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: gr...@nmr.mgh.harvard.edu > > To: caoa...@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: gr...@nmr.mgh.harvard.edu > > > > To: caoa...@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: gr...@nmr.mgh.harvard.edu > > > > > > To: caoa...@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: gr...@nmr.mgh.harvard.edu > > > > > > > > To: caoa...@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; > > > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > > > 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: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > > 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 th e e-mail. > > > > > > > > > > > > > > > > > > > > -- > > > > > > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > > > > > > > > > -- > > > > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > > > -- > > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > * -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
