- ynic-users

[Fwd: PhD scholarships, Heidelberg University]

by Gary Green

FYI ------------------------ -------- Original Message -------- Subject: PhD scholarships, Heidelberg University Date: Tue, 5 Jul 2011 22:37:26 +0200 From: Sebastian Padó <pado(a)cl.uni-heidelberg.de> Reply-To: Sebastian Padó <pado(a)cl.uni-heidelberg.de> To: researchers(a)pascal-network.org 5 PhD scholarships in Computational Linguistics: "Semantics beyond the sentence" (Date: July 5th 2011, Deadline: July 31st) We are soliciting applications for 5 PhD scholarships (EUR 1310 per month, tax-free) within the research initiative "Coherence in Language Processing: Semantics Beyond the Sentence". They are associated with the Graduate Program "Semantic Processing", jointly organized by the Computational Linguistics Department (ICL) at Heidelberg University [1] and the NLP Group at HITS gGmbH [2] in Heidelberg, Germany. The scholarships are available from October 1st, 2011, and will run three years (dependent on positive evaluations after the first and second years). The goal of the research initiative "Coherence in Language Processing: Semantics Beyond the Sentence" is to investigate computational models of semantic phenomena at the discourse level by (a) analysing semantic phenomena at the discourse level and represent them; (b) using these representatons to improve semantic analysis; (c) evaluating (a) and (b) in NLP applications, including SMT. See [3] for details. Candidates should have a strong background in computational linguistics and possess a Masters or a Diploma degree in either Computational Linguistics or Computer Science/Linguistics with a specialization in Natural Language Processing. Experience with machine learning, corpus-based methods and statistics is a plus. Strong programming skills (Java, C++, or Python) are required. Scholarship holders will become members of the graduate program "Semantic Processing" [4]. They will participate in a PhD colloquium and may attend lectures at the university and the Heidelberg Graduate School "MathComp" [5]. The graduate program provides a lively research environment with about ten PhD students already enrolled. Interdisciplinary research links exist to computer science, linguistics, and other disciplines. Applications should include a research statement indicating the candidates' interests and plans (which should fall into the area outlined above), university transcripts and a CV. They should also indicate a preference for a primary supervisor matching their plans (Anette Frank, Sebastian Pado, Stefan Riezler, Michael Strube). For more details, see the links below. Please send your application, including all documents, as a single PDF file before **July 31st 2011** to: Anke Sopka & Corinna Schwarz Sekretariat Computerlinguistik sekretariat(a)cl.uni-heidelberg.de Questions should be sent to Sebastian Pado, pado(a)cl.uni-heidelberg.de Links: [1] ICL (http://www.cl.uni-heidelberg.de) [2] HITS (http://www.h-its.org/nlp) [3] Research Initiative Discourse Semantics http://semproc.cl.uni-heidelberg.de/discourse-semantics/ [4] Graduate Program Semantic Processing http://semproc.cl.uni-heidelberg.de [5] Heidelberg Graduate School in Mathematical and Computational Methods for the Sciences http://www.mathcomp.uni-heidelberg.de/ -- Sebastian Pado pado(a)cl.uni-heidelberg.de Institut für Computerlinguistik www.cl.uni-heidelberg.de/~pado Universität Heidelberg Tel. 06221 - 54 3591 Im Neuenheimer Feld 325, 69120 HD Fax 06221 - 54 3242 -- Gary Green

13 years, 10 months

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multimodal imaging methods job - CBU, Cambridge]

