Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas

Dear Matt,

Thanks for sending me this paper. I will read it. I would be absolutely okay doing it surface to surface, I am just not sure how. If you could give me a suggestion I can try. Thank you so much and sorry for all the bothering.

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 Glasser, Matthew glasserm@wustl.edu Sent: Sunday, May 16, 2021 9:50 PM To: Freesurfer support list Subject: [External] Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas

External Email - Use Caution Why not go directly surface to surface? You lose an enormous amount of precision going to the volume (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1vYBUtrqtPaubN3C6ATprkXO6ao6WzxWUGc6v_ITfRNf9sr...https://secure-web.cisco.com/1EmF4yT0huFgd-5CTXgyST_Nvchh6xXZHohWYFkGGNY6GgIP93yAwv5J1CNpi0iMSCUb8HurHMwuegb9C2LYfvSKllDEQyJYYXuUGTMpulkJJ5f31ZwU-O6YKR7Uu1GGZvYqIyiew4Hc7pKmTyHdGKXoQdxlGZ00okS6Pji3fI-HZpqMz1in2q2ZeVOZsRf5sW4CknAKt0gGW23-fOqBpBQ7QJuF3spTRg1AauMosng12GaBZBCufK6OG5gzKYlthsGj06kIa8SX3LxL1k8B_ng/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F129h7FK-zYnFPmjtoOZBCeExQUX7Akm5719AvgT3P9OynVehg_z4G1zvN7diSyupIWwn1aQ5CqNf2zDndOqo1ZJSDghdY1ykv0Aun3SdIa1CRmTMAB-Jo1bzPxJN7Ik3y5KdHQjImgJSxNUXbDTJ7Zet6e4VOjvy6mGat06Wee3ZSDCeQwE7fU-B5TIKCnbYozUX_jUUfz3g3LWyzAtHd2SUKEW85uHqppIyqzPTNq6pzpXjt1Ty5qrU7f_dhFlv5RjfJpslPZpNIrhDu3G9elw%2Fhttps%2A3A%2A2F%2A2Fwww.pnas.org%2A2Fcontent%2A2F115%2A2F27%2A2FE6356.short__%3BJSUlJSUlJQ%21%21CvMGjuU%21t56cia2idYK-SDP7o2pXZXIaWOe9mS7tXTJ__a2xKnfU0-0EzT28nIdTjHZLb8Xm0kpenHQ%24).

Matt.

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Romanella,Sara (BIDMC - Wilkinson - Neurology SF)" sromanel@bidmc.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Sunday, May 16, 2021 at 8:47 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas

Hi Matt and Bruce,

Thank you for answering me. I understand. Actually it is simpler than that. I have MNI coordinates of the surface resulting from a computational study and I need to see where they fall in the areas of the DK atlas. Do you have any suggestion?

About Connectome Workbench I was asking for a different project. I was hoping to map the entire Brodmann atlas on fsaverage but Bruce kindly advised me it is not possible for now.

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 Glasser, Matthew glasserm@wustl.edu Sent: Sunday, May 16, 2021 9:38 PM To: Freesurfer support list Subject: [External] Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas

External Email - Use Caution One reason Bruce may be asking why you need MNI coordinates is that MNI coordinates are a very poor substitute for surface-based statistical maps and a terrible way to compare across subjects. It’s much better to align subjects on the surface and then make much more accurate comparisons. If you have volume coordinates from an individual subject, you can project those accurately onto that subject’s cortical surface. In Connectome Workbench we do this with Foci, but I bet FreeSurfer has something similar. You just need to ensure that the coordinates and the surface are in the same volume space (i.e. are aligned with eachother). This could be in the subject’s physical space or MNI space (keep in mind that FreeSurfer never puts surfaces in MNI space, but we make copies of them there in the HCP Pipelines).

I also see you asked how to convert .mgh to a Connectome Workbench readable format. I must admit I’m not entirely sure what .mgh contains. If it is a value per vertex, you could likely use mris_convert to do the conversion to .func.gii. .annot can be converted to .label.gii with mris_convert.

Matt.

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Fischl, Bruce" BFISCHL@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Sunday, May 16, 2021 at 7:34 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas

Hi Sara

Why do you need MNI coordinates at all?

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Romanella,Sara (BIDMC - Wilkinson - Neurology SF) Sent: Sunday, May 16, 2021 5:57 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas

Hi Bruce,

I can convert the MNI coordinates to subject space. But how do I enter them in freeview when I open the DK atlas of the subject to see where they fall?

thank you for the help!

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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Sunday, May 16, 2021 10:31 AM To: Freesurfer support list Subject: [External] Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas

Hi Sara

Why do you need MNI at all? Why not just do it in individual subject space? Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Romanella,Sara (BIDMC - Wilkinson - Neurology SF) Sent: Saturday, May 15, 2021 8:43 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas

I am actually not sure. I have some MNI coordinates for the GM surface and I should check if they fall into a specific area of the DK. I could sacrifice accuracy in order to check this.

Could you please me tell me how if possible?

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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Saturday, May 15, 2021 6:04 PM To: Freesurfer support list Subject: [External] Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas

Do you need to do that in a common space? The DK is a surface atlas and won’t map very accurately to MNI. I think Doug has something for this, but you will definitely sacrifice accuracy

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Romanella,Sara (BIDMC - Wilkinson - Neurology SF) Sent: Saturday, May 15, 2021 5:56 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas

Thank you in any case! Do you maybe know if I can enter MNI coordinates in freeview and see where it falls into the areas of DK atlas?

Thank you!

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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Saturday, May 15, 2021 5:47 PM To: Freesurfer support list Subject: [External] Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas

Sorry, I don’t know what SimNIBS is (or how you can easily save a sphere in nifti format). Maybe someone else can comment?

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Romanella,Sara (BIDMC - Wilkinson - Neurology SF) Sent: Saturday, May 15, 2021 5:41 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas

Oh got it! It makes sense why I could not find it then! Thank you!

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?

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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Saturday, May 15, 2021 5:09 PM To: freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Saturday, May 15, 2021 2:58 PM To: freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Saturday, May 15, 2021 11:45 AM To: freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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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