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2794 discussions

Change in default matlab version
by Mark Hymers 29 Sep '10

29 Sep '10

Dear all, Earlier in the year, we added Matlab 2010a to the YNiC systems and asked for it to be tested against anything people were using. At the same time we announced that as detailed at: https://www.ynic.york.ac.uk/doc/ITPages/FAQ/Misc/SupportedVersions we would be changing the default matlab version from 2009a (7.8) to 2010a (7.10) in September 2010. As we've had no feedback, we'll be going ahead with this change - most likely towards the end of next week but certainly by the end of the month. Matlab 2009a (7.8) will still be available on the system until January (when 2011a will be added and 2009a withdrawn). Thanks, Mark -- Mark Hymers York Neuroimaging Centre

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MEG Software
by Mark Hymers 28 Sep '10

28 Sep '10

Dear all, As you're probably aware, we're working on a new release of the MEG analysis software. As part of this, there will be some changes to how we use the XML input files. It would therefore be really helpful if anyone who has used the MEG software in the past could send me some of their sample XML files so I can check that we can still read them properly. Cheers, Mark -- Mark Hymers York Neuroimaging Centre

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[Fwd: Job Opening: MEG Scientist at University of Washington]
by Gary Green 24 Sep '10

24 Sep '10

FYI - see attached email

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FW: [NLC2010] Postdoctoral Fellow / Research Scientist Position at The Center for BrainHealth at UT Dallas
by Ekaterini Klepousniotou 23 Sep '10

23 Sep '10

FYI **************************************************************** Dr. Ekaterini Klepousniotou Lecturer in Cognitive Neuroscience & Neuropsychology Institute of Psychological Sciences University of Leeds Leeds LS2 9JT UK Tel: +44 (0)113 3435716 Fax: +44 (0)113 3435749 From: nlc_distribution-bounces(a)nlc2009.angularis.org [mailto:nlc_distribution-bounces@nlc2009.angularis.org] On Behalf Of Jones, Bruce L Sent: 22 September 2010 20:50 To: nlc_distribution(a)nlc2009.angularis.org Subject: [NLC2010] Postdoctoral Fellow / Research Scientist Position at The Center for BrainHealth at UT Dallas Postdoctoral Fellow / Research Scientist Position Cognitive Neuroscientist in Adolescent Reasoning and Brain Development The Center for BrainHealth at The University of Texas at Dallas in collaboration with The University of Texas Southwestern Medical Center seeks to fill a Postdoctoral Research position in Cognitive Neurosciences with a productive and innovative investigator whose research interests address brain plasticity, cognitive training and reasoning. Applicable research experience desired includes an understanding of hierarchical cognitive strategies that support higher-order reasoning processes to foster deeper understanding and strengthen overall brain function and reasoning during adolescence in daily life. Additional experience would be useful but not required in multi-modality neuroimaging platforms (electrophysiology, MR technology, PET, etc.) and genetic factors related to frontal lobe and higher order cognitive development in adolescence. The research may be applied to elucidate the emergence and treatment effects acquired during normal development and in brain injuries or psychiatric diseases such as Traumatic Brain Injury, Attention Deficit/Hyperactivity Disorder (ADHD), Addictions, Obsessive-Compulsive Disorders, Mood Disorders, and Schizophrenia. The Center for BrainHealth<http://www.brainhealth.utdallas.edu/> School of Behavioral & Brain Sciences<http://bbs.utdallas.edu/> Qualifications for the position include: PhD, preferably completed in neuroscience, neuropsychology, neurocognition, or related field; familiarity with fMRI, EEG, and physiological measures; an ability to work well in a multidisciplinary, highly collaborative research team; an interest in translational research between neuroscience and clinical populations; and a strong record or potential for scholarly productivity. The Center for BrainHealth is located in downtown Dallas adjacent to The University of Texas Southwestern Medical Center. The Center's research is dedicated to applying cutting edge brain research to clinical populations to study brain plasticity. These projects cover a wide range of cognitive functions across the life-span, across a multitude of disorders, and across the most current functional brain imaging technologies. Established access available to special subject populations including: Alzheimers Disease (AD), Frontotemporal Lobar Degeneration (FTLD), Traumatic Brain Injury (TBI), ADHD, Autism, Military and Former Military, as well as healthy Aging, Stroke, Adolescent, and Pediatric groups. Access to state of the art facilities including: Philips 3T research-dedicated MRI scanner and Four Neuroscan SynAmps2 systems equipped for both 64 and 128 channel recordings. Benefits of the job include: *Ability to be involved with established, innovative, multidisciplinary collaborations. *Ability to work on research projects highly relevant to health outcomes. *Potential for high publication rate *High potential for innovation in research design *Competitive salary and benefits *One year position, renewable for 2nd year based upon available funding, performance, and productivity Submit application materials at http://provost.utdallas.edu/facultyjobs/welcome/jobdetail/pbv100810 Review of applicants will begin immediately and will continue until the position is filled. The starting date for this position is September 1, 2010. Indication of gender and ethnicity for affirmative action statistical purposes is requested as part of the application. The University of Texas at Dallas is an Equal Opportunity / Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, age, citizenship status, Vietnam era or special disabled veteran's status, or sexual orientation. UT Dallas strongly encourages applications from candidates who would enhance the diversity of the University's faculty and administration.

