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

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

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

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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Tim Schäfer ts+ml@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" 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

---

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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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