- ynic-users

MEG unavailable
by Gary Green 13 Sep '07

13 Sep '07

I am sorry to have to report that MEG is currently unavailable. An electronics board that is the interface between the scanner and the main computer rack has failed. 4D have been informed and are trying to get a board to us as fast as possible. Unfortunately this may take more than a week as the new board will need substantial testing before it can be installed. I will keep you informed as to when MEG will be available again. I know this will cause some inconvenience and I apologise for the problems that this will undoubtedly bring to some projects. -- Gary Green York Neuroimaging Centre The Biocentre York Science Park Innovation Way Heslington York YO10 5DG http://www.ynic.york.ac.uk tel. 01904 435349 fax 01904 435356 mobile 07986 778954

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Stimulus Delivery at YNiC - Presentation licenses
by Andre Gouws 28 Aug '07

28 Aug '07

The Presentation licenses at YNiC have now been renewed for another year. If any users experience problems with the stimulus delivery PCs (especially if there are prompts for license files) please contact the DSO and / or email it-support(a)ynic.york.ac.uk Thanks -- ************************************************************************ Andre Gouws User Support Manager York Neuroimaging Centre The Biocentre York Science Park Heslington YO10 5DG Tel: +44 (0) 1904 435328 Fax: +44 (0) 1904 435356

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Thursday Seminars
by Sam Johnson 09 Aug '07

09 Aug '07

Hello all, Due to the inevitable summer lull, and the long awaited arrival of some sunny weather, the Thursday evening sessions are being put on hold till the beginning of September. So those of you who are around can make the most of the balmy summer's evenings and we'll recommence in a month or so by which time normal weather service will no doubt be resumed, the winter evenings will be drawing in and a YNiC seminar will be a welcome respite from the rain and snow. Thanks, Sam

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Interesting MRI
by Michael Simpson 01 Aug '07

01 Aug '07

Sorry, the link should be: https://www.ynic.york.ac.uk/doc/Miscellaneous apologies. Michael -- Dr Michael Simpson Science Liaison Officer York Neuroimaging Centre Innovation Way York YO10 5DG Tel: 01904 567614 Web: http://www.ynic.york.ac.uk

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Interesting MRI
by Michael Simpson 01 Aug '07

01 Aug '07

Dear all, The .pdf named WhiteCollarBrain, located here: https://www.ynic.york.ac.uk/docwiki/Miscellaneous may be of interest to you. Download it and have a look. It received a 'That's amazing!' from Prof. Morland when he saw it on my screen earlier! Michael -- Dr Michael Simpson Science Liaison Officer York Neuroimaging Centre Innovation Way York YO10 5DG Tel: 01904 567614 Web: http://www.ynic.york.ac.uk

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Thursday evening seminar 2nd August.
by Michael Simpson 01 Aug '07

01 Aug '07

Dear all, just a reminder that at this weeks Thursday evening seminar, Sam and Tony will be presenting the new streamlined Science and Ethics applications procedure. It will be beneficial to attend this if you are interested in carrying out any studies at YNiC. Also, for the oenologists in YNiC, you'll be pleased to know that this weeks refreshments have already been procured from the York Beer and Wine shop. Usual time, usual place (4pm, YNiC open plan). Thanks, Michael -- Dr Michael Simpson Science Liaison Officer York Neuroimaging Centre Innovation Way York YO10 5DG Tel: 01904 567614 Web: http://www.ynic.york.ac.uk

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NAGTY at YNiC
by Sam Johnson 27 Jul '07

27 Jul '07

Hello all, This is just a heads up to let people know that there is a NAGTY group visiting the centre next Monday, the 30th. This means that Open Plan will be very busy for periods, and people may have limited access to machines. It might be a good reading day :) Thanks, Sam -- Sam Johnson Science Manager, York NeuroImaging Centre University of York http://www.ynic.york.ac.uk

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Thursday evening seminar tonight
by Michael Simpson 26 Jul '07

26 Jul '07

Dear all, Just a reminder of the Thursday evening seminar that Piers Cornelissen will be giving tonight. He'll be discussing some interesting MEG data from one of the undergraduate projects. Hope to see you all there, usual time, usual place (4pm, YNiC open plan). Michael -- Dr Michael Simpson Science Liaison Officer York Neuroimaging Centre Innovation Way York YO10 5DG Tel: 01904 567614 Web: http://www.ynic.york.ac.uk

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Thursday 2/8/07
by a.morland＠psychology.york.ac.uk 24 Jul '07

