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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Fischl, Bruce <bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>> Sent: Saturday, May 15, 2021 2:58 PM To: freesurfer@nmr.mgh.harvard.edu<mailto: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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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<mailto: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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Fischl, Bruce <bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>> Sent: Saturday, May 15, 2021 11:45 AM To: freesurfer@nmr.mgh.harvard.edu<mailto: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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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<mailto: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 ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. 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