External Email - Use Caution
Why not go directly surface to surface? You lose an enormous amount of
precision going to the volume
(https://secure-web.cisco.com/129h7FK-zYnFPmjtoOZBCeExQUX7Akm5719AvgT3P9OynVehg_z4G1zvN7diSyupIWwn1aQ5CqNf2zDndOqo1ZJSDghdY1ykv0Aun3SdIa1CRmTMAB-Jo1bzPxJN7Ik3y5KdHQjImgJSxNUXbDTJ7Zet6e4VOjvy6mGat06Wee3ZSDCeQwE7fU-B5TIKCnbYozUX_jUUfz3g3LWyzAtHd2SUKEW85uHqppIyqzPTNq6pzpXjt1Ty5qrU7f_dhFlv5RjfJpslPZpNIrhDu3G9elw/https%3A%2F%2Fwww.pnas.org%2Fcontent%2F115%2F27%2FE6356.short).
Matt.
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Romanella,Sara
(BIDMC - Wilkinson - Neurology SF)" <sroma...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Glasser, Matthew
<glass...@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-boun...@nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce"
<bfis...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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-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: 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-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 8:43 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto: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-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 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-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 5:56 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto: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-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 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-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 5:41 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto: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-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 5:09 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto: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-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 4:56 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,
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
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