[Freesurfer] Postdoctoral Position in Division of Neurotherapeutics at MGH/HMS (Boston, MA)

[Afzal, Afsana]

Hi everyone,

The Division of Neurotherapeutics at Massachusetts General Hospital (Boston, 
MA) has an open postdoctoral position. The posting is below:



NEUROIMAGING POSTDOCTORAL POSITION IN DIVISION OF NEUROTHERAPEUTICS AT HARVARD 
MEDICAL SCHOOL/ MASSACHUSETTS GENERAL HOSPITAL


The Division of Neurotherapeutics at the Massachusetts General Hospital is 
looking for a neuroimaging postdoctoral fellow to join the research group of 
Drs. Darin Dougherty MD, Thilo Deckersbach PhD and Alik Widge MD PhD.


Overview

Research projects will focus on developing pipelines for multi-modal MRI 
analysis with the aim of investigating psychopathology along transdiagnstic 
domains under the TRANSFORM DBS project, using task-based and resting-state 
fMRI and structural MRI data. The post-doctoral fellow will have the 
opportunity to collaborate and work with an interdisciplinary team of 
clinicians, neuroscientists and engineers and have significant opportunities to 
advance their career.


Your Profile

We seek a postdoctoral candidate with a Ph.D. in psychology, neuroscience, or 
related discipline with an interest translational neuroscience with a strong 
background in Python, Matlab, or R. The ideal candidate would have extensive 
knowledge of computational neuroimaging. Expertise in cognitive modeling, graph 
theory, or machine learning is also highly desirable. Knowledge of common 
neuroimaging software, especially FreeSurfer and FSL, is also appreciated. 
Interest in understanding mechanisms underlying major psychiatric disorders and 
enthusiasm for working with psychiatric populations is necessary. Highly 
motivated individuals with a record of productive research are encouraged to 
apply.


Benefits

Benefits of this postdoctoral position include (1) access to numerous sets of 
high-quality, multi-modal MRI data; (2) opportunities to analyze and publish on 
these datasets; (3) mentoring for career development; and (4) access to imaging 
experts from around the world and to state-of-the-art tools for the development 
of neuroscientific and clinical research at the Martinos Center.


Lab Description

The Division of Neurotherapeutics at MGH is a multidisciplinary translational 
neuroscience group located at the Athinoula A. Martinos Center for Biomedical 
Imaging in Charlestown, MA. Our focus is on neurotherapeutic interventions for 
severe, treatment-resistant psychiatric illnesses, particularly for major 
depressive disorder, obsessive compulsive disorder, anxiety disorders, and 
eating disorders.

Our research spans both mechanistic studies, clinical trials, and device-based 
interventions employing a variety of techniques, including neuroimaging and 
electrophysiology. We also provide clinical services and surgical treatments 
for psychiatric illness.

Our work utilizes functional and structural magnetic resonance imaging (fMRI), 
positron emission tomography (PET), electroencephalography (EEG), 
magnetoencephalography (MEG) to further understanding of psychiatric illness 
and treatment. We use transcranial magnetic stimulation (TMS), vagus nerve 
stimulation (VNS) and deep brain stimulation (DBS) as tools to both treat 
disease and understand the neural correlates of mental illness.

Lab Website: 
http://www.massgeneral.org/psychiatry/research/researchlab.aspx?id=1659

Contact: Afsana Afzal - aaf...@mgh.harvard.edu

__
Afsana Afzal
Clinical Research Coordinator
Massachusetts General Hospital
Division of Neurotherapeutics
Department of Psychiatry: Neurosciences
149 13th St, Room 2612
Charlestown, MA 02129
Phone: 617-643-5129
Fax: 617-726-4078
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Re: [Freesurfer] longitudinal tracula error

[Yendiki, Anastasia]

Hi Barbara – Thank you for your kind words. As you’ve read, if the output files 
are generated, then you’re good to go. Bedpost does not differentiate between 
longitudinal and cross-sectional data, so it’s run separately on each time 
point’s …/dmri/ folder.

