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" <ZNASIRIAVANAKI@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. <DGREVE@mgh.harvard.edu<mailto:DGREVE@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
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu<mailto: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

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer