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Hi Bruce, I have my subject's T1 image that I use as input in my recon -all call. But all the output from freesurfer (eg, surfaces in surf directory, labels in the label directory) are in freesurfer's space, aren't they? When I load the label with T1.mgz it appears in the correct location, but not when I load the native T1 image of the subject the label is not correct. So I simply want to have the labels in the native T1w-space of my subject. The same way I can for example convert a volume in from freesurfer space into native anatomical space ( https://secure-web.cisco.com/18dzfcomDtZKgTXJmODZL5YQnaa7EaSXDzc-sFiqm5_S_ti...) can I do the same with freesurfer labels? Best regards, Sam
On Fri, Jun 3, 2022 at 4:59 PM Fischl, Bruce BFISCHL@mgh.harvard.edu wrote:
The conformed space is an anatomical one, so I’m still not clear what “anatomical space” you want to map it to. What are you trying to do with it? And when you visualize the label in freeview in the volume does it appear in the correct location?
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Sam W *Sent:* Friday, June 3, 2022 10:46 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] labels in anatomical space
External Email - Use Caution *Hi Bruce,
Thanks for your help!
I got the label after running mri_annotation2label using the label\lh.aparc.annot file on an individual subject. I always assumed (maybe wrongly) that labels correspond to surfaces and are defined in freesurfer's conformed space.
Best regards,
Sam
On Fri, Jun 3, 2022 at 4:33 PM Fischl, Bruce BFISCHL@mgh.harvard.edu wrote:
Hi Sam
We need more information. What do you mean by “freesurfer space”? Is it on an individual subject or fsaverage? Volume or surface? How did you create it?
Cheers
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Sam W *Sent:* Friday, June 3, 2022 9:12 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] labels in anatomical space
External Email - Use Caution *Hello!
I have a label in freesurfer space, and I would like it to be in anatomical space. Is this possible?
Best regards,
Sam
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