Best,
a.y

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Bárbara Avelar Pereira 
mailto:barbara.avelar.pere...@ki.se>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, January 30, 2017 at 10:48 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks again for the help! And congrats on tracula — it's a great tool, and the 
online support is really good :)

I do have a follow-up question, if that’s OK. I’m currently running bedpost, 
and it gives the following error:

(…)
53 slices processed
54 slices processed
54 slices processed
55 slices processed
Queuing post processing stage
64 slices processed
For some reason the bedpostX process DOES NOT appear to have successfully 
completed. Please examine your results carefully.
/usr/local/freesurfer/bin/bedpostx_mgh: line 345: kill: (21128) - No such 
process

I was not running this on a cluster, but I was running a few subjects at the 
same time so I was wondering if it could be a memory problem? Or a 
compatibility problem between FSL and freesurfer?

It seems strange that it shows the same slice more than once on the monitor. 
But from what I read, the monitor is not entirely reliable and the best way to 
check whether everything ran smoothly is to look at the output. I have all the 
files that should have been created, but I’m still suspicious that something 
might be wrong. For example, my merged_xxx files are 50 volumes (should they 
have the same number of volumes as my original nii file? Because this is not 
the case...).

I’ve also tried running it directly from the command line and the error is the 
same (however, since this is longitudinal, when running bedpost from the 
command line, can I simply run it for each timepoint separately as if it was 
cross-sectional or is there an extra step?)

Many thanks!

On 26 Jan 2017, at 14:51, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Glad to hear it, thanks for checking! If the final 6.0 works, there's no need 
to dig up the beta.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
[freesurfer-boun...@nmr.mgh.harvard.edu]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se]
Sent: Thursday, January 26, 2017 3:29 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your help! Sorry for the delay in replying -- just wanted to 
make sure the was problem was indeed solved. Since I'm using a server for which 
I have no administrative rights, I had to wait before the update was installed. 
It seems to run perfectly now.
I can't find the beta version I was using at the time (just deleted it once I 
realised I was having the same problem), but if I manage to trace it back, I'll 
let you know.

Once again, thanks, I'm super grateful!


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
[freesurfer-boun...@nmr.mgh.harvard.edu]
 on behalf of Yendiki, Anastasia 
[ayend...@mgh.harvard.edu]
Sent: Sunday, January 22, 2017 7:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Barbara - If you're using the 5.3 version, then you'll have to download the 
update from 2014:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

This should fix the problem. But if there's a version of the 6.0 beta that was 
having the same problem, please let me know (by sending the trac-all copy of 
that version) so I can fix that asap.

Thanks!

a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
[freesurfer-boun...@nmr.mgh.harvard.edu]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se]
Sent: Friday, January 20, 2017 7:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your quick reply. I've only tried version 6.0 to determine 
whether the error was possibly version-related, but that doesn’t seem to be the 
case… I'm actually working with version 5.3 so I'll send attach the 
trac-all.local-copy for that if that’s OK. Once again, thank you!

On 20 Jan 2017, at 23:52, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Barbara - If

[Freesurfer] Binary images multiplication

[Sahil Bajaj]

Hi,

I would like to multiply two binary images (standard brain image with an
ROI) using fslmaths (or may be using some other way) command. Although both
are in standard space but image dimensions are different. I was wondering
if there is any way I can do that without any co-registration step.

Thanks,
Sahil
-- 
-- 
-
Sahil Bajaj
Post-doctoral Fellow
Nantz National Alzheimer's Center, Department of Neurology
The Houston Methodist Research Institute (THMRI)
Houston, TX, USA.
E-mail:sahil.br...@gmail.com 
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Re: [Freesurfer] Command for Reverse Normalizing with mri_vol2vol Using CVS m3z Morphs (REPOST)

[Douglas Merkitch]

Hello,

I'm reposting the following just in case anyone has any ideas. Any input would 
be greatly appreciated!

Thank you very much for the suggestion. Here then are my attempts at putting 
what you said into two sequential commands:

mri_vol2vol --targ $SUBJECTS_DIR/$subj/mri/norm.mgz \
--m3z 
$SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \
--noDefM3zPath --inv-morph \
--mov $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \
--o temporary_volume.mgz \
--interp trilin --no-save-reg

mri_vol2vol --targ temporary_volume.mgz \
--reg $SUBJECTS_DIR/$subj/dtrecon/register.dat \
--inv \
--mov $SUBJECTS_DIR/$subj/dtrecon/lowb.nii \
--o lowb.ANAT+CVS-to-avg35.mgz \
--interp trilin --no-save-reg

Do the above commands look OK? I tried these commands, but the results were not 
great so I suspect that something is incorrect in the syntax and/or inputs.

