ynic-users June 2011

ynic-users@ynic.york.ac.uk

3 participants
12 discussions

Matlab / SPM versions
by Mark Hymers 30 Jun '11

30 Jun '11

Hi, We've added Matlab 7.12 (R2011a) to the YNiC systems. The default has not yet changed and remains 7.10 (R2010a). Details of the supported versions are at: https://www.ynic.york.ac.uk/doc/ITPages/FAQ/Misc/SupportedVersions#Matlab At the same time, we've updated SPM8 to the latest revision which is 8+svn4290. Can people please test the new Matlab version as we'll change the default in September unless any major issues are found. We'll also be looking to withdraw Matlab 7.8 in September (as previously announced) as part of a major set of software upgrades. More on this later. Thanks, Mark -- Mark Hymers York Neuroimaging Centre

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YNiC seminar today
by rem 30 Jun '11

30 Jun '11

Dear Users Today (4-5 pm in YNiC) there will be a project proposal presentation by Carin Whitney. The title of the project is "Investigating semantic cognition with MEG, fMRI and TMS". Please see below for the talk abstract. Everyone is welcome to attend and refreshments will be provided after the talk. Best wishes Rebecca Abstract: Beth Jefferies, Carin Whitney, Piers Cornelissen and Andy Ellis This project investigates how semantic cognition – referring to our ability to understand the meaning of words, pictures, faces, sounds, and smells – is represented in the brain. We will focus on semantic control, which is one of two principal components of semantic cognition and relates to executive mechanisms that enable us to retrieve and select conceptual knowledge according to the current task or context. Research has been plentiful in describing the spatial extent of the brain regions that underpin semantic control, and has identified a distributed fronto-temporo-parietal network. However, it remains largely unknown how this system is organised (i.e., what the specific functions of each component are) and how well they interact. In the proposed project, we will apply a novel approach to investigate these questions by combining MEG with TMS and fMRI. In particular, we will use MEG to track neural activity, allowing us to generate predictions about likely patterns of communication within the semantic control network and its relation to other components of semantic cognition (i.e., brain areas that encode conceptual knowledge). Follow-up TMS will then be used to impair brain functioning at specific time points to prove causality. Equivalent fMRI data – taken from the same participants and tasks – will guide coil positioning for TMS and act as a spatial localiser for MEG. The project hence aims to establish a neural model of semantic cognition that is based on convergent evidence across different methods, generating potentially strong conclusions about how meaning retrieval is achieved. -- ************************************************************************ Dr. Rebecca E. Millman Science Liaison Officer York Neuroimaging Centre The Biocentre York Science Park Heslington YO10 5DG Tel: +44 (0) 1904 567614 Fax: +44 (0) 1904 435356

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YNiC seminar 30th June
by rem 27 Jun '11

27 Jun '11

Dear Users This Thursday (4-5 pm in YNiC) there will be a project proposal presentation by Carin Whitney. The title of the project is "Investigating semantic cognition with MEG, fMRI and TMS". Please see below for the talk abstract. Everyone is welcome to attend and refreshments will be provided after the talk. Best wishes Rebecca Abstract: Beth Jefferies, Carin Whitney, Piers Cornelissen and Andy Ellis This project investigates how semantic cognition – referring to our ability to understand the meaning of words, pictures, faces, sounds, and smells – is represented in the brain. We will focus on semantic control, which is one of two principal components of semantic cognition and relates to executive mechanisms that enable us to retrieve and select conceptual knowledge according to the current task or context. Research has been plentiful in describing the spatial extent of the brain regions that underpin semantic control, and has identified a distributed fronto-temporo-parietal network. However, it remains largely unknown how this system is organised (i.e., what the specific functions of each component are) and how well they interact. In the proposed project, we will apply a novel approach to investigate these questions by combining MEG with TMS and fMRI. In particular, we will use MEG to track neural activity, allowing us to generate predictions about likely patterns of communication within the semantic control network and its relation to other components of semantic cognition (i.e., brain areas that encode conceptual knowledge). Follow-up TMS will then be used to impair brain functioning at specific time points to prove causality. Equivalent fMRI data – taken from the same participants and tasks – will guide coil positioning for TMS and act as a spatial localiser for MEG. The project hence aims to establish a neural model of semantic cognition that is based on convergent evidence across different methods, generating potentially strong conclusions about how meaning retrieval is achieved. -- ************************************************************************ Dr. Rebecca E. Millman Science Liaison Officer York Neuroimaging Centre The Biocentre York Science Park Heslington YO10 5DG Tel: +44 (0) 1904 567614 Fax: +44 (0) 1904 435356