by Gary Green

FYI -------forwarded message---------- Programme Leader/Programme Leader Track Cambridge The MRC Cognition and Brain Sciences Unit (CBSU) is an internationally renowned research institute with state-of-the-art cognitive neuroscience facilities, including a research dedicated 3T Siemens TIM Trio MRI scanner and 306-channel Elekta Neuromag MEG scanner. We are seeking a talented new Group Leader to lead and manage the Methods group at the Unit. The role of the group is both to provide support for analysis of behavioural, fMRI, M/EEG data, DTI and other data, and to develop and apply innovative methods to support the CBSU mission to deliver world-class research on human cognition and its biological underpinnings. The post will be ideal for a senior postdoctoral scientist with an outstanding record of scientific achievement, wishing to establish an independent career in the field of cognitive neuroscience. You will have a strong background in a relevant discipline (e.g., training in signal processing, mathematics, physics, statistics, or computer science), and experience of the type of methods and questions addressed within human cognitive neuroscience. This appointment may be made at either Programme Leader (starting salary £44,314) or Programme Leader Track (starting salary £35,935) level. This is supported by a flexible pay and reward policy, and optional MRC final salary Pension Scheme. We offer 30 days annual leave entitlement. 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. Applicants who would like to receive this advert in an alternative format (e.g. large print, Braille, audio or hard copy), or who are unable to apply online should contact us by telephone on 01793 867003, Please quote reference number IRC24431. Closing date: 31st August 2011 --

13 years, 10 months

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YNiC seminar 7th July

by Rebecca E Millman

Dear Users This Thursday (4-5 pm) there will be a project proposal presentation given by Rich Harris. The title of Rich's talk is "The neural representation of perceived changes in facial expression". Please see below for the talk abstract. Everyone is welcome to attend and refreshments will be provided. Best wishes Rebecca Abstract: How the brain represents different aspects of faces remains controversial. This experiment will present participants with stimuli drawn from morphed continua between two different emotional facial expressions. In paired presentations, a second face could: (1) be identical to the first; (2) share the perceived expression category but differ physically along the morphed continuum (within-expression change); (3) differ physically by the same distance along the continuum but in a direction that leads participants to classify the face pairs as showing expressions of different basic emotions (between-expression change). Using an fMR-adaptation paradigm, our aim is to reveal regions of the brain whose activity corresponds to our sensitivity to changes in facial expression. -- 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

13 years, 10 months

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Matlab / SPM versions

by Mark Hymers

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

13 years, 10 months

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YNiC seminar today

by rem

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

13 years, 10 months

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YNiC seminar 30th June

by rem

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

13 years, 10 months

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YNiC seminar today (external speaker)

by rem

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

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

13 years, 11 months

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MEG Analysis Code Changes

by Mark Hymers

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

13 years, 11 months

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YNiC Downtime

by Mark Hymers

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

13 years, 11 months

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[Fwd: [megcommunity] PhD and Post Doc position]

by Gary Green

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

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

13 years, 11 months

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YNiC seminar today

by rem

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

13 years, 11 months

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At risk period tomorrow lunchtime

by Mark Hymers

Hi, The UPS in the YNiC server room will be undergoing its yearly maintanence tomorrow from around 11:30. This should have no effect on users unless we suffer from a power cut at exactly the same time as the UPS is being maintained (a highly unlikely scenario). In this case, there will be a short outage whilst we bring the servers back up again. Thanks, and sorry for the short notice. Mark -- Mark Hymers York Neuroimaging Centre

13 years, 11 months

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[ lecturerships in aberdeen]

by Gary Green

FYI *********************************** UNIVERSITY OF ABERDEEN SCHOOL OF PSYCHOLOGY LECTURESHIPS As part of its continuing development, the School of Psychology invites applications for lectureships from individuals with a strong research record that extends the School’s activities in any of the following areas: Cognition, Perception & Attention, and Social Cognition. The successful candidate will show exceptional promise as an independent researcher and the ability to deliver inspiring teaching. Salary will be at the appropriate point on the Grade 7 scale (£36,862-£44,016 per annum), with placement according to qualifications and experience. / / Informal enquiries may be made to Prof. Neil Macrae (tel: 01224 272245, email c.n.macrae(a)abdn.ac.uk <mailto:c.n.macrae@abdn.ac.uk>). * * *Should you require a visa to undertake paid employment in the UK you will be required to fulfil the minimum points criteria to be granted a Certificate of Sponsorship and Tier 2 visa. As appropriate, at the time an offer of appointment is made you will be asked to demonstrate that you fulfil the criteria in respect of financial maintenance and competency in English. Please do not hesitate to contact Lynda Johnston, HR Adviser, for further information on this.* * * To apply online for this position visit www.abdn.ac.uk/jobs <http://www.abdn.ac.uk/jobs> Job Reference Number: YPS243A. The closing date for the receipt of applications is 24 June 2011. Promoting Diversity and Equal Opportunities throughout the University Dr Jasna Martinovic School of Psychology University of Aberdeen William Guild Building Aberdeen AB24 2UB tel: 01224 272240 email: j.martinovic @ abdn.ac.uk web: http://www.abdn.ac.uk/~psy527/dept/ -- 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 - Claire Fox : +44 (0) 1904 435329 or Claire.Fox(a)ynic.york.ac.uk fax +44 (0) 1904 435356 mobile +44 (0) 788 191 3004