24 Jul '07

Dear All, At the Thursday evening session on 2/8 Sam Johnson and Tony Morland will provide an introduction to the new applications procedures that will be used at YNiC. This will cover: 1) Project Proposal forms 2) Project Presentations 3) Research Science and Ethics forms We have also been working on documentation concerning new arrangements for support of users. This will be introduced at a subsequent Thursday session. Tony

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Thursday Evening
by Sam Johnson 24 Jul '07

24 Jul '07

Hello all, Just a reminder that after a couple of quiet weeks this Thursday evening Piers Cornelissen will be talking. He'll be discussing some interesting MEG data from one of the undergraduate projects. Hope to see you all there, usual time, usual place (4pm, YNiC open plan). Thanks, Sam

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MEG status
by a.morland＠psychology.york.ac.uk 20 Jul '07

20 Jul '07

Dear All, The 4-D engineer has repaired the dewar positioning system. We are hopeful that the system will be up and running as normal from Monday onwards. Some final checks and testing will be performed before then. Tony

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DSO arrangements
by a.morland＠psychology.york.ac.uk 18 Jul '07

18 Jul '07

Dear All, As Gary mentioned at the end of a recent Thursday evening meeting, the DSO will now occupy a desk in the open plan area so that he/she is more accessible to users. The desk is in the corner of the room and will have the name of the DSO on the desk. If the DSO is not at the desk and is working elsewhere in the centre, details of where he/she can be found will be on the desk. Please note that the DSO can be approached 10am-12pm and 2pm-4pm. Tony

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Fwd: BrainVoyager QX advanced course July 19 & 20 2007
by a.morland＠psychology.york.ac.uk 17 Jul '07

17 Jul '07

>Sorry for the late notice: >This may be of interest to AVA members; we are running an advanced training >course on Brain Voyager (see schedule attached) on July 19th and 20th at the >Birmingham University Imaging Centre. Basic knowledge of the software is >necessary, as the course will be covering only advanced topics. > >Please contact Zoe Kourtzi directly if you are interested. > >Zoe Kourtzi, PhD >Chair of Brain Imaging >Behavioural and Brain Sciences >School of Psychology >University of Birmingham >Edgbaston, Birmingham >B15 2TT UK > >tel: 121 414 8509 >fax: 121 414 4897 >e-mail: z.kourtzi(a)bham.ac.uk >web: http://psg275.bham.ac.uk/cnil/ > > >BrainVoyager QX advanced course > >Birmingham, July 19 & 20, 2007 > >Program > >Day 1 Analysis and visualization of structural MRI data > > >09:00 10:00 Overview - Tools and methods: Image enhancement, Region >Growing, Edge detection, Image matching and averaging >10:00 - 10:45 Demonstration: Contrast, intensity, inhomogeneity correction, >filtering. Automatic/ semi-automatic segmentation of structural data >10:45 - 11:00 Demonstration: Coregistration/ averaging of structural data >11:00 - 11:15 - Tea break - >11:15 - 12:15 Exercise: Data preprocessing, automatic/ semi-automatic >segmentation >12:15 - 13:00 Cortex-based inter-subject alignment > >13:00 14:00 - Lunch break - > >14:00 15:00 Exercise: A) Cortex-based alignment B) Transfer of Broadman >areas >15:00 15:30 Cortical thickness analysis >15:30 16:30 Exercise: Cortical thickness analysis >16:30 - 16:45 - Tea break - >16:45 17:15 DTI data analysis and visualization >17:15 18:15 Exercise: DTI data analysis and visualization > > > >BrainVoyager QX advanced course > >Birmingham, July 19 & 20, 2007 > >Program > >Day 2 Analysis of functional MRI data > > >09:00 09:30 Overview: Tools and methods, concepts, VTC/MTC, ROI/POI >09:30 11:00 Multi-subjects/ multi-study statistics in BVQX: Fixed and >random effects group analysis (GLM, RFX ANCOVA) >11:00 11:15 - Tea break - >11:15 12:15 Volume-based/ cortex-based single-subject and group ICA >12:15 12:45 Granger causality mapping >12:45 13:00 Exercise: Coregistration - fMRI data with structural 3d data > patient data with deformed brains > >13:00 14:00 - Lunch break - > >14:00 15:00 Exercise: A) Volume-based and cortex-based ICAB) RFX ANCOVA, >C) GLM analysis on aligned cortices >15:00 15:30 Mapping: Localizer and follow up >data analysis (VOI, MSK, POI) >15:30 16:30 Demonstration: Mapping visual areas field sign maps as >preparation for VOI/ POI data analysis >16:30 16:45 - Tea break - >16:45 17:15 Future Tools 1: Combined fMRI/MRI and EEG analysis >17:15 17:45 Future Tools 2: Simulation of brain processes >17:45 18:00 Discussion Dr Peter Thompson, Executive Editor, Perception National Teaching Fellow British Association - Royal Society Millennium Fellow Department of Psychology, University of York, YO10 5DD, UK P.Thompson(a)psych.york.ac.uk tel: +44 1904 433150 fax +44 1904 433181 Creator of the solar system: www.solar.york.ac.uk Try www.viperlib.com your one-stop visual perception image site