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YNiC seminar today (external speaker)
by rem 23 Jun '11

23 Jun '11

Dear Users Today (4-5 pm in YNiC) there will be a talk by Prof. Peter Redgrave from the University of Sheffield. http://www.sheffield.ac.uk/psychology/staff/academic/peter-redgrave The title of Prof. Redgrave's talk is "Goal-directed and habitual control in the basal ganglia: implications for Parkinson's disease". Please see below for the talk abstract. Everyone is welcome to attend and refreshments will be provided after the talk. Best wishes Rebecca Abstract: Progressive loss of the ascending dopaminergic projection in the basal ganglia is a fundamental pathological feature of Parkinson’s disease. Studies in animals and humans have identified spatially segregated functional territories in the basal ganglia for the control of goal-directed and habitual actions. In patients with Parkinson’s disease the loss of dopamine is predominantly in the posterior putamen, a region of the basal ganglia associated with the control of habitual behaviour. These patients may therefore be forced into a progressive reliance on the goal-directed mode of action control that is mediated by comparatively preserved processing in rostro-medial striatum. Thus, in addition of the loss of habits, the behavioural difficulties of Parkinson patients may also be subject to distorting output signals from habitual control circuits which impede the expression of goal-directed action. -- ************************************************************************ Dr. Rebecca E. Millman Science Liaison Officer York Neuroimaging Centre The Biocentre York Science Park Heslington YO10 5DG Tel: +44 (0) 1904 567614 Fax: +44 (0) 1904 435356

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YNiC seminar 23rd June (external speaker)
by rem 20 Jun '11

20 Jun '11

Dear Users This Thursday (4-5 pm in YNiC) there will be a talk by Prof. Peter Redgrave from the University of Sheffield. http://www.sheffield.ac.uk/psychology/staff/academic/peter-redgrave The title of Prof. Redgrave's talk is "Goal-directed and habitual control in the basal ganglia: implications for Parkinson's disease". Please see below for the talk abstract. Everyone is welcome to attend and refreshments will be provided after the talk. Best wishes Rebecca Abstract: Progressive loss of the ascending dopaminergic projection in the basal ganglia is a fundamental pathological feature of Parkinson’s disease. Studies in animals and humans have identified spatially segregated functional territories in the basal ganglia for the control of goal-directed and habitual actions. In patients with Parkinson’s disease the loss of dopamine is predominantly in the posterior putamen, a region of the basal ganglia associated with the control of habitual behaviour. These patients may therefore be forced into a progressive reliance on the goal-directed mode of action control that is mediated by comparatively preserved processing in rostro-medial striatum. Thus, in addition of the loss of habits, the behavioural difficulties of Parkinson patients may also be subject to distorting output signals from habitual control circuits which impede the expression of goal-directed action -- ************************************************************************ Dr. Rebecca E. Millman Science Liaison Officer York Neuroimaging Centre The Biocentre York Science Park Heslington YO10 5DG Tel: +44 (0) 1904 567614 Fax: +44 (0) 1904 435356

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MEG Analysis Code Changes
by Mark Hymers 13 Jun '11

