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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.edumailto: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
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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