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MRI and MEG
by a.morland＠psychology.york.ac.uk 17 Jul '07

17 Jul '07

Dear All, The MEG scanner has a problem with the dewar, as has been previously reported. Until further notice, no scanning. The radiographer is off sick this week and currently Andre is assisting with as much MRI scanning as he can. It will be necessary however to cancel or shorten some scanning sessions. Please do not book any more MRI sessions this week. Tony

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IMPORTANT - VALIDATING BEAMFORMING OUTPUTS
by Andre Gouws 13 Jul '07

13 Jul '07

We have always stressed the importance of checking a few of the manual steps in the beamforming processing stream where possible. These include the outputs generated by the co-registration routines which co-register your MEG headshape to your structural MRI for each subject, and simultaneously calculate the local sphere sources for each channel in the MEG sensor array. This information, calculated early in the processing tree is obviously vital for all post-processing steps. You should be routinely checking that the co-registration itself is accurate and that the spheres generated make are 'sensible' for each sensor. If you are not doing this you are STRONGLY ENCOURAGED to do so. Whilst there have been very few instances of the outputs failing (only 2 in the last year!) they have had significant effects on results for both individuals and groups. These errors are easily resolved if detected. Please see the following page for more information: https://www.ynic.york.ac.uk/doc/BeamformerUsage and see "/STEP 3 - Visually check that the co-registration is reasonable for each subject and associated MEG run/" (Thanks to those who brought this to our attention!) -- ************************************************************************ Andre Gouws User Support Manager York Neuroimaging Centre The Biocentre York Science Park Heslington YO10 5DG Tel: +44 (0) 1904 435328 Fax: +44 (0) 1904 435356

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Thursday Evening
by Sam Johnson 09 Jul '07

09 Jul '07

Hello all, Due to the rearranging of sessions there's a bit of a hole in the schedule and the next Thursday evening will be the 26th, when Piers will talk. Unless of course we have any volunteers, or (without making any promises) requests for more training biased sessions. Thanks, Sam

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re: use of fridge, kitchen and toilets
by Gary Green 05 Jul '07

05 Jul '07

Dear users and staff Just a gentle reminder. Please, please do not use the fridge in ynic reception for food. I have just had to do archeology on someone's lunch. It is not very good for public relations when people try and get some milk but are faced with fungal blooms. Also, please can everyone use the kitchen in the link corridor between the biocentre and the innovation centre rather than the one near biocentre reception. This is because the reception kitchen is for the use of the biocentre team rather than tenants. The other kitchen does have a fridge for your lunches, etc. Last, and sorry to keep on, please can you use the toilets by the biocentre reception rather than the toilet in the mri corridor. The toilet in the mri corridor is really for patients and participants rather than users. The problem is that the mri toilet is not keeping up with demand! thanks Gary ps Good news. Work starts very soon on the new cafeteria at the Biocentre. Details are on the notice board in the Open Plan office. It should be available in the autumn. -- Gary Green York Neuroimaging Centre The Biocentre York Science Park Innovation Way Heslington York YO10 5DG http://www.ynic.york.ac.uk tel. 01904 435349 fax 01904 435356 mobile 07986 778954

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re: Today YNiC Thursday evening seminar. 5th July, 4pm.]
by Gary Green 05 Jul '07

05 Jul '07

Dear all, just a reminder that tonight's seminar features Gary and Tim reviving their 'good-cop bad-cop' style interrogation of a journal article and the associated correspondence. Continuing with the face processing theme, they will be looking at the following paper relating to the N170 response. Article http://www.nature.com/neuro/journal/v10/n4/full/nn1864.html And then they will discuss the following correspondence and replies. Correspondence http://www.nature.com/neuro/journal/v10/n7/full/nn0707-801.html Reply http://www.nature.com/neuro/journal/v10/n7/full/nn0707-802.html Supplementary Figures http://www.nature.com/neuro/journal/v10/n7/suppinfo/nn0707-801_S1.html Please read the above in advance if you get the chance. Usual time 4pm, usual place, YNiC Open Plan. Refreshments will be provided afterwards.