13 Jun '11

Hi, We have just pushed some core changes to the YNiC NAF Beamforming code. The change is that nafEpochRejection will no longer produce what have become known as "Epoch Rejection Files" but will instead produce "Slice Rejection Files". "Epoch Rejection File" are simply a list of epochs of data which should be rejected during analysis due to artifacts. This can be problematic, as if you change your pre-trigger or epoch duration, the timings of the epochs will move around and you will reject data you didn't mean to, whilst not rejecting the data around your artifacts. The replacement for these are "Slice Rejection Files". These are a list of slice ranges containing bad data - simply a list of comma separated slice ranges; one per line. The analysis (beamformer) code itself will continue to accept Epoch Rejection Files which are listed in YAML files for analysis, but will produce "Deprecation Warnings" to remind you that you should consider converting. If you wish to convert an existing Epoch Rejection File to a Slice Rejection File, you can do one of the following: * Use the nafEpochRejectToSliceReject tool (documented at /mnt/common/naf/naf-doc/userref/scripts/nafEpochRejectToSliceReject.html ) * Load the Epoch Rejection file into nafEpochRejection using the -e flag and it will output a slice rejection file. * Load you study into the Study Definer Tool (nafStudyDefiner) and it will offer to convert all epoch rejection files into slice rejection files and update the YAML file for you at the same time. Although the nafEpochRejection and nafStudyDefiner tool will still read Epoch Rejection Files (to perform conversions), they will no longer allow you to edit or output them; they will only work with and output slice rejection files. It should be noted that internally, all of the code now converts Epoch Rejection Files to Slice Rejection Files. This means that strictly speaking, if you have overlapping epochs, a single epoch number in an epoch rejection may now result in more than one epoch being rejected. This should be a rare corner case and if you want to fully understand and see what is going on, you can use the nafShowEpochs tool to list the epochs you have and, if a epoch or slice rejection file is present in your YAML file, whether or not they will be rejected. This is one of the final big changes before we make the NAF tools available by default on the system. More on that soon. Thanks, Mark -- Mark Hymers York Neuroimaging Centre

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YNiC Downtime
by Mark Hymers 09 Jun '11

09 Jun '11

Dear all, We need to reboot the main fileservers at YNiC over the weekend, most likely on Saturday. Can I therefore ask that people log off at the end of Friday and do not leave jobs running on the cluster which will continue beyond Saturday morning - any jobs running at that point will be cancelled. This does not affect the Psychology email server. Thanks, Mark -- Mark Hymers York Neuroimaging Centre

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[Fwd: [megcommunity] PhD and Post Doc position]
by Gary Green 07 Jun '11

07 Jun '11

FYI ------------------------------- Dear colleagues, please find below two separate announcements for open positions in our research team. Kind regards, Alfons Schnitzler & Katja Biermann-Ruben /**********************************************************************/ PhD Position in Düsseldorf A *PhD position* is available at the Institute of Clinical Neuroscience and Medical Psychology, Heinrich-Heine-University Düsseldorf, to study neural representations of action related concepts. The successful candidate will be expected to work within the interdisciplinary collaborative research center (CRC/SFB 991) "The Structures of Representation in Language, Science and Cognition" starting July 2011. Within this linguistic CRC and on the theoretical basis of embodiment and the mirror neuron system our neuroscientific project investigates the functional relevance of the motor cortex for conceptual representation of verbs and nouns which derived from action verbs. Methods will be non-invasive 306-channel MEG, TMS and behavioural priming. Successful candidates will have a MSc in psychology, neuroscience or related fields and are highly motivated to learn MEG and TMS measurement and data analysis. Preference will be given to candidates with experimental practice. We offer a stimulating and inspiring atmosphere in a young, interdisciplinary team of neurologists, psychologists, physicists, and biologists. The position is for an initial period of two years but may be extended. Earliest start for the position is July 2011. Applications will be accepted until the position is filled. To apply, please send a full CV, a brief outline of current research and interests, certificates, and contact information of two academic references via email to/: schnitza(a)med.uni-duesseldorf.de and K.Biermann-Ruben(a)uni-duesseldorf.de/ / / Or via regular mail to: Dr. Katja Biermann-Ruben, Heinrich-Heine-University Düsseldorf, Institute of Clinical Neuroscience and Medical Psychology, Moorenstr. 5, D-40225 Düsseldorf // /**********************************************************************/ // // PostDoc Position in Düsseldorf A *postdoctoral position* is available at the Institute of Clinical Neuroscience and Medical Psychology, Heinrich-Heine-University Düsseldorf, to study neural representations of action related concepts. The successful candidate will be expected to play a key role in our neuroscientific the interdisciplinary collaborative research center (CRC/SFB 991) "The Structures of Representation in Language, Science and Cognition" starting July 2011. Within this linguistic CRC and on the theoretical basis of embodiment and the mirror neuron system our project investigates the functional relevance of the motor cortex for conceptual representation of verbs and nouns which derived from action verbs. Methods will be non-invasive 306-channel MEG, TMS and behavioural priming. Successful candidates will have a PhD in neuroscience or related fields. Preference will be given to candidates with a strong background in systems level neurophysiological research (MEG/EEG, TMS) and related signal analysis methods (MEG/EEG analysis in frequency and time domain). We offer a stimulating and inspiring atmosphere in a young, interdisciplinary team of neurologists, psychologists, physicists, and biologists. The position is for a period of four years. Earliest is July 2011. Applications will be accepted until the position is filled. To apply, please send a full CV, a brief outline of current research and interests, certificates, and contact information of two academic references via email to/: //schnitza(a)med.uni-duesseldorf.de// and //K.Biermann-Ruben(a)uni-duesseldorf.de/ / / Or via regular mail to: Dr. Katja Biermann-Ruben, Heinrich-Heine-University Düsseldorf, Institute of Clinical Neuroscience and Medical Psychology, Moorenstr. 5, D-40225 Düsseldorf // //**********************************************************************// // *Alfons Schnitzler, MD* Professor and Chairman Institute of Clinical Neuroscience and Medical Psychology Heinrich Heine University Düsseldorf Universitätstr. 1, D-40225 Düsseldorf tel. ++49 211-81-13014 fax ++49 211-81-13015 & Movement Disorders and Neuromodulation Department of Neurology, University Hospital Düsseldorf Moorenstr. 5, D-40225 Düsseldorf tel. ++49 211-81-16756 fax ++49 211-81-19032 *Katja Biermann-Ruben, PhD* Postdoctoral scientist Institute of Clinical Neuroscience and Medical Psychology Heinrich-Heine-University Düsseldorf Universitätsstr. 1, D-40225 Düsseldorf tel. ++49 211-81-13015 fax ++49 211-81-13015

