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[Fwd: [megcommunity] Postdoctoral Fellowship: Multimodal Neuroimaging -MGH/Harvard Medical School]
by Gary Green 13 Apr '11

13 Apr '11

FYI ---------------------- Postdoctoral Fellowship: Multimodal Neuroimaging -MGH/Harvard Medical School Job Description A postdoctoral position is available with the TRANSCEND Research Program (www.transcendresearch.org <http://www.transcendresearch.org/>) at the Martinos Center for Biomedical Imaging in Charlestown, MA (www.martinos.org <http://www.martinos.org/>) which is affiliated with the Massachusetts General Hospital, Harvard Medical School and MIT. We are seeking a candidate with a strong basis in magnetic resonance imaging. Emphasis will be on MRI (DTI, spectroscopy, morphometry, ASL as well as resting state fMRI), and on co-registering MEG with MRI. This position will involve analysis of existing multimodal imaging data and collection of new data. The emphasis of the postdoctoral fellowship will be analysis of existing datasets with secondary activity in piloting data for new studies. It will involve working closely with a multidisciplinary team and with children, and will also involve some research oriented analysis of data collected for clinical purposes. After initial phase-in, ample opportunity will also be provided to the candidate to self-explore and lead research. Datasets to be analyzed include: MRI (including DTI and 1H-spectroscopy) and MEG data on 6-12 and teenage matched autism spectrum and control subjects with phenotyping data MRI data ( (morphometry, DTI, spectroscopy) plus laboratory and phenotyping data) on 70 children with autism plus epilepsy and/or mitochondrial dysfunction, along with one or more overnight EEGs on each patient data from children ages 2-10 with and without autism. Overall objectives: To perform multimodal analyses of research and clinical research data, to develop new approaches for performing these analyses, and to design pipelines for data analysis. To write papers and grants which will be high priorities all along the way and will be actively supported by senior faculty. To take advantage of the world class faculty and facilities of the Martinos Center for Biomedical Imaging to perform the above activities to their maximal potential. The program’s emphasis is on pathophysiologically grounded brain research and application of advanced imaging acquisition and analysis techniques to neurological and sensory aspects of autism spectrum disorders. Requirements: Candidates must have PhD in neuroscience, physics, biomedical engineering, electrical engineering, computer science or other related fields. Prior experience in MRI analysis is required. Experience with EEG will be an added advantage. Salary will be consistent with Massachusetts General Hospital, Harvard Medical School policies for Postdoctoral trainees and will range between $45,000 to $55,000 depending upon qualifications and experience. Compensation also includes full staff benefits, including health insurance, and vacation time. Contact: Interested applicants may send a CV and statement of interest addressing background and specific pertinence of the candidate’s interest to Dr. Martha R. Herbert at mherbert1(a)partners.org <mailto:mherbert1@partners.org> and cc transcend(a)partners.org <mailto:transcend@partners.org>. Applications will be considered until the position is filled. -- Gary Green York Neuroimaging Centre The Biocentre York Science Park Innovation Way Heslington York YO10 5DG http://www.ynic.york.ac.uk https://www.ynic.york.ac.uk/about-us/people/ggrg tel. +44 (0) 1904 435349 PA +44 (0) 1904 435329 or reception(a)ynic.york.ac.uk fax +44 (0) 1904 435356 mobile +44 (0) 788 191 3004

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Beamforming questions
by Luis Peraza 07 Apr '11

07 Apr '11

More about Beamforming files In a previous mail-list I was told that the *spheres.txt and *transform.txt file are obtained after coregistration of the MEG data to the MRI structural before beamforming. So I imagine that transform.txt matrix takes the NAI voxel values to the MNI space with a 5mm or 2mm volume grid, from the individual/subject brain to the MNI standard. Am I right? Is it MNI standard or the MNI space of the individual structural MRI? But anyway, (and this is a supposition) coregistration should be done first between MEG and the individual MRI structure to perform Beamforming in world/real or physical coordinates (right?). So there should be a previous space transform in world coordinates to perform beamforming, then the NAI values are obtained in world coordinates and finally transformed to MNI space together with the individual structural MRI. Am I right about this? The reason why I am to eager to know this, is because I am doing Beamforming for my project using python-vtk, and so far I have learned how to extract the cortical voxels of individual structrual MRI using BET-FAST from FSL. But in order to run my beamforming I need to transform the structural voxels (in MNI) to world coordinates and also do coregistration between the fiducial skin points, which I imagine were obtained using the stylus pen for 3D modelling during the MEG acquisition with the surface of the subject skin from the MRI. I was wondering if the transform.txt file does the coregistration skin-points-to-skin-surface for the Beamforming, Now I know that it does not. Maybe I will have to program my own coregistration algorithm anyway. I only wanted to know If there were a less painful way to do it. My fifth question is the following. According to the ynic-wiki, it says that I am able to define any voxel in MNI coordinates to define virtual electrodes using the Beamforming functions. The problem is that the wiki does not say how to define this coordinates. From where can I take them? > From the structural MRI or from the MRI standard? Can they be only the cortex or any voxel inside the brain? And my last question is about the sphere.txt file. It is composed of 248 lines, they should be the MEG coils, but I can not imagine the meaning of the rest of the four columns. I was thinking they where x,y,z coordinates, but there is a fourth one that tells me I am wrong. Many thanks, Luis R. Peraza