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YNiC Thursday evening seminar. 5th July, 4pm.
by Michael Simpson 03 Jul '07

03 Jul '07

Dear all, in a change to the previously advertised schedule, Gary and Tim will be reviving their 'good-cop bad-cop' style interrogation of a journal article and the associated correspondence. Continuing with the face processing theme, they will be looking at the following paper relating to the N170 response. Article http://www.nature.com/neuro/journal/v10/n4/full/nn1864.html And then they will discuss the following correspondence and replies. Correspondence http://www.nature.com/neuro/journal/v10/n7/full/nn0707-801.html Reply http://www.nature.com/neuro/journal/v10/n7/full/nn0707-802.html Supplementary Figures http://www.nature.com/neuro/journal/v10/n7/suppinfo/nn0707-801_S1.html Please read the above in advance if you get the chance. Usual time 4pm, usual place, YNiC Open Plan. Refreshments will be provided afterwards. Thanks, Michael -- Dr Michael Simpson Science Liaison Officer York Neuroimaging Centre Innovation Way York YO10 5DG Tel: 01904 567614 Web: http://www.ynic.york.ac.uk

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[Fwd: ScienceDirect Alert: Trends in Neurosciences, Vol. 30, Iss. 7, 2007]
by Tim Andrews 03 Jul '07

03 Jul '07

The latest Trends in Neurosciences has a whole issue on oscillations that might be of interest. http://www.sciencedirect.com/science/journal/01662236 Tim -- Dr Tim Andrews Department of Psychology University of York York, YO10 5DD UK Tel: 44-1904-434356 Fax: 44-1904-433181 http://www-users.york.ac.uk/~ta505/ http://www.york.ac.uk/depts/psych/www/admissions/cns/

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(no subject)
by Claire Fox 03 Jul '07

03 Jul '07

Does any body know a Caroline Creep? There is some post in reception to be collected Thank you

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[Fwd: ScienceDirect Alert: Trends in Neurosciences, Vol. 30, Iss. 7, 2007]
by Tim Andrews 02 Jul '07

02 Jul '07

The latest Trends in Neurosciences has a whole issue on oscillations that might be of interest. Tim -------- Original Message -------- Subject: ScienceDirect Alert: Trends in Neurosciences, Vol. 30, Iss. 7, 2007 Date: Mon, 2 Jul 2007 05:07:40 -0400 From: ScienceDirect Message Center <valert(a)prod.sciencedirect.com> To: ta505(a)york.ac.uk ScienceDirect <http://www.sciencedirect.com/science> New Volume/Issue is now available on ScienceDirect Trends in Neurosciences <http://www.sciencedirect.com/science/issue/4872-2007-999699992-661931> Trends in Neurosciences <http://www.sciencedirect.com/science/journal/01662236> Volume 30, Issue 7 <http://www.sciencedirect.com/science/issue/4872-2007-999699992-661931>, Pages 307-374 (July 2007) July INMED/TINS special issue—Physiogenic and pathogenic oscillations: the beauty and the beast Edited by Y. Ben-Ari 1. Editorial Board <http://www.sciencedirect.com/science?_ob=GatewayURL&_method=citationSearch&…> Page i Editorial 2. Physiologic and pathologic oscillations <http://www.sciencedirect.com/science?_ob=GatewayURL&_method=citationSearch&…> Pages 307-308 Yehezkel Ben-Ari Review 3. The gamma cycle <http://www.sciencedirect.com/science?_ob=GatewayURL&_method=citationSearch&…> Pages 309-316 Pascal Fries, Danko Nikolić and Wolf Singer 4. Human gamma-frequency oscillations associated with attention and memory <http://www.sciencedirect.com/science?_ob=GatewayURL&_method=citationSearch&…> Pages 317-324 Ole Jensen, Jochen Kaiser and Jean-Philippe Lachaux 5. Network and intrinsic cellular mechanisms underlying theta phase precession of hippocampal neurons <http://www.sciencedirect.com/science?_ob=GatewayURL&_method=citationSearch&…> Pages 325-333 Andrew P. Maurer and Bruce L. McNaughton 6. Are corticothalamic ‘up’ states fragments of wakefulness? <http://www.sciencedirect.com/science?_ob=GatewayURL&_method=citationSearch&…> Pages 334-342 Alain Destexhe, Stuart W. Hughes, Michelle Rudolph and Vincenzo Crunelli 7. Role of GABAergic inhibition in hippocampal network oscillations <http://www.sciencedirect.com/science?_ob=GatewayURL&_method=citationSearch&…> Pages 343-349 Edward O. Mann and Ole Paulsen 8. Thalamic synchrony and dynamic regulation of global forebrain oscillations <http://www.sciencedirect.com/science?_ob=GatewayURL&_method=citationSearch&…> Pages 350-356 John R. Huguenard and David A. McCormick 9. Pathological synchronization in Parkinson's disease: networks, models and treatments <http://www.sciencedirect.com/science?_ob=GatewayURL&_method=citationSearch&…> Pages 357-364 Constance Hammond, Hagai Bergman and Peter Brown 10. Analysis of dynamic brain oscillations: methodological advances <http://www.sciencedirect.com/science?_ob=GatewayURL&_method=citationSearch&…> Pages 365-373 Michel Le Van Quyen and Anatol Bragin Send my e-mail in plain text format <http://www.sciencedirect.com/science/account> Modify or Remove My Alerts <http://www.sciencedirect.com/science/alerts> Access the ScienceDirect Info site <http://www.info.sciencedirect.com> if you have questions about this message or other features of this service. This email has been sent to you by ScienceDirect, a division of Elsevier B.V., Radarweg 29, 1043 NX Amsterdam, The Netherlands, Tel.+31 20 485 3911. ScienceDirect respects your privacy and does not disclose, rent or sell your personal information to any non-affiliated third parties without your consent, except as may be stated in the ScienceDirect online privacy policy <http://www.sciencedirect.com/science/privacy>. By using email or alert services, you agree to comply with the ScienceDirect Terms and Conditions <http://www.sciencedirect.com/science/termsandcond>. To unsubscribe to alert services, please go to the Alerts <http://www.sciencedirect.com/science/alerts> page. Copyright © 2007 ScienceDirect. All rights reserved. Any unauthorized use, reproduction, or transfer of this message or its contents, in any medium, is strictly prohibited. ScienceDirect® is a registered trademark of Elsevier B.V. Delivery Job ID: 1929:107515196:1929:092584350 -- Dr Tim Andrews Department of Psychology University of York York, YO10 5DD UK Tel: 44-1904-434356 Fax: 44-1904-433181 http://www-users.york.ac.uk/~ta505/ http://www.york.ac.uk/depts/psych/www/admissions/cns/