13 years, 11 months

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YNiC seminar 2nd June

by Rebecca E Millman

Dear Users This Thursday (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 York Neuroimaging Centre The Biocentre York Science Park York YO10 5DG Email: rem(a)ynic.york.ac.uk Tel: 01904 435 5373

13 years, 11 months

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Freesurfer

by Mark Hymers

Hi, FreeSurfer has recently announced a new version (5.1.0) where they've finally sorted out the license issues after several years. We don't have packages built for it yet, but will be looking at it very soon (in conjunction with the neurodebian team) to replace the semi-working 4.5.0 packages we have now. Release notes can be found at: http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes Thanks, Mark -- Mark Hymers York Neuroimaging Centre

13 years, 11 months

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Tonight in YNiC

by Gary Green

This evening we are hosting a visit from members of the York Philosophical Society. They will be in YNiC from 6-8pm. If anyone would like to help us show people around, please contact me Gary -- 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

13 years, 11 months

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YNiC seminar today

by Rebecca E Millman

Dear Users Today (4-5 pm in YNiC) there will be a YNiC project proposal presentation given by Chris Racey. The title of the talk is "The effects of parametrically manipulating view exposure range on representational invariance in object selective cortex". Please see the abstract below. Everyone is welcome to attend. N.B. The starting time of the YNiC seminars will be 4 pm this term. Best wishes Rebecca *Abstract* Previously we have carried out two experiments in which view shift of objects and landscape scenes was parametrically manipulated. In both experiments participants viewed blocks of stimuli changing in view by 0, 5, 10, and 15°. Different levels of adaptation across these view shift conditions allow us to derive a measure of view sensitivity for any given voxel or region. We were able to show variation in the degree of view sensitivity between category selective regions for both objects and landscape stimuli. Our previous work has shed new light on how category specific visual information is processed and represented during perception. However, it is not yet clear what the effect of object learning and long term storage is on these ventral stream representations. Previous research on this issue is limited, and there have been few studies investigating the effects of prior learning on neural adaptation. We aim to apply our parametric manipulation of view shift paradigm during an encoding experiment with unfamiliar objects prior to scanning. Participants will under training, and learn to recognise objects where their range of view exposure will vary parametrically, from 0°, 10°, and 20°. In the scanner, all of the stimuli will be presented from previously unseen views in an fMR-adaptation block design, with blocks of images shifting in view in 10° steps. For each pre-exposure condition, the presentation conditions in the scanner will be identical, and any differences across conditions must be due to differences during the encoding of items. We predict that objects learned with a greater range of views will be associated with richer, more invariant, representations, and show greater degrees of invariant adaptation than objects learned under a narrower range of views. -- 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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[Fwd: [SPM] Vacancy for one postdoc and one PhD student in Leuven, Belgium]