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Questions about beamforming
by Luis Peraza 07 Apr '11

07 Apr '11

More about Beamforming files In a previous mail-list I was told that the *spheres.txt and *transform.txt file are obtained after coregistration of the MEG data to the MRI structural before beamforming. So I imagine that transform.txt matrix takes the NAI voxel values to the MNI space with a 5mm or 2mm volume grid, from the individual/subject brain to the MNI standard. Am I right? Is it MNI standard or the MNI space of the individual structural MRI? But anyway, (and this is a supposition) coregistration should be done first between MEG and the individual MRI structure to perform Beamforming in world/real or physical coordinates (right?). So there should be a previous space transform in world coordinates to perform beamforming, then the NAI values are obtained in world coordinates and finally transformed to MNI space together with the individual structural MRI. Am I right about this? The reason why I am to eager to know this, is because I am doing Beamforming for my project using python-vtk, and so far I have learned how to extract the cortical voxels of individual structrual MRI using BET-FAST from FSL. But in order to run my beamforming I need to transform the structural voxels (in MNI) to world coordinates and also do coregistration between the fiducial skin points, which I imagine were obtained using the stylus pen for 3D modelling during the MEG acquisition with the surface of the subject skin from the MRI. I was wondering if the transform.txt file does the coregistration skin-points-to-skin-surface for the Beamforming, Now I know that it does not. Maybe I will have to program my own coregistration algorithm anyway. I only wanted to know If there were a less painful way to do it. My fifth question is the following. According to the ynic-wiki, it says that I am able to define any voxel in MNI coordinates to define virtual electrodes using the Beamforming functions. The problem is that the wiki does not say how to define this coordinates. From where can I take them? >From the structural MRI or from the MRI standard? Can they be only the cortex or any voxel inside the brain? And my last question is about the sphere.txt file. It is composed of 248 lines, they should be the MEG coils, but I can not imagine the meaning of the rest of the four columns. I was thinking they where x,y,z coordinates, but there is a fourth one that tells me I am wrong. Many thanks, Luis R. Peraza

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Beamforming files
by Luis Peraza 07 Apr '11

07 Apr '11

After doing beamforming there are two files besides the NAI ones, a *spheres.txt and *transform.txt files. My question is which is the purpose of these files. What do they represent? Many thanks. Luis Peraza

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Beamforming files
by Luis Peraza 07 Apr '11

07 Apr '11

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MRI help
by Philip Quinlan 26 Mar '11

26 Mar '11

Are there any useful rules of thumb about what the critical cluster size should be in reporting results. I have a results with a cluster size of 1 that reaches the 2.3 threshold. (i) this cant be a real ROI - can it? (ii) why is the critical z val set at 2.3 anyway? Any help gratefully received. Thanks Philip. ******************************************************************** Philip Quinlan E-Mail: ptq1(a)york.ac.uk Department of Psychology FAX: (01904) 323181 The University of York Tel: (01904) 320000 Ext. 3135 Heslington Direct : (01904) 323135 York YO10 5DD U.K. ********************************************************************

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[Fwd: [megcommunity] MEG Research Associate - University of Cambridge]
by Gary Green 25 Mar '11

