[Freesurfer] Postdoctoral Fellowship at Harvard Medical School

[Baran, Bengi]

Dear members,

Please feel free to distribute the job ad below as you see fit.

Best,


Bengi Baran, Ph.D.
Instructor in Psychiatry, Harvard Medical School
Massachusetts General Hospital
Martinos Center for Biomedical Imaging
149 13th Street, Room 2626
Charlestown Navy Yard
Charlestown, MA 02129
email: bba...@mgh.harvard.edu
phone: 617-643-7964
fax: 617-726-4078




Postdoctoral Fellowship at the Martinos Center for Biomedical Imaging and the 
Psychiatric Neuroimaging Division of the Psychiatry Department at Massachusetts 
General Hospital, Charlestown, MA and Harvard Medical School
Position Description: Clinical/Cognitive Neuroscience Research
Project: Multimodal neuroimaging studies of sleep and memory
PI: Dara S. Manoach, Ph.D.

The position will involve investigating the role of sleep in memory 
consolidation, how these processes go awry in schizophrenia and autism, and the 
effects of pharmacological and other interventions.  Our work has linked 
cognitive deficits to specific heritable mechanisms (sleep spindles and other 
sleep oscillations) and we are seeking effective interventions.  In 
collaboration with Dr. Robert Stickgold’s lab at Beth Israel Deaconess Medical 
Center, we are extending and expanding this basic and clinical research program 
using state-of-the art tools including high density EEG, MEG, DTI, functional 
connectivity MRI, fMRI, and behavioral studies.  We are seeking someone to 
participate in these foundation and NIMH-funded investigations who is familiar 
with cognitive neuroscience, neuroimaging methodology including MEG and/or EEG 
and data analysis, and is interested in developing research questions and 
optimizing analysis streams tailored to the study aims and populations.  New 
approaches and ideas are encouraged, as are independent projects that dovetail 
with current studies.  The position requires working closely with the PI, as 
well as with Dr. Stickgold, other Martinos Center investigators, particularly 
Dr. Matti Hamalainen, Director of the MEG Core Lab, and lab mates to design 
studies, acquire data, and develop, explore, improve and apply data analytic 
techniques. Training in clinical research and in the acquisition, analysis, and 
interpretation of neuroimaging data will be provided.

Requirements: PhD (or MD) in neuroscience, psychology, engineering or a related 
discipline and a strong research background are required. Ideal candidates 
would have extensive experience in data analysis, a background in computational 
neuroscience and/or signal processing, be proficient in Matlab/Python and be 
interested in methods development. The following are also beneficial: 
experience with MEG/EEG data analysis/methodology, background in cognitive 
neuroscience, experimental psychology and sleep; interest/experience with 
clinical populations; and experience in task design and analysis for cognitive 
experiments.


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[Freesurfer] Postdoctoral Fellowship at the Martinos Center

[Baran, Bengi]

We believe this posting may be of interest for some members of the group:


Postdoctoral Fellowship at the Martinos Center for Biomedical Imaging and the 
Psychiatric Neuroimaging.
Division of the Psychiatry Department at Massachusetts General Hospital, 
Charlestown, MA.
Project: Multimodal neuroimaging studies of sleep and memory
PI: Dara S. Manoach, Ph.D.


The position will involve investigating the role of sleep in memory 
consolidation, how these processes go awry in schizophrenia and autism, and the 
efficacy of pharmacological and other interventions. Our work has linked 
cognitive deficits to a specific heritable mechanism (sleep spindles) and we 
are seeking effective interventions. In collaboration with Dr. Robert 
Stickgold’s lab at Beth Israel Deaconess Medical Center, we are extending and 
expanding this basic and clinical research program using state-of-the art tools 
including high density EEG (polysomnography), MEG, DTI, functional connectivity 
MRI, fMRI, and behavioral studies. We are seeking someone to participate in 
these foundation and NIMH-funded investigations who is familiar with MEG/EEG 
methodology and data analysis, comfortable with methodological innovation, and 
is interested in optimizing and developing analysis streams tailored to the 
study aims and populations. New approaches and ideas are encouraged, as are 
independent projects that dovetail with current studies. The position requires 
working closely with the PI, as well as with Dr. Stickgold, other Martinos 
Center investigators, particularly Dr. Matti Hamalainen, Director of the MEG 
Core Lab, and lab mates to design studies, acquire data, and develop, explore, 
improve and apply data analytic techniques. Training in clinical research and 
in the acquisition, analysis, and interpretation of neuroimaging data will be 
provided.

Requirements: PhD or MD Experience with MEG/EEG data analysis/methodology 
and/or other signal processing. Background in cognitive neuroscience, 
experimental psychology, and an interest in clinical applications are a plus.

Position available immediately. Interested applicants should email: (a) CV, (b) 
statement of post-doctoral and career goals, (c) writing sample (e.g., a 
published manuscript), and (d) letters and/or contact information for three 
references to Dara Manoach 
dara.mano...@mgh.harvard.edu
Stipend levels are in line with experience and NIH. A two-year commitment is 
required.



Best,




Bengi Baran, Ph.D.
Post-Doctoral Fellow
Martinos Center for Biomedical Imaging
Harvard Medical School
Massachusetts General Hospital
149 13th Street
Charlestown Navy Yard
Charlestown, MA 02129
email: bba...@mgh.harvard.edu
phone: 617-643-7964
fax: 617-726-4078
https://sleep.med.harvard.edu/people/trainees/1598/Bengi+Baran+MA+PhD



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but does not contain patient information, please contact the sender and properly
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[Freesurfer] segmentation of the thalamus?

[Baran, Bengi]

Dear FreeSurfer developers and users,

I’m wondering if any of you worked on further segmentation of the thalamus into 
thalamic nuclei or e.g. dorsal vs. medial thalamus.


Thanks,
Bengi



Bengi Baran, Ph.D.
Post-Doctoral Fellow
Martinos Center for Biomedical Imaging
Harvard Medical School
Massachusetts General Hospital
149 13th Street
Charlestown Navy Yard
Charlestown, MA 02129
email: bba...@partners.org
phone: 617-643-7964
fax: 617-726-4078
https://sleep.med.harvard.edu/people/trainees/1598/Bengi+Baran+MA+PhD

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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
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but does not contain patient information, please contact the sender and properly
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[Freesurfer] missing raw.fsnr files

[Baran, Bengi]

Hi,

We’re trying to run isxconcat -sess and ran into the following error:

ERROR: cannot determine format for stem …./raw.fsnr

Apparently our individual subject analysis files do not include a raw.fsnr file 
instead we have fsnr.nii in all the contrast folders.

This error terminates isxconcat so we’re unable to get the surface based 
ces.nii etc files

Any idea why that may be the case or is there any flag to remove this step?

Best,



Bengi Baran, Ph.D.
Post-Doctoral Fellow
Martinos Center for Biomedical Imaging
Harvard Medical School
Massachusetts General Hospital
149 13th Street
Charlestown Navy Yard
Charlestown, MA 02129
email: bba...@partners.org
phone: 617-643-7964
fax: 617-726-4078
https://sleep.med.harvard.edu/people/trainees/1598/Bengi+Baran+MA+PhD

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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
http://www.partners.org/complianceline . 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.