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FW: [NLC2010] Two postdoctoral positions (fMRI, MEG) and RA/Lab Manager position; University of Trento, Italy.
by Ekaterini Klepousniotou 22 Sep '10

22 Sep '10

FYI ****************************************************************** Dr. Ekaterini Klepousniotou Lecturer in Cognitive Neuroscience & Neuropsychology Institute of Psychological Sciences University of Leeds Leeds LS2 9JT UK Tel: +44 (0)113 3435716 Fax: +44 (0)113 3435749 ________________________________ From: nlc_distribution-bounces(a)nlc2009.angularis.org [nlc_distribution-bounces(a)nlc2009.angularis.org] On Behalf Of Uri Hasson [uhasson(a)gmail.com] Sent: 22 September 2010 07:00 To: nlc_distribution(a)nlc2009.angularis.org Subject: [NLC2010] Two postdoctoral positions (fMRI, MEG) and RA/Lab Manager position; University of Trento, Italy. Dear all: Applications are invited for two postdoctoral positions and one RA/Lab-manager position funded by an ERC (European Research Council) Starting Grant (PI: Uri Hasson; http://www.hasson.org). Individuals of all nationalities are encouraged to apply. Inquiries can be addressed to uri.hasson(a)unitn.it<mailto:uri.hasson@unitn.it>, and meetings can be arranged at the Neurobiology of Language Conference. Application forms will be posted at http://bit.ly/bntHrv within 14 days. The 4-year project examines the cognitive mechanisms and neural systems by which the human brain codes the recent past and predicts the immediate future. It uses neuroimaging, behavioral studies, and eye tracking methods. The ideal candidates are highly motivated and creative individuals, capable of working independently and in groups, who will thrive in a dynamic startup-like work environment. Experience with computational modeling of complex systems is helpful, as is prior work on neuroimaging of syntax/semantics. The research takes place at the Center for Mind/Brain Sciences at the University of Trento, located in the autonomous region of Trentino in Northern Italy. Salaries are comparable to those offered by research institutions in the US and Europe, include benefits and health insurance, and are commensurate with training and experience. Expected starting date for all positions is Jan 1st, 2011. Positions offered: a. Postdoctoral position (2-4 years) for fMRI research. The person will be responsible for the design of several fMRI studies, conducting data analysis and leading the write-up of scientific work. The person will have access to the center’s onsite 4T fMRI scanner. REQUIREMENTS: expertise with fMRI design and analysis methods and a solid background in cognitive neuroscience. HELPFUL: knowledge of functional connectivity methods including those applicable to resting state data, analysis of perfusion (ASL) data, R/Matlab programming, good understanding of UNIX. Interest in MEG methods. b. Postdoctoral position (2-4 years) for Magnetoencephalography (MEG) research. The person will be responsible for the design of several MEG studies, conducting data analysis and leading the write-up of scientific work. The person will have access to the center’s onsite MEG apparatus and 4T fMRI scanner. REQUIREMENTS: expertise with MEG techniques and a solid background in cognitive neuroscience. HELPFUL: Knowledge of coherence analysis and pattern classifier methods; knowledge of fMRI analysis techniques and the integration of fMRI and MEG data. C. Research Assistant/ Lab Manager. A 2-year position is available. The individual will be responsible for analysis of fMRI datasets, programming and conducting fMRI studies, and monitoring computer hardware. This position is ideal for recent college graduates considering future graduate study in cognitive neuroscience. REQUIREMENTS: Experience with fMRI analysis and good knowledge of Italian. HELPFUL: a bachelor's degree in psychology, cognitive science, neuroscience, or computer science. Experience with diverse computing environments (Linux/OSX/Windows), programming (python/perl/shell scripting, or R) and relational databases. About the University of Trento: In 2009, The University of Trento ranked first in the Italian national ranking published by the Italian Ministry of Education. The ranking is based on the quality of the research and teaching activities, as well as the success in attracting funds from the European Commission, awarded for international research projects.

