MNE and estimating subcortical sources like amygdala

✉️ Mailing List Archive (read-only)
1

Hi MNE Listserv.

I am looking to employ MNE to examine subcortical surfaces like amygdala and perhaps thalamus. Two studies have used MNE in part to accomplish this :

1) J Vis Exp. 2013 Jun 3;(76). doi: 10.3791/50212.

How to detect amygdala activity with magnetoencephalography using source imaging.

Balderston NL1, Schultz DH, Baillet S, Helmstetter FJ.

2) Article Source: MEG Evidence for Dynamic Amygdala Modulations by Gaze and Facial Emotions

Dumas T, Dubal S, Attal Y, Chupin M, Jouvent R, et al. (2013) MEG Evidence for Dynamic Amygdala Modulations by Gaze and Facial Emotions. PLoS ONE 8(9): e74145. doi: 10.1371/journal.pone.0074145

These studies however do not make clear however how to do the following:

-Merge amygdala surface with cortical surfaces

-Create and add sources at the amygdala vertices to those found in the cortex for subsequent model creation and source estimation.

If anyone has been down this road or has some suggestions I would be most appreciative.

Thanks// dave
David I. Leitman PhD

Research Assistant Professor
Department of Psychiatry-
Neuropsychiatry program
Perelman School of Medicine
University of Pennsylvania
Gates Pavilion 10th floor room 1042
3400 Spruce St
Philadelphia, PA 19104-4283
P: (215) 662-7389
F: (215) 662-7903
E: leitman at mail.med.upenn.edu
Faculty page: http://www.med.upenn.edu/apps/faculty/index.php/g275/p8174343
Lab website:
http://davidileitman.com

The information contained in this e-mail message is intended only for the personal and confidential use of the recipient(s) named above. If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this document in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please notify the the Neuropsychiatry Section immediately by e-mail, and delete the original message.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140220/b2c5722c/attachment.html

2

hi David,

what you want to do has been on the MNE wish list
for some time. It's also the first topic proposed for the Google summer code:

https://github.com/mne-tools/mne-python/wiki/GSOC-Ideas

So I fear the answer is no, nobody did this with MNE, but the good
news is that a few people could team up to make this happen.

If you know a good student who could apply for a GSOC that could help.

Best,
Alex

PS : I know very well the authors of 2) and they did for sure a lot of
engineering with in-house development to make it work.

3

OK Thanks,

I wish I had a student competent in python for the project. sadly I do not.

I know there is a way in brainstorm... though I have put off doing so because I like MNE and am not thrilled with the large footprint of Brainstorm...

It might be nice if there was some hack ... to use brainstorm for just one stage and then go back to MNE or vice versa.

thanks// dave

hi David,

what you want to do has been on the MNE wish list
for some time. It's also the first topic proposed for the Google summer code:

GSoC Ideas · mne-tools/mne-python Wiki · GitHub

So I fear the answer is no, nobody did this with MNE, but the good
news is that a few people could team up to make this happen.

If you know a good student who could apply for a GSOC that could help.

Best,
Alex

PS : I know very well the authors of 2) and they did for sure a lot of
engineering with in-house development to make it work.

Hi MNE Listserv.

I am looking to employ MNE to examine subcortical surfaces like amygdala and
perhaps thalamus. Two studies have used MNE in part to accomplish this :

1) J Vis Exp. 2013 Jun 3;(76). doi: 10.3791/50212.

How to detect amygdala activity with magnetoencephalography using source
imaging.

Balderston NL1, Schultz DH, Baillet S, Helmstetter FJ.

2) Article Source: MEG Evidence for Dynamic Amygdala Modulations by Gaze and
Facial Emotions

Dumas T, Dubal S, Attal Y, Chupin M, Jouvent R, et al. (2013) MEG Evidence
for Dynamic Amygdala Modulations by Gaze and Facial Emotions. PLoS ONE 8(9):
e74145. doi: 10.1371/journal.pone.0074145

These studies however do not make clear however how to do the following:

-Merge amygdala surface with cortical surfaces

-Create and add sources at the amygdala vertices to those found in the
cortex for subsequent model creation and source estimation.

If anyone has been down this road or has some suggestions I would be most
appreciative.

Thanks// dave
David I. Leitman PhD

Research Assistant Professor
Department of Psychiatry-
Neuropsychiatry program
Perelman School of Medicine
University of Pennsylvania
Gates Pavilion 10th floor room 1042
3400 Spruce St
Philadelphia, PA 19104-4283
P: (215) 662-7389
F: (215) 662-7903
E: leitman at mail.med.upenn.edu
Faculty page: http://www.med.upenn.edu/apps/faculty/index.php/g275/p8174343
Lab website:
http://davidileitman.com

The information contained in this e-mail message is intended only for the
personal and confidential use of the recipient(s) named above. If the
reader of this message is not the intended recipient or an agent responsible
for delivering it to the intended recipient, you are hereby notified that
you have received this document in error and that any review, dissemination,
distribution, or copying of this message is strictly prohibited. If you
have received this communication in error, please notify the the
Neuropsychiatry Section immediately by e-mail, and delete the original
message.

_______________________________________________
Mne_analysis mailing list
Mne_analysis at nmr.mgh.harvard.edu
Mne_analysis Info Page

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
MyComplianceReport.com: Compliance and Ethics Reporting . If the e-mail was sent to you in
error
but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.

David I. Leitman PhD

Research Assistant Professor
Department of Psychiatry-
Neuropsychiatry program
Perelman School of Medicine
University of Pennsylvania
Gates Pavilion 10th floor room 1042
3400 Spruce St
Philadelphia, PA 19104-4283
P: (215) 662-7389
F: (215) 662-7903
E: leitman at mail.med.upenn.edu
Faculty page: http://www.med.upenn.edu/apps/faculty/index.php/g275/p8174343
Lab website:
http://davidileitman.com

The information contained in this e-mail message is intended only for the personal and confidential use of the recipient(s) named above. If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this document in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please notify the the Neuropsychiatry Section immediately by e-mail, and delete the original message.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140221/a989da90/attachment.html