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Useful links for the Matlab-inclined
by Pádraig Kitterick 28 Jun '07

28 Jun '07

Dear all, While struggling to co-exist with Matlab, I have found some excellent documentation online which I thought others might find useful. The first, and probably most useful for those already familiar with using Matlab, is a tips & tricks document which covers various techniques of array and matrix manipulation, which can save you a lot of coding and time searching through the Matlab help library. You can download/view it online here: http://home.online.no/~pjacklam/matlab/doc/mtt/doc/mtt.pdf For those who are just starting Matlab, or need a more extensive reference, the official Matlab 'Getting Started' guide is worth a read: http://www.mathworks.com/access/helpdesk/help/pdf_doc/matlab/getstart.pdf as is the suitabily named 'Matlab for Psychologists': http://www.dartmouth.edu/~antonia/matlab_for_psychologists.pdf Finally, the following page contains lots of useful links to similar documents, including guides to speed up Matlab code through vectorizing: http://www.ee.columbia.edu/~marios/matlab/matlab_tricks.html I hope these are a useful resource for the Matlab users out there. Best wishes, Padraig -- Pádraig Kitterick Graduate Student Department of Psychology University of York Heslington York YO10 5DD UK Tel: +44 (0) 1904 43 3170 Email: p.kitterick(a)psych.york.ac.uk

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Seminar reminder
by Michael Simpson 28 Jun '07

28 Jun '07

Dear all, just a reminder about the seminar this afternoon. Andy Young will be presenting his seminar on: 'Neural responses to moving faces' Usual time 4pm, usual place, YNiC open plan. Michael -- Dr Michael Simpson Science Liaison Officer York Neuroimaging Centre Innovation Way York YO10 5DG Tel: 01904 567614 Web: http://www.ynic.york.ac.uk

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MRI status
by Gary Green 25 Jun '07

25 Jun '07

Dear colleagues The MRI system RF amplifier will be replaced tomorrow (Tuesday the 26th) afternoon. For the rest of the week we will be soak testing the new amp and the new receiver system. If you use the new system and detect ANY problems, please let us know. We are interested in even the smallest of problems. I will email you all with an update later in the week. Other news: We now have MEG compatible lenses and lens holder. We need people/projects who use subjects that normally wear glasses to try it out and give us feedback. A 'how-to' session will be included in the Thursday session on the 5th of July. -- Gary Green York Neuroimaging Centre The Biocentre York Science Park Innovation Way Heslington York YO10 5DG http://www.ynic.york.ac.uk tel. 01904 435349 fax 01904 435356 mobile 07986 778954

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