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Old news?
by Philip Quinlan 21 Sep '10

21 Sep '10

PsychoPy: “PsychoPy is an open-source application to allow the presentation of stimuli and collection of data for a wide range of neuroscience, psychology and psychophysics experiments. It’s a free, powerful alternative to Presentation™ or e-Prime™ . It’s written in Python (a free alternative to Matlab™ )”. http://www.psychopy.org/ ******************************************************************** Philip Quinlan E-Mail: ptq1(a)york.ac.uk Department of Psychology FAX: (01904) 433181 The University of York Tel: (01904) 430000 Ext. 3135 Heslington Direct : (01904) 433135 York YO10 5DD U.K. ********************************************************************

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Last call
by Antony Morland 21 Sep '10

21 Sep '10

Hi Everyone, The visit by the Times Higher Education judging panel will commence at 4pm at YNiC. Pleas come and show your support..... Thanks Tony

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YNiC Visit
by Antony Morland 20 Sep '10

20 Sep '10

Dear All, Apparently, we are in the running for THE University of the Year. The folks who make the decision are visiting YNiC tomorrow. To make a good impression on them, I'd value the presence of those who are or have been engaged in neuroimaging research at YNiC. The tour of YNiC starts at 4pm and should finish at 4:30pm. Apologies for cross postings. Thanks Tony

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YNiC seminar today
by Rebecca E Millman 16 Sep '10

16 Sep '10

Dear Users Today (4-5 pm YNiC open plan) Miriam Johnson from the Hull York Medical School will give a talk on "Magnetoencephalography appearances in breathless patients with and without air flow directed to the face." Everyone is welcome to attend. Best wishes Rebecca Background: Intractable breathlessness is a common and devastating consequence of many diseases. Breathlessness affects all aspects of life, causing major distress for both patient and caregiver. Many patients face psychological, social and physical repercussions of persistent breathlessness, which require, long-term NHS support especially out of hours. Research into possible mechanisms for the perception of breathlessness has largely concentrated on peripheral pathways. However there is a growing interest in functional brain imaging using positron electron tomography scanning and functional MRI (fMRI), mainly in induced breathlessness in healthy volunteers. Similarities with pain perception are striking. However, little is known of these processes in patients with chronic breathlessness due to lung disease, indeed, one study suggests that patients with asthma demonstrate habituation and down-regulation of perceived unpleasantness due to breathlessness. Moreover we know nothing of the effect of interventions to improve breathlessness; patients with chronic breathlessness tolerate fMRI poorly. Magnetoencephalography (MEG) scanning is a possibly tolerated method but has not been tried. There is some clinical evidence that the use of a handheld fan reduces the sensation of breathlessness and may reduce the need for nebulisers and oxygen. The fan directs airflow to the area innervated by the 2nd and 3rd branches of the trigeminal nerve. It is universally available, cheap, non-invasive and easy to use in any setting alongside any other breathlessness intervention with no contra-indications. As the cost to the NHS of oxygen, nebulisers and inhalers and hospital admission are considerable, this area warrants research both with regard to clinical effect but also to mechanism of action. -- Dr. Rebecca E. Millman York Neuroimaging Centre The Biocentre York Science Park York YO10 5DG Email: rem(a)ynic.york.ac.uk Tel: 01904 435 5373

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Re: BET settings
by Chris Racey 15 Sep '10

15 Sep '10

I ran 3 identical first level FSL analyses of a localiser scan in order to compare the different bet settings (applied to all structural and functional images). I can confirm that BET with the recursive flag (-R) produces the best outcomes with higher Z values when transformed to standard space. The -B option looks good when examining the resulting BET images, and deals nicely with residual neck artefacts, but actually produces worse results at the level of the statistics. Below are images showing zstats from each first level analysis (face-place localiser), converted to standard space and displayed on the MNI brain. PPA (blue), FFA (orange), standard space - BET with no options http://i.imgur.com/q3FdX.png PPA (blue), FFA (orange), standard space - BET with -B option http://i.imgur.com/QC9al.png PPA (blue), FFA (orange), standard space - BET with recursive option (-R) http://i.imgur.com/Nqob1.png Activation is more extensive and more significant with the -R option. Images of the structural scans after each bet extraction can be seen in the album below http://laserdragon.imgur.com/brainimaging It seems that the standard pipeline involves using the -R option anyway, but I thought people might be interested to see the difference it makes, and that the -B option turns out to be pretty bad. Chris

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