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[Fwd: [Eeglablist] Research Assistant Position "Transitions of Consciousness" Cambridge, UK.]
by Gary Green 06 Jun '11

06 Jun '11

FYI - MRC Cognition and Brain Sciences Unit – Cambridge Research Assistant The MRC Cognition and Brain Sciences Unit (CBSU) is an internationally renowned research institute with state-of-the-art cognitive neuroscience facilities, including on-site fMRI, MEG, and EEG laboratories, and neuropsychological patient panel and large panel of healthy volunteers. Applications are invited for a Research Assistant to provide scientific support for Dr Tristan Bekinschtein’s 5 year programme on Transition of Consciousness in Sleep and Sedation, particularly for acquiring behavioural, EEG and fMRI data (and the combination of both) during cognitive experiments on volunteers, patients with sleep disorders and people under sedation. This is a 2 year post initially, funded by the Wellcome Trust. You will be highly motivated and proactive, with a degree in psychology, biology, computer science or physics. Experience in scientific research, particularly with human volunteers, is important, as is familiarity with computer programming and statistics. Experience of research in the area of sleep and polysomnography is desirable. Experience with EEG or MRI acquisition and/or analysis would be an advantage. Good communication skills plus the ability to work as part of a large, multi-disciplinary team are essential. The starting salary will be in the range of £20,074 - £27,271 per annum, depending upon qualifications and experience. We offer a flexible pay and reward policy, 30 days annual leave entitlement, and an optional MRC final salary Pension Scheme. On site car and bicycle parking is available. Applications are handled by the RCUK Shared Services Centre; to apply please visit our job board at https://ext.ssc.rcuk.ac.uk and complete an online application form. If you are unable to apply online please contact us on 01793 867003 quoting reference IRC23030. Closing date: 2nd July 2011 This position is subject to pre-employment screening The Medical Research Council is an Equal Opportunities Employer ------------------------- Gary Green

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YNiC seminar today
by rem 02 Jun '11

02 Jun '11

Dear Users This afternoon (4-5 pm in YNiC) there will be a talk on "Measuring the spatial resolution of MEG beamformers" given by Sam Johnson. Everyone is welcome to attend. Best wishes Rebecca -- ************************************************************************ Dr. Rebecca E. Millman Science Liaison Officer York Neuroimaging Centre The Biocentre York Science Park Heslington YO10 5DG Tel: +44 (0) 1904 567614 Fax: +44 (0) 1904 435356

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ynic-users June 2011