Nick- Doug wrote:
>Try this: >mri_vol2vol --mov aseg.mgz --targ rawavg.mgz --o aseg-in-native.mgz >--regheader --interp nearest >doug Sure enough, this worked. What I mean by "norm" is the file /mri/norm.mgz which gets created in the CA Normalize section of recon-all. Mike was kind enough to point out that this is the same as orig.mgz but, this was not what I was going after. What I meant by "native" was the T1 volume I input into freesurfer (before conversion from Analzye to mgz via mri_convert). After running Doug's command, and converting back to Analyze format, I now have a working copy of "aseg" (sub-cortical) that can be overlaid onto my, original, native space T1 MRI. Thanks everyone for your help. -Joel On Nov 13, 2007 12:43 PM, Nick Schmansky <[EMAIL PROTECTED]> wrote: > Joel, > > All freesurfer volume files, including aseg.mgz, are in native MRI > space. The various talairach transforms are used to align to the > atlases used in freesurfer. I'm not sure what you mean by 'norm' space. > The --apply_transform flag of mri_convert can be used to convert a > volume to talairach space (see mri_convert --help for details). > > Nick > > On Tue, 2007-11-13 at 12:01 -0600, joel bruss wrote: > > > Hello- > > > > I'm running FreeSurfer v4.01on SUSE Linux > > > > I'm interested in viewing the sub-cortical parcels, /mri/aseg.mgz, but > > in the native MRI space. I see that the output of "CA Label" produces > > a file that is fit to the "CA Normalize" step but I can't figure out > > the transform that was used. Specifically, for CA Normalize, if I > > look under /mri/transforms, and sort by time, I have both the > > talairach.lta and talairach.m3z files, but neither will get me from > > native to norm space (or vice-versa). Is there a transform file that > > I'm missing or is this a process of intermediate steps to get from > > native to norm space? Please help! > > > > Thanks, > > Joel > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
