: Wed, 9 Feb 2011 11:44:15 -0500 > > From: greve@nmr.mgh.harvard.edu > > To: caoaize@hotmail.com > > CC: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] Whole brain gray matter image > > > > > > Do you want cortical and subcortical or just cortical? > > doug > > > > > > caoaize wrote: > > > 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 > > >
& gt; > > > > > > >
>
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> > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve@nmr.mgh.harvard.edu > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop:
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve