Hi Tim
Thanks for you reply.
I did use the command you recommended ( tksurfer subject23 lh inflated -ov
sig.nii.gz )
But, I don't see any activation on it. However, when I use ( tksurfer
fsaverage lh inflated -ov sig.nii.gz ), I see patches of activation.
Is it because my whole analysis is done on fsaverage and not native space?
Zahra (Mona) Nasiriavanaki
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Tim Schäfer
<ts...@rcmd.org>
Sent: Monday, October 28, 2019 10:28 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] view labels in native space
External Email - Use Caution
If I get the question correctly, all you have to do is:
1) not run mri_label2label at all
2) replace 'fsaverage' with the subject identifier in the command, e.g.:
tksurfer subject23 lh inflated -ov sig.nii.gz
Best,
Tim
> On October 28, 2019 at 3:21 PM "Nasiriavanaki, Zahra"
> <znasiriavan...@mgh.harvard.edu> wrote:
>
>
> Hi Doug
>
> Thanks for your reply.
> Could you pleas let me know how I can solve this issue?
> How should I view those labels on the subject’s native space?
>
> Thanks
> Mona
>
> On Oct 28, 2019, at 10:18 AM, Greve, Douglas N.,Ph.D.
> <dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> wrote:
>
> yes, the vertices in one subject do not have any correspondence to vertices
> in an other subject
>
> On 10/25/19 12:08 PM, Nasiriavanaki, Zahra wrote:
> Hi Freesurfer experts
>
> I have a few labels that correspond to activation clusters in fsaverage space
> for an individual subject. I used mri_label2label to transfer them to native
> space of the subject.
>
> export
> SUBJECTS_DIR=/autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR
> mri_label2label --srclabel
> ./first_levels/$subj/label/aparc/pos/lh-0001.label --trglabel lh-new.label
> --srcsubject fsaverage --trgsubject ${subj} --regmethod surface --hemi lh
>
> When I overlay the native label on top of the fsaverage significance map
> (tksurfer fsaverage lh inflated -ov sig.nii.gz), it looks like small dots all
> over the map.
> Is this because I'm viewing the native label in fsaverage space?
> Is there a way to view these labels in this subject's native space instead of
> fsaverage, something like tksurfer native(instead of fsaverage) lh inflated
> -ov sig.nii.gz?
>
> Thank you very much in advance
> Mona
>
>
> Zahra (Mona) Nasiriavanaki
> Postdoctoral Research Fellow
> Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> 149 13th Street, 149-2615
> Charlestown, MA, USA, 02129
>
>
>
>
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--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
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