Re: [HCP-Users] source MEG icablpenv projection

[Jan Mathijs Schoffelen]

Dear Ola,

You can directly average across subjects, no morphing is needed.
Best wishes,
Jan-Mathijs


J.M.Schoffelen, MD PhD
Senior Researcher, VIDI-fellow - PI, language in interaction
Telephone: +31-24-3614793
Physical location: room 00.028
Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands

> On 14 Nov 2017, at 18:24, Ola Choukair  wrote:
> 
> Hi! 
> using the source MEG dtseries from the icablpenv pipeline, 
> if I want to average data across groups, do I need to compute the morph 
> matrix ( transfomation matrix of the xyz-individual suface model  for the 
> 8004 vertex onto the fsaverage template)or is it already projected?
> 
> thank you, 
> -- 
> Ola
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> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> 


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[HCP-Users] source MEG icablpenv projection

[Ola Choukair]

Hi!
using the source MEG dtseries from the icablpenv pipeline,
if I want to average data across groups, do I need to compute the morph
matrix ( transfomation matrix of the xyz-individual suface model  for the
8004 vertex onto the fsaverage template)or is it already projected?

thank you,
-- 
Ola

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[HCP-Users] tfMRI: Converting EPrime text file to EVs

[Sang-Young Kim]

Dear Experts:

I’m new to analyze task-based fMRI data. We have acquired tfMRI data with 
stimulus paradigm similar to HCP protocol.
And we have EPrime text text file showing stimulus information. But I’m 
struggling to make EV files from EPrime text file. 

Is there a script available for that purpose? Or could someone kindly provide 
an example script for converting EPrime text file to EV file (e.g., 
${Subject}/unprocessed/${tfMRIName}/LINKED_DATA/EPRIME/EVs)?
If not available, please give me some advise how to do that.

Thanks in advance. 

Sang-Young Kim, Ph.D

Postdoctoral Fellow
University of Pittsburgh


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Re: [HCP-Users] access to files with realilgnment parameter in language task

[Harms, Michael]

Sure, you can download individual files using REST calls – see previous posts 
in the list for example syntax.  Or, you could access the files via Amazon S3 
and identify the subjects that way.

The Movement_RelativeRMS_mean.txt file that accompanies each fMRI run is the 
mean of the relative (frame-to-frame) movement during the run.  So, no need to 
compute any movement metrics, if you are willing to use that as your measure 
for identifying subjects.

Cheers,
-MH


--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu

On 11/14/17, 4:46 AM, "hcp-users-boun...@humanconnectome.org on behalf of Cesar 
Caballero"  wrote:

Dear all,

We would like to download low movers only of the language task-fMRI data from 
the entire database. Is it possible to access or download only the text files 
of the realignment parameters in order to compute movement metrics?

Thanks very much,
Cesar


--
Cesar Caballero
MRI engineer
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
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[HCP-Users] PostDoctoral Position in Connectomics and Neuromodulation Available at MGH

[Camprodon, Joan A.,M.D.,M.P.H.,Ph.D.]

POST-DOCTORAL RESEARCH FELLOW
LABORATORY FOR NEUROPSYCHIATRY AND NEUROMODULATION
MASSACHUSETTS GENERAL HOSPITAL, HARVARD MEDICAL SCHOOL

Background:

The Laboratory for Neuropsychiatry and Neuromodulation (Camprodon Lab) in the 
Division of Neuropsychiatry at Massachusetts General Hospital (Harvard Medical 
School) is seeking a full time Post-Doctoral Research Fellow for an NIMH 
RO1-funded project studying the mechanisms of action of neuromodulation 
therapies (TMS and ECT) in neuropsychiatric disorders.

This project will use multimodal MRI Human Connectome sequences to study 
structural and functional circuit dynamics longitudinally with a dimensional 
neuropsychiatric focus. There will be opportunities to address basic and 
pathophysiological systems neuroscience questions, in addition to develop 
translational and clinical research skills (e.g. target discovery, 
individualized treatment development and biomarker/predictor development).

The Laboratory for Neuropsychiatry and Neuromodulation is located in the 
incredible scientific and translational environment of the MGH/HMS Charlestown 
Navy Yard campus, affiliated with the Martinos Center for Biomedical Imaging. 
We are a multidisciplinary team conducting clinical, translational and basic 
research with healthy and neuropsychiatric human populations, using 
device-based neuromodulation interventions (TMS, tDCS, ECT, DBS, etc.), 
neuroimaging, EEG, behavioral and clinical methods. Additionally, the program 
includes the Transcranial Magnetic Stimulation (TMS) clinical service, tightly 
integrated with our research mission, where we treat neuropsychiatric patients.

The laboratory, clinical service and the Division of Neuropsychiatry are 
directed by Joan Camprodon, MD MPH PhD; you will work directly with him and an 
array of collaborators and co-investigators.
There will be many opportunities to lead high impact publications starting on 
day one, working with rich and unique existing datasets.
Extensive mentorship will be provided to facilitate the transition to an 
independent research career.

Duties and Responsibilities:

The Post-Doctoral Fellow’s responsibilities will include, but are not limited 
to:
1. Analyze longitudinal multimodal MRI data (functional connectivity, 
task-based fMRI, diffusion tractography and volumetrics).
2. Model complex datasets including imaging, behavioral and clinical data.
3. Coordinate the acquisition of high quality connectome data working with 
a team of research assistants.
4. Be inquisitive, curious and publish!