Thanks,

Doug

Douglas Merkitch
Neurological Sciences
Rush University Medical Center



On Jan 26, 2017, at 2:41 PM, Douglas Merkitch 
mailto:douglas_merki...@rush.edu>> wrote:

Hello Lilla,

Thank you very much for the suggestion. Here then are my attempts at putting 
what you said into two sequential commands:

mri_vol2vol --targ $SUBJECTS_DIR/$subj/mri/norm.mgz \
--m3z 
$SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \
--noDefM3zPath --inv-morph \
--mov $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \
--o temporary_volume.mgz \
--interp trilin --no-save-reg

mri_vol2vol --targ temporary_volume.mgz \
--reg $SUBJECTS_DIR/$subj/dtrecon/register.dat \
--inv \
--mov $SUBJECTS_DIR/$subj/dtrecon/lowb.nii \
--o lowb.ANAT+CVS-to-avg35.mgz \
--interp trilin --no-save-reg

Do the above commands look OK? I tried these commands, but the results were not 
great so I suspect that something is incorrect in the syntax and/or inputs.

Thanks for your help!

Doug

Douglas Merkitch
Neurological Sciences
Rush University Medical Center
Email: douglas_merki...@rush.edu





On Jan 26, 2017, at 8:42 AM, Lilla Zollei 
mailto:lzol...@nmr.mgh.harvard.edu>>
 wrote:


Hi Doug,

In order to compute and apply the inverse of an m3z transform you would need to 
use the --inv-morph flag instead of the --m3z and reverse your targ and mov 
inputs. With the current implementation of mri_vol2vol though I do not think 
that you can specify the order of the transforms (which is important here), so 
you would need to apply the inverse non-linear trasform first and then the 
inverse rigid.

Lilla

On Wed, 25 Jan 2017, Douglas Merkitch wrote:

Hello Freesurfer experts,
>From your wiki page, I understand how to normalize volumes in subject 
>diffusion space to the CVS template:
mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \
   --m3z 
$SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \
   --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \
   --mov fa-masked.mgz \
   --o fa-masked.ANAT+CVS-to-avg35.mgz \
   --interp trilin --no-save-reg
However, how would one take take a volume in CVS template space and reverse 
normalize it back to subject diffusion space? Is this possible? If so, what 
would that command look like and what other st
eps would be necessary to get the required inputs?
Thanks,
Doug
Douglas Merkitch
Neurological Sciences
Rush University Medical Center
Email: douglas_merki...@rush.edu
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Re: [Freesurfer] Neighborhood thickness in a 10mm radius

[Douglas N Greve]

You can smooth it. This would give you a gaussian kernel instead of the 
box kernel that you describe. Set the fwhm to the radius you want 
(mris_fwhm with --smoothonly option)


On 01/31/2017 04:48 PM, Dorian P. wrote:
> Hi Freesurfers,
>
> Thank you for the help you provide through this list.
>
> Is there a way to get, for each vertex, the identify (or thickness 
> values) of the surrounding vertices in a 10mm radius? The command 
> mris_convert has the '-v' option, but that produces only 5-6 vertices 
> and there is no option to query a particular radius.
>
> I imagine this can be done manually outside Freesurfer by first 
> identifying the neighbors for each vertex based on the coordinates, 
> then getting the respective thickness value, but I wanted to check 
> whether there is any easier way or any advice on how to proceed.
>
> Dorian
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Neighborhood thickness in a 10mm radius

[Dorian P.]

Douglas, thank you for the quick reply.

I am trying to figure out how can mri_fwhm help in this contect but can't
grasp it. I tried some of the example commands in the wiki, applied on a
XX.thickness file, but the outcome is NaN.

To clarify, what I am trying to do is detect local variations in thickness
which might be a biomarker of pathology. A generic value for the whole
brain does not help, I will need to localize the "anomaly". I thought I can
do this by something like raw neighboring values, but maybe an estimation
of the smoothing of thethickness surface might do the trick. I just can't
find out how to compute it (sorry, not an experienced user of freesurfer).
Any help in terms of raw commands to use is welcome.

