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 nicks@nmr.mgh.harvard.edu 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