I would have thought it would show properly on your input T1 image since that
is just a header updating of the coordinates. You might have to use
mri_label2label, but I defer to Doug who knows more about this stuff than I do
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Sam W
Sent: Friday, June 3, 2022 12:03 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] labels in anatomical space
External Email - Use Caution
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 (MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat<https://secure-web.cisco.com/18dzfcomDtZKgTXJmODZL5YQnaa7EaSXDzc-sFiqm5_S_ti1SsYzb9jJcW91yyAIetFqdYWWqFTbZvpEq8BUY0_Jqq9s6yLMhtA1J2_MM06vmMim_16wjJfSILdm1MDzlX2B5KnvnnscKzhpRtYAYCS-MsKoPi2FCUavsTmrAqi0F--8HVzcU-S06NO3ZR_Z4S8UFw0eCJiTTo44QvMRfhR-t4ozX1ycpYpHV-h9MQl8KE0DV-OrqsV7uQU_gxbaLIl7SQeLo9fLKXARb5PZ9X-IHyfQhf_PIcOb6l4jJqZME_CByZqGbYbpvpD3tYyXIg3Q5SZyGvjmG_QnzD_xw6Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsAnat-to-NativeAnat>)
can I do the same with freesurfer labels?
Best regards,
Sam
On Fri, Jun 3, 2022 at 4:59 PM Fischl, Bruce
<bfis...@mgh.harvard.edu<mailto:bfis...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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<mailto: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
<bfis...@mgh.harvard.edu<mailto:bfis...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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<mailto: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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