Dorian




On Tue, Jan 31, 2017 at 4:52 PM, Douglas N Greve 
wrote:

> You can smooth it. This would give you a gaussian kernel instead of the
> box kernel that you describe. Set the fwhm to the radius you want
> (mris_fwhm with --smoothonly option)
>
>
> On 01/31/2017 04:48 PM, Dorian P. wrote:
> > Hi Freesurfers,
> >
> > Thank you for the help you provide through this list.
> >
> > Is there a way to get, for each vertex, the identify (or thickness
> > values) of the surrounding vertices in a 10mm radius? The command
> > mris_convert has the '-v' option, but that produces only 5-6 vertices
> > and there is no option to query a particular radius.
> >
> > I imagine this can be done manually outside Freesurfer by first
> > identifying the neighbors for each vertex based on the coordinates,
> > then getting the respective thickness value, but I wanted to check
> > whether there is any easier way or any advice on how to proceed.
> >
> > Dorian
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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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.
>
>
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[Freesurfer] flip4fsl missing in stable6

[Fan, Qiuyun]

Hi FreeSurfer experts,

I figured 'flip4fsl' is missing from /usr/local/freesurfer/stable6/bin/.  Can 
someone help to make a copy from 
/usr/local/freesurfer/stable5_3_0/bin/flip4fsl, if possible?

Thanks a lot!

Best,
Qiuyun

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Re: [Freesurfer] flip4fsl missing in stable6

[Z K]

Hello Qiuyun,

What command did you call that complained about this? And what was the 
error exactly?




On 01/31/2017 06:03 PM, Fan, Qiuyun wrote:
> Hi FreeSurfer experts,
>
>
>
> I figured 'flip4fsl' is missing from
> /usr/local/freesurfer/stable6/bin/.  Can someone help to make a copy
> from /usr/local/freesurfer/stable5_3_0/bin/flip4fsl, if possible?
>
>
>
> Thanks a lot!
>
>
>
> Best,
>
> Qiuyun
>
>
>
>
>
> ___
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Re: [Freesurfer] flip4fsl missing in stable6

[Yendiki, Anastasia]

Hi Qiuyun - You can use orientLAS instead.

Hope this helps,
a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fan, Qiuyun 
[qiuyun@mgh.harvard.edu]
Sent: Tuesday, January 31, 2017 6:03 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] flip4fsl missing in stable6

Hi FreeSurfer experts,

I figured 'flip4fsl' is missing from /usr/local/freesurfer/stable6/bin/.  Can 
someone help to make a copy from 
/usr/local/freesurfer/stable5_3_0/bin/flip4fsl, if possible?

Thanks a lot!

Best,
Qiuyun

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[Freesurfer] Fwd: Cortical thickness from ROI in volume format

[Martin Juneja]

-- Forwarded message --
From: Martin Juneja 
Date: Tue, Jan 31, 2017 at 4:38 PM
Subject: Cortical thickness from ROI in volume format
To: Freesurfer support list 


Hi FreeSurfer experts,

My goal is to extract cortical thickness of several ROIs, which are in
volume space. I am following instructions from this page:
https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness

My ROIs and T1 image are in the form of binary mask and are already in same
standard space (MNIT1.nii). So following the instructions, I am able to
perform until step 3 (I created registration file X.dat using fslregister
command to register MNIT1.nii with fslaverage).

After that I am using this command:
tksurfer fsaverage lh inflated -overlay lh.fsaverage.ROI5.mgh -fthresh 0.5

to make sure that the ROI in surface format is at correct place. But after
I run this command I do not see the region anywhere on surface. I tried to
view it using FreeView also. From FreeView, it looks like the ROI is now a
brain mask and is all over the brain with a constant value of ~0.5
everywhere. I am not sure why this is happening.

Next, I have 26 ROIs, 12 on left hemisphere, 12 on right hemisphere and 2
in the midline. Somehow, 11/12 ROIs on left hemisphere and 2 ROIs in the
midline are working fine when I view those in tksurfer or FreeView but rest
all are showing me value of 1 all over the brain.

For left hemisphere and midline ROIs, I am using exactly same steps as
mentioned in the instructions but for right hemisphere, I just replaced
'lh' with 'rh' in step 3.

Any help would be really appreciated.
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