by Gary Green

FYI --------------------- We are looking for two bright and motivated researchers to work on a research project in which we will use *brain imaging and advanced brain decoding methods to investigate the neural basis of deviant mental representations in neurodevelopmental disorders such as autism, dyslexia, and dyscalculia*. This project is an interdisciplinary collaboration between the Laboratory of Biological Psychology (Hans Op de Beeck), the Parenting and Special Education Research Group (Bert De Smedt), and Child Psychiatry (Jean Steyaert, Bart Boets), all part of the University of Leuven (K.U.Leuven) in Belgium. We offer one PhD position and one Post-doc position. Eligible candidates should have or should soon obtain a master’s degree (for the PhD position) and a PhD (for the postdoc position) in a relevant field such as neuroscience, psychology, psychiatry, neurobiology, or medical engineering. Specific positive points for the evaluation will be experience with brain imaging (in particular functional magnetic resonance imaging), a computational background in a relevant field (e.g., brain imaging data analysis, neural networks, etc.), and good computer skills (e.g., Matlab). A background in neurodevelopmental disorders is a plus, but not mandatory. Good English (oral and written) communicative skills are necessary. The two positions are full-time, for a period of 4 years (PhD position) and 2-3 years (postdoc), and start in October 2011. The two positions are strongly research oriented, and teaching and/or administration load will be minimal. The research will be embedded in a very stimulating environment with state-of-the-art technical facilities and with ample opportunities for interaction with experts on neurodevelopmental disorders and brain imaging. The K.U.Leuven is consistently ranked within the top of European Universities and is located in the city of Leuven, which has an strong international appeal. For more information about our university, please visit http://www.kuleuven.be/about/ Formal applications should be sent by email to Hans Op de Beeck, and should include a scientific CV (mentioning past research positions and education, and publications), motivation letter, and the names and contact information of 2 senior researchers that are willing to write a recommendation letter if necessary (no letters have to be sent yet). Application deadline is June 20^th 2011. For further information please contact Hans Op de Beeck (hans.opdebeeck(a)psy.kuleuven.be <mailto:hans.opdebeeck@psy.kuleuven.be>), Bert De Smedt (Bert.DeSmedt(a)ped.kuleuven.be <mailto:Bert.DeSmedt@ped.kuleuven.be>), or Bart Boets (Bart.Boets(a)ped.kuleuven.be <mailto:Bart.Boets@ped.kuleuven.be>). Bart Boets, PhD Postdoctoral fellow of the Research Foundation - Flanders Leuven Autism Research Consortium Child and Adolescent Psychiatry Herestraat 49 - box 7003, B-3000 Leuven, BELGIUM Tel. +32 (0)16/ 34.22.45 Fax. +32 (0)16/ 34.38.30 Email: bart.boets(a)ped.kuleuven.be <mailto:bart.boets@ped.kuleuven.be> -- Gary Green

13 years, 11 months

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YNiC seminar 26th May

by Rebecca E Millman

Dear Users This Thursday (4-5 pm in YNiC) there will be a YNiC project proposal presentation given by Chris Racey. The title of the talk is "The effects of parametrically manipulating view exposure range on representational invariance in object selective cortex". Please see the abstract below. Everyone is welcome to attend. N.B. The starting time of the YNiC seminars will be 4 pm this term. Best wishes Rebecca *Abstract* Previously we have carried out two experiments in which view shift of objects and landscape scenes was parametrically manipulated. In both experiments participants viewed blocks of stimuli changing in view by 0, 5, 10, and 15°. Different levels of adaptation across these view shift conditions allow us to derive a measure of view sensitivity for any given voxel or region. We were able to show variation in the degree of view sensitivity between category selective regions for both objects and landscape stimuli. Our previous work has shed new light on how category specific visual information is processed and represented during perception. However, it is not yet clear what the effect of object learning and long term storage is on these ventral stream representations. Previous research on this issue is limited, and there have been few studies investigating the effects of prior learning on neural adaptation. We aim to apply our parametric manipulation of view shift paradigm during an encoding experiment with unfamiliar objects prior to scanning. Participants will under training, and learn to recognise objects where their range of view exposure will vary parametrically, from 0°, 10°, and 20°. In the scanner, all of the stimuli will be presented from previously unseen views in an fMR-adaptation block design, with blocks of images shifting in view in 10° steps. For each pre-exposure condition, the presentation conditions in the scanner will be identical, and any differences across conditions must be due to differences during the encoding of items. We predict that objects learned with a greater range of views will be associated with richer, more invariant, representations, and show greater degrees of invariant adaptation than objects learned under a narrower range of views. -- ************************************************************************ 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

13 years, 11 months

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YNiC Closed 27th May

by Jen Downing

Hi Everyone, Due to an important event taking place, please be aware that YNiC will be closed all day on Friday 27 May and there will be no scanning or access to the computers. The centre will be closed on Monday 30th due to the bank holiday and open again as usual on Tuesday 31st May. Best Wishes Jen