Qualifications:

1. Ph.D. in Neuroscience, Psychology, Engineering or a related field.
2. Background in systems/cognitive neuroscience, neuroanatomy and 
psychological/clinical constructs.
3. A demonstrated capacity to drive first author publications.
4. Strong proficiency in various neuroimaging analysis platforms, 
multivariate modeling strategies and connectivity toolboxes.
5. Established quantitative and statistical skills, including programming 
and comfort with diverse computing environments.
6. Great writing skills, motivated and driven to publish.

Additional Qualifications:

1. Connectomics network analysis and machine learning modeling confer a 
significant advantage.
2. Management/coding of neuroimaging databases (XNAT or others) preferred.

Additional Information:
This is an NIH-funded 2 to 5-year term position with great opportunities for 
training in human systems neuroscience, translational/clinical applications and 
diverse integrated methodologies (including neuromodulation).

Applications must be sent by email to Dr. Joan Camprodon 
(jcampro...@mgh.harvard.edu) CCing Lauren 
Johnson (ljohnso...@mgh.harvard.edu) and 
include a CV, cover letter and names of three references.
Expected start date: Fall 2017/Winter 2018






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[HCP-Users] Neuroimaging Data Analyst Position at MGH, Harvard Medical School (Boston, MA)

[Camprodon, Joan A.,M.D.,M.P.H.,Ph.D.]

RESEARCH AND DATA ANALYST
LABORATORY FOR NEUROPSYCHIATRY AND NEUROMODULATION
MASSACHUSETTS GENERAL HOSPITAL, HARVARD MEDICAL SCHOOL

Background:
The Laboratory for Neuropsychiatry and Neuromodulation at the Massachusetts 
General Hospital, Harvard Medical School, is seeking a full time Research and 
Data Analyst for a series of exciting large-scale projects aimed at 
understanding the circuit dynamics underlying neuropsychiatric disorders and 
their treatments. The laboratory is a multidisciplinary group conducting 
clinical, translational and basic human neuroscience research with healthy and 
neuropsychiatric populations, using device-based neuromodulation interventions 
(TMS, tDCS, ECT, DBS, etc.), neuroimaging, EEG, behavioral and clinical 
methods. The program is directed by Joan Camprodon, MD MPH PhD and includes the 
Transcranial Magnetic Stimulation (TMS) clinical service, tightly integrated 
with our research mission, where we provide individualized treatments for 
neuropsychiatric patients.

Duties and Responsibilities:
The Scientific and Data Analyst responsibilities will include, but are not 
limited to:

  1.  Implement and support processing pipelines for multimodal neuroimaging 
analysis, including resting‐state and task-based fMRI, DTI and volumetric data.
  2.  Implement and support statistical analyses and scripts for behavioral, 
clinical and neuroscience data.
  3.  Assist in the creation of databases, query tools for data mining, and 
documentation on their effective use. Behavioral (RedCap, etc.) and 
neuroimaging databases (XNAT, etc.) are emphasized.
  4.  Maintain quality control and integrity of neuroimaging and behavioral 
data by developing, implementing and overseeing data entry and QC protocols.
  5.  Implement web-based behavioral questionnaires (e.g. RedCap) and program 
behavioral tasks with presentation software (e.g. Psychophysics Toolbox, 
PsychoPy, Presentation).
  6.  Provide programming and analysis support for lab members.
  7.  Coordinate general lab computer/network administration (including data 
management and archiving).
  8.  Assist with the preparation of scientific reports and publications.

Qualifications:

  1.  B.A., B.S. or equivalent with background in neuroscience, computer 
science, engineering or related fields. Masters or PhD degree preferred but not 
required. 2+ years of prior technical experience.
  2.  Quantitative and extremely proficient with multiple neuroimaging analysis 
platforms (HCP Pipeline, FreeSurfer, SPM, FSL, AFNI, etc.).
  3.  Strong programming skills and comfort with diverse computing environments 
required.
  4.  Strong background in statistics and statistical software scripting (R 
preferred).
  5.  Strong interpersonal skills and a high level of organization with careful 
attention to detail are absolutely required. This position requires a high 
degree of motivation and self‐sufficiency, although extensive training and 
supervision will be provided.

Additional Qualifications:

  1.  Experience with neuroimaging and behavioral databases.
  2.  Experience with network analyses, machine learning and modeling confer a 
significant advantage.
  3.  Experience with EEG analysis is preferred.
  4.  Graphic or Web design skills are considered a plus, but not required for 
consideration.

Additional Information:
Applications must be sent by email to Dr. Joan Camprodon 
(jcampro...@mgh.harvard.edu) CCing Lauren 
Johnson (ljohnso...@mgh.harvard.edu) and 
include a CV, cover letter and names of three references.
Expected start date: Fall 2017/Winter 2018




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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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[HCP-Users] access to files with realilgnment parameter in language task

[Cesar Caballero]

Dear all,

We would like to download low movers only of the language task-fMRI data from 
the entire database. Is it possible to access or download only the text files 
of the realignment parameters in order to compute movement metrics?

Thanks very much,
Cesar


--
Cesar Caballero
MRI engineer
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
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