?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 <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce <bfis...@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-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 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-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. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.
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