13 years, 12 months

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Lies and statistics?

by Philip Quinlan

http://neuroskeptic.blogspot.com/2009/09/fmri-gets-slap-in-face-with-dead-f… ******************************************************************** 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. ********************************************************************

13 years, 12 months

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smoking

by Gary Green

Dear Users Please do not smoke just outside the entrance to YNiC. Thank you Gary -- 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

14 years

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[Fwd: Re: poststats inquiry pls]

by Gary Green

This email to the FSL mailserver list may be of interest to local YNiC FSL users Gary ---------------------------------- Dear David, The short answer is, no, there is no way to justify Z=1.7 as a cluster-forming threshold in FEAT. The problem is that the cluster size P-values are based on Random Field Theory (RFT), and RFT makes various approximation that are only valid for high thresholds. While one early reference (Petersson et al, 1999) specified cluster-forming threshold P=0.01 / Z=2.33 as a practical lower limit for accurate results, later work (Hayasaka & Nichols, 2003; Silver et al, 2010; K. Worsley personal communication) found even that level was unstable, and instead recommended P=0.001 / Z=3.09 as a lower limit on a cluster-forming threshold to ensure accurate inferences. On the other hand, if you are using randomise, you can safely use any cluster-forming threshold (though if you go too low, the clusters might be too extended and spindly to be interpretable). If using randomise, though, check out TFCE as away to avoid specifying any particular cluster-forming threshold. To answer your second question, the cluster-forming threshold used at lower-levels is only used to make inferences *at* the lower level, and is ignored at higher levels. Only the cluster-forming threshold specified in the top-level FEAT analysis matters for the top-level results. -Tom Petersson, K. M., Nichols, T. E., Poline, J.-B., & Holmes, A. P. (1999). Statistical limitations in functional neuroimaging II. Signal detection and statistical inference. /Phil. Trans. R. Soc. Lond. B/, /354/, 1261-1281. Hayasaka, S., & Nichols, T. (2003). Validating cluster size inference: random field and permutation methods. /NeuroImage/, /20/, 2343-2356. Silver, M., Montana, G., & Nichols, T. E. (2010). False positives in neuroimaging genetics using voxel-based morphometry data. /NeuroImage/. Elsevier Inc. doi: 10.1016/j.neuroimage.2010.08.049. On Mon, May 9, 2011 at 1:06 PM, David Soto <d.soto.b(a)gmail.com <mailto:d.soto.b@gmail.com>> wrote: Hello, I am finding that when I use a Z<1.7 to define the cluster size at he highest level analyses, I am getting some interesting activations in regions that I don't see when I use Z<2.3. In both cases I use cluster thresholding and p<0.05 whole brain corrected..... I know the Z value used to define cluster size prior to correction for multiple comparisons is arbitrary, but is it there any paper that I can use to justify in my study why a Z<1.7 was used instead of Z<2.3? Would it be right to say that poststat results with a Z<1.7 are more lenient than with a Z<2.3? I feel it this is not necessarily right but can you please advise? A second question I have is about poststats as implemented in FEAT.... Say that I have done a lower level analyses - for session, a 2nd level -across session within subjects- and 3rd level -across subjects- do I need to set up the Z<1.7 at the first and second level and third level analyses - or does FEAT bring the unthresholded data from lower level analyses to the higher levels and then use the Z score specified at the highest level analyses? in other words, will I get the same results if I specify Z<1.7 across all levels or whether I do Z<2.3 for first and second level and Z<1.7 at the higher level? Many thanks, David -- ____________________________________________ Thomas Nichols, PhD Principal Research Fellow, Head of Neuroimaging Statistics Department of Statistics & Warwick Manufacturing Group University of Warwick Coventry CV4 7AL United Kingdom Email: t.e.nichols(a)warwick.ac.uk <mailto:t.e.nichols@warwick.ac.uk> Phone, Stats: +44 24761 51086, WMG: +44 24761 50752 Fax: +44 24 7652 4532

14 years

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