Sorry for bothering again, but I have a similar issue on the DK atlas and I was wondering if you could also help me.

I have some spheres saved in nifti in both MNI and/or subject's space (from SimNIBS), and I would like to see if they fall into a specific area of the DK atlas in FS. Do you have any suggestion how can I check this?

Should I open the aparc+aseg DK atlas of the subject in freeview and somehow convert the nifti sphere and overlap them? The subject's space from SimNIBS and from FS output would be different?

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce <BFISCHL@mgh.harvard.edu>
Sent: Saturday, May 15, 2021 5:09 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [External] Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas

There should be the same BA labels on every subject, And no, not all of them, that is an ongoing project for neuroscience!
Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Romanella,Sara (BIDMC - Wilkinson - Neurology SF)
Sent: Saturday, May 15, 2021 4:56 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas

Hi Bruce,

I did see there are some BA labels for each subjects, but not all of them is that right?

Thank you!

Sara Romanella

Fellow (Ph.D. in Neuroscience)

Berenson-Allen Center for Noninvasive Brain Stimulation

Department of Neurology | Beth Israel Deaconess Medical Center
330 Brookline Avenue, 02215 Boston, MA, USA

Phone Nr: +1-339-229-7645

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce <BFISCHL@mgh.harvard.edu>
Sent: Saturday, May 15, 2021 2:58 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [External] Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas

Hi Sara

We keep statistics on each of the BAs separately, as stored in the various label files. During recon-all we put them together into a single non-overlapping .annot file that you can use for visualization on individual subjects. I thought he had done that for fsaverage also, but I looked briefly and didn’t see it, so you can just do it yourself if it would be useful. We’ll probably included it in future releases

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Romanella,Sara (BIDMC - Wilkinson - Neurology SF)
Sent: Saturday, May 15, 2021 12:23 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas

Hi Bruce,

thanks for the help, but I do not understand. Is there no template of BA atlas in fsaverage? Do I have to create it manually with the mris_label2annot? And in this case how should I do it? Thank you so much

Sara

Sara Romanella

Fellow (Ph.D. in Neuroscience)

Berenson-Allen Center for Noninvasive Brain Stimulation

Department of Neurology | Beth Israel Deaconess Medical Center
330 Brookline Avenue, 02215 Boston, MA, USA

Phone Nr: +1-339-229-7645

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce <BFISCHL@mgh.harvard.edu>
Sent: Saturday, May 15, 2021 11:45 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [External] Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas

Hi Sara

You can assemble all the BA labels on fsaverage into a .annot file and display it that way if you want. mris_label2annot should do the trick. Just give it all the appropriate either with/without thresh (?h.BA*_exvivo.label or ?h.BA*_exvivo.thresh.label)

Or just load the individual labels, which would be easy enough to do in a script to build the freeview command line

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Romanella,Sara (BIDMC - Wilkinson - Neurology SF)
Sent: Saturday, May 15, 2021 8:59 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Overlay of MGH clusters on Broadmann atlas

Hi FreeSurfer community,

I have a cluster.mgh file (along with the .annot and .summary) resulting from correlation analysis of cortical thickness in a group of patients. I can open it as overlay in freeview but I was wondering if there was any chance to overlay it to a Broadmann atlas (hopefully in freeview) so I can visually show the overlap of the clusters with the BA areas. I cannot seem to find a Broadmann atlas in fsaverage to open in freeview.

Also I was wondering, if I want to convert .mgh and open it on Connectome Workbench what extension do you think I should use (e.g., .gii). Should I use mri_convert or mris_convert? I am not sure if .mgh should be converted as a surface.

Thank you so much for your help!

Sara

Sara Romanella

Fellow (Ph.D. in Neuroscience)

Berenson-Allen Center for Noninvasive Brain Stimulation

Department of Neurology | Beth Israel Deaconess Medical Center
330 Brookline Avenue, 02215 Boston, MA, USA

Phone Nr: +1-339-229-7645

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