- ynic-users

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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At risk period tomorrow lunchtime
by Mark Hymers 01 Jun '11

01 Jun '11

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

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[ lecturerships in aberdeen]
by Gary Green 01 Jun '11

01 Jun '11

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

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YNiC seminar 2nd June
by Rebecca E Millman 31 May '11

31 May '11

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

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Freesurfer
by Mark Hymers 28 May '11

28 May '11

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

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Tonight in YNiC
by Gary Green 26 May '11

26 May '11

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

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YNiC seminar today
by Rebecca E Millman 25 May '11

25 May '11

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 23 May '11

23 May '11

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

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YNiC seminar 26th May
by Rebecca E Millman 22 May '11

22 May '11

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

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YNiC Closed 27th May
by Jen Downing 19 May '11

19 May '11

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

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Lies and statistics?
by Philip Quinlan 19 May '11

19 May '11

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. ********************************************************************

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smoking
by Gary Green 13 May '11

13 May '11

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

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[Fwd: Re: poststats inquiry pls]
by Gary Green 10 May '11

10 May '11

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

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External Seminar Today
by Julian Oldmeadow 10 May '11

10 May '11

Dear All, Today's external seminar will be delivered by Prof. Michelle Ryan from Exeter. Her talk will follow on nicely from last wednesday's Athena Swan talk, as she will be presenting her research on the "Glass Cliff", a precarious and obscured obstacle faced by women in leadership. As usual there will be drinks in the foyer afterwards. 4:15 in B020. Please come. Julian Julian Oldmeadow, PhD Department of Psychology University of York York, YO10 5DD julian.oldmeadow(a)york.ac.uk

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[Fwd: Neuroimaging post]
by Gary Green 10 May '11

10 May '11

FYI ---------------------------------- Applications are invited for a position at a Hospital Research Center in Barcelona, Spain. The position is full-time for 15 months (with a probable extension to 18 months). It entails working mainly on neuroimaging data. The postholder will help in analyzing functional, structural, and diffusion tensor data. Essential skills include knowledge of fMRI and/or structural MRI techniques, a proficient management of SPM and programming skills in MATLAB. The position is available to start 1st of September 2011. Annual salary will be around €26,000 (plus social security, health and unemployment benefits). Please send enquiries or applications (which must include a covering letter detailing professional objectives and interests, CV, all in one pdf file) to cenicogni(a)gmail.com, with the subject line "Neuroimaging position". -- Gary

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[Fwd: Postdoctoral fellowships at Oxford University on brain basis of visual attention and associative processing and disruption and retraining of these mechanisms in anxiety]
by Gary Green 10 May '11

10 May '11

FYI ----------------------- Positions to be based at The Centre for Functional Magnetic Resonance Imaging of the Brain (FMRIB), Oxford University. From June 2011 part of my lab (primarily at UC Berkeley) will be based at The Centre for Functional Magnetic Resonance Imaging of the Brain (FMRIB), Oxford University. I am looking for two postdoctoral researchers to join the group there. The positions are to play a key role in a programme of research aimed at identifying and retraining the brain mechanisms underlying disrupted attentional and associative processing in anxiety. The research is supported by funding from the European Research Council and conducted in collaboration with Drs K Weich, I Tracey and E Holmes. Candidates are sought with a doctorate in a relevant discipline and research experience in neuroimaging and programming (ideally in matlab or python). Employment is for an initial period of 1 year with the possibility of extension for an addition 2-4 years. Salary is from £33084. Start date is flexible between July 1 and Dec 1 2011. Further details can be obtained from sbishop(a)berkeley.edu <mailto:sbishop@berkeley.edu>. Prof. Sonia Bishop Assistant Professor Dept Psychology & Helen Wills Neuroscience Institute, UC Berkeley; visiting Senior Researcher, FMRIB, Oxford University

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[Fwd: PostDoc- and PhD-positions at the Central Institute of Mental Health in Germany (ZI Mannheim)]
by Gary Green 10 May '11

10 May '11

FYI -------------------------------------------------------------------------------------------------------------- The Central Institute of Mental Health in Mannheim, Germany, is an internationally renowned research institute in the field of psychiatry and neuroscience, home of the Department of Psychiatry and Psychotherapy of the Medical Faculty Mannheim of the University of Heidelberg, and a psychiatric hospital with 255 inpatient and 52 day-clinic beds. To strengthen our recently established independent neuroscience research group funded by the Federal Ministry of Education and Research (BMBF), the Clinic for Psychiatry and Psychotherapy (Medical Director: Prof. Dr. med. Andreas Meyer-Lindenberg) offers * * *1 PostDoc and 1 PhD-Student Position* * * in the area of functional and structural magnetic resonance imaging (MRI). Positions are initially limited to 2 years, a prolongation is intended. The Central Institute of Mental Health is equipped, among others, with two Siemens 3 Tesla research MR scanners. Our research group consists of an interdisciplinary team of psychologists, psychiatrists, neurologists, biologists and technical assistants (http://www.zi-mannheim.de/ag_imaging.html). The main goal of the international research project is to examine fronto-striatal plasticity processes and their molecular genetic basis in healthy individuals and psychiatric patients using multimodal magnetic resonance imaging techniques (fMRI, morphometry, DTI, spectroscopy). Ideally, potential applicants will have previous experience with the acquisition, processing and analysis of MRI data, as well as a strong interest in the application of systems neuroscience methods in the context of neuropsychiatric research questions. We offer an interesting job in a pleasant working environment at a leading German research institute. Salary is according to the German TV-L pay scale, including the social benefits of the German public service sector. For further information please contact Dr. Dr. Heike Tost, Tel. +49 621 1703-6508, E-Mail heike.tost(a)zi-mannheim.de <mailto:heike.tost@zi-mannheim.de>. ____________________________________ Maria Zangl, PhD-Student Central Institute of Mental Health Research Group Imaging in Psychiatry J5, 68159 Mannheim, Germany Phone: +49-621-1703-6514 Email:maria.zangl@zi-mannheim.de <mailto:maria.zangl@zi-mannheim.de>

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Niedermeyer's Electroencephalography
by michael＠ynic.york.ac.uk 19 Apr '11

19 Apr '11

Dear all, does anyone have a recent edition of Niedermeyer's Electroencephalography: Basic Principles, Clinical Applications and Related Fields? If so, would I be able to borrow it? Thanks, Michael

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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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