25 Mar '11

FYI Research Associate *University of Cambridge, Department of Experimental Psychology* *Vacancy Ref: PJ07992* * * *Salary: £27,428 - £35,788 pa* Applications are invited for a post-doctoral researcher to develop, implement, and analyse MEG studies investigating cognitive and motor abilities across the adult life-span for an interdisciplinary BBSRC funded research project (Cambridge Centre for Ageing and Neuroscience (Cam-CAN) www.cam-can.com). This collaborative project involves researchers in a number of University of Cambridge Departments and at the MRC-Cognition and Brain Sciences Unit. The applicant will be based in the Centre for Speech, Language and the Brain, Department of Experimental Psychology, led by Professor Lorraine K Tyler. The post-holder will be expected to interact frequently with members of the CSLB and other members of the Cam-CAN team. The Centre has access to a research-dedicated 3T Siemens MR scanner, EEG and MEG facilities housed at the MRC-CBU. Applicants must have a PhD in a relevant discipline and experience in MEG imaging analysis, particularly connectivity in both sensor and source space. Excellent computer programming (MATLAB and/or Python) and MEG analysis (SPM, Fieldtrip) skills are essential. A background in cognitive neuroscience, particularly ageing, would be beneficial. /Closing date: 4 May 2011, Start date: 1 October 2011/ /Limit of tenure: The funds for this post are available for one year in the first instance, with a possibility to extend for a further two-three years./ / / For further details, please see our website at http://csl.psychol.cam.ac.uk/vacancies.html or http://www.cam-can.org/vacancies/index.html Applications should include a covering letter, CV, publications list and a completed form CHRIS/6 Parts I and III (downloadable from http://www.admin.cam.ac.uk/offices/hr/forms/chris6), and should be sent to Mrs M Dixon at csladmin(a)csl.psychol.cam.ac.uk <mailto:csladmin@csl.psychol.cam.ac.uk> or by post to Mrs M Dixon, Centre for Speech, Language and the Brain, Department of Experimental Psychology, University of Cambridge, Downing Street, Cambridge, CB2 3EB. /The University values diversity and is committed to equality of opportunity./ /The University has a responsibility to ensure that all employees are eligible to live and work in the UK./

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post-doc positions
by Gary Green 23 Mar '11

23 Mar '11

FYI -------- Original Message -------- Date: Tue, 22 Mar 2011 16:53:49 +0000 (GMT) From: Klaas Enno Stephan <klaasenno(a)yahoo.de> Reply-To: Klaas Enno Stephan <k.stephan(a)fil.ion.ucl.ac.uk> To: Klaas Enno Stephan <klaasenno.stephan(a)econ.uzh.ch> Dear colleagues, The Max-Planck Society and University College London recently launched a joint initiative in Computational Psychiatry & Aging. This program currently offers a number of open postdoctoral positions (application deadline: 31 March 2011). We would be grateful if you could forward the information below to students in your department who may have an interest in applying for these positions. With many thanks and my very best wishes, Klaas Max Planck Society – University College London Joint Initiative in Computational Psychiatry and Aging The Max Planck Society (MPS) and University College London (UCL) are launching a joint initiative, funded by contributions from MPS and UCL, commencing in May 2011 (for details, see www.mpib-berlin.mpg.de/research-initiative-mps-ucl <http://www.mpibberlin.mpg.de/research-initiative-mps-ucl>). The initiative will involve laboratories including the Max Planck Institute for Human Development (Berlin) and the Max Planck Institute for Cognitive and Brain Sciences (Leipzig), in Germany, and the Wellcome Trust Centre for Neuroimaging (London) and the Gatsby Computational Neuroscience Unit (London) in the UK. The goal of the initiative is to develop novel neuroscience approaches to understanding psychopathology and cognitive aging that exploit computational and mechanistic perspectives. We are seeking applicants for a number of post-doctoral positions with an interest or background in computational neuroscience who would like to use such approaches to understand psychiatric disorders and cognitive aging. The applicants should forward their CVs to Helena Maravilla (MPSUCL(a)mpib-berlin.mpg.de), Max Planck Institute for Human Development, Lentzeallee 94, 14195 Berlin, Germany. The deadline for the first round of applications is March 31, 2011. For further information, please see http://www.mpib-berlin.mpg.de/en/research/research-initiative-mps-ucl http://www.mpib-berlin.mpg.de/sites/default/files/media/pdf/25/mps-ucl-anno… __________________________________________________ Prof. Klaas Enno Stephan, MD Dr.med. PhD Laboratory for Social and Neural Systems Research, Dept. of Economics, University of Zurich Tel. +41-44-6343799/-6345520 http://www.socialbehavior.uzh.ch/stephan.html Wellcome Trust Centre for Neuroimaging, Institute of Neurology, University College London Tel. +44-207-8337472 http://www.fil.ion.ucl.ac.uk/Staff/

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Science Trail
by Michael Simpson 22 Mar '11

22 Mar '11

Dear all, The university Science Trail will be on tomorrow. As per usual, YNiC will be taking part. Availability of Open Plan will not be affected, however, there may be background noise from excitable secondary school students between 10 am and 3 pm. Michael -- Dr Michael Simpson Science Liaison Officer York Neuroimaging Centre Innovation Way York YO10 5DG Tel: 01904 567614 Web: http://www.ynic.york.ac.uk

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Useful Tool for Meta-analysis and Functional Anatomy
by Tom Hartley 17 Mar '11

17 Mar '11

I've just come across pubbrain.org. It looks like a fantastic tool for cognitive neuroscience. Search for a term (e.g. "working memory") and find out how many PubMed papers have referred to different brain regions (a "heat map" is provided), together with a list of citations. For example, Pubmed find 161 papers linking "working memory" and "inferior frontal gyrus". Of course this is only the first step in understanding the brain basis of a given function, but I think it should be very useful for gaining a quick overview. Tom

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