- ynic-users

YNiC ASC - Wednesday 14th May - Piers Cornelissen
by Michael Simpson 06 May '08

06 May '08

Dear all, this is just a quick mailing to advertise a YNiC ASC on Wednesday May 14th. It will be chaired by Piers Cornelissen and will be on the subject of his MEG priming study. Nearer the time, Piers will forward an agenda. And as before, the session will take place in Psychology B020, at 4pm. Please come along and join in the discussion. Following the YNiC ASC, there will hopefully be a short digest of the session emailed to ynic-users. 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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YNiC seminar 8th May
by rem 06 May '08

06 May '08

Dear Users This week's seminar (4 pm at YNiC) will be given by Matthew Brett from the CBU at the University of Cambridge. http://www.mrc-cbu.cam.ac.uk/people/matthew.brett/ The title of his talk will be "Finding and using regions of interest". Everyone is welcome to attend and there will be wine and soft drinks available after the talk. 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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This just in
by Philip Quinlan 02 May '08

02 May '08

Current Directions in Psychological Science Vol 17 (2) April 2008 is a special issue entitled The interface between neuroscience and psychological science subtitle A Sun Reader's Guide to Head Magnetics so very good for those (like me) who dont want to read the proper literature. -- ******************************************************************************** Philip Quinlan E-Mail: ptq1(a)york.ac.uk Department of Psychology FAX: (01904) 433181 University of York Tel: (01904) 430000 Ext. 3135 Heslington Direct : (01904) 433135 York Telex: 57933 YORKUL YO10 5DD U.K. ********************************************************************************

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Correction to doc wiki e-mail
by Michael Simpson 01 May '08

01 May '08

Dear all, I have made my usual mistake. The links for the pages on the doc wiki should be: https://www.ynic.york.ac.uk/doc/MEGFrontPage https://www.ynic.york.ac.uk/doc/MRIFrontPage https://www.ynic.york.ac.uk/doc/ITFrontPage https://www.ynic.york.ac.uk/doc/Miscellaneous https://www.ynic.york.ac.uk/doc/TechnicalInfo https://www.ynic.york.ac.uk/doc/YNiCGlossary I shouldn't send emails at the end of the day! 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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Changes to the doc wiki
by Michael Simpson 01 May '08

01 May '08

Dear all, the more observant of you may have noticed that there have been a number of changes to the Doc wiki recently. In particular there are now six areas about which there is documentation: https://www.ynic.york.ac.uk/docwiki/MEGFrontPage https://www.ynic.york.ac.uk/docwiki/MRIFrontPage https://www.ynic.york.ac.uk/docwiki/ITFrontPage https://www.ynic.york.ac.uk/docwiki/Miscellaneous https://www.ynic.york.ac.uk/docwiki/TechnicalInfo https://www.ynic.york.ac.uk/docwiki/YNiCGlossary There has also been a little bit of tidying up here and there. In particular, the MEG Front Page was getting rather long. Don't panic, we haven't deleted everything! The re-organisation just means that the documentation for MEG now has five separate pages. These pages are linked from the MEG Front Page, and are on the following areas; Establishing Key Parameters; Processing Epoch Data; MEG Data Visualisation; Sensor Space Analysis; Source Space Analysis. As ever, there may have been an odd error in the re-edit. If you spot any errors, please email <support(a)ynic.york.ac.uk> and let us know the problem. With 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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Help offered
by Antony Morland 29 Apr '08

29 Apr '08

Dear All, I am forwarding a message from Theresa Jones, who is a highly motivated second-year student. As you can read in her message, she is keen to gain research experience at the imaging centre. She can only help during this term, because she has work organized over the summer vacation. Could you please email her directly if you have anything for her to do? Thanks Tony -----Original Message----- From: tej500(a)york.ac.uk [mailto:tej500@york.ac.uk] Sent: 25 April 2008 13:59 To: arm501(a)york.ac.uk Subject: Research experience Hi just a qucik email following my supervisor meeting. I'm really keen to get involved in some of the research going on in the neuroimaging centre. If you could ask around if anyone needs any sort of help I would be very grateful! Many thanks, Theresa Jones

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YNiC seminar TODAY
by rem 24 Apr '08

24 Apr '08

Dear Users This Thursday (24th April) there will be a seminar at YNiC from 4-5 pm about "Hyperpolarised gas MR physics and engineering". The speaker is Dr. Jim Wild from the University of Sheffield: http://www.shef.ac.uk/medicine/staff/wild.html All are welcome and drinks will be available afterwards. Best wishes Rebecca -- ************************************************************************ Dr. Rebecca E. Millman Science Liaison Officer York Neuroimaging Centre The Biocentre York Science Park Heslington YO10 5DG Tel: +44 (0) 1904 567614 Fax: +44 (0) 1904 435356

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YNiC Thursday seminars
by rem 22 Apr '08

22 Apr '08

Dear Users We are planning the content of the YNiC Thursday seminars during the summer term. There are already some interesting external speakers lined up (please see below): 8th May: Matthew Brett, MRC Cognition and Brain Sciences Unit, University of Cambridge. http://www.mrc-cbu.cam.ac.uk/people/matthew.brett/ 15th May: Ekaterini Klepousniotou, University of Leeds http://www.psyc.leeds.ac.uk/people/ekaterini/index.htm 29th May: Jonathan Peirce, University of Nottingham http://www.psychology.nottingham.ac.uk/research/vision/jwp/home.html We also hope to secure another speaker for 26th June. For the other sessions that are still available we would like to run journal clubs and internal User presentations. We invite Users to suggest journal articles that they would like to present as part of a series of journal clubs. The available dates for the summer term are: 1st May 22nd May 5th June 12th June 19th June Please let me know if you have a journal article that you would like to present. Best wishes Rebecca -- ************************************************************************ Dr. Rebecca E. Millman Science Liaison Officer York Neuroimaging Centre The Biocentre York Science Park Heslington YO10 5DG Tel: +44 (0) 1904 567614 Fax: +44 (0) 1904 435356

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YNiC seminar 24th April
by rem 21 Apr '08

21 Apr '08

Dear Users This Thursday (24th April) there will be a seminar at YNiC from 4-5 pm about "Hyperpolarised gas MR physics and engineering". The speaker is Dr. Jim Wild from the University of Sheffield: http://www.shef.ac.uk/medicine/staff/wild.html All are welcome and drinks will be available afterwards. 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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[Fwd: REMINDER- PENS Training Center “Imaging Brain Function: From Synapses to Networks” - Deadline approaching]
by Gary Green 14 Apr '08

14 Apr '08

<http://fens.org> <http://fens.mdc-berlin.de/> */Federation of European Neuroscience Societies/* ............................................................................................................................................................................................... ------------------------------------------------------------------------ ................................................................................................................................................................................................ *FENS Office Berlin* Max Delbrück Center for Molecular Medicine (MDC) Berlin-Buch Robert-Rössle-Str. 10 13092 Berlin Tel.: +49 30 9406 3336 Fax: +49 30 9406 3819 e-mail: gibson(a)mdc-berlin.de <mailto:gibson@mdc-berlin.de>, a.buchheister(a)mdc-berlin.de <mailto:a.buchheister@mdc-berlin.de> <http://mars.glia.mdc-berlin.de/pens/> <http://fens.mdc-berlin.de/pens/> <http://www.ibro.info/> .......................................................................................................................................................................................... * PENS Training Center *Imaging Brain Function: From Synapses to Networks* * * **This is to remind you that the **PENS Training Center**: * *Imaging Brain Function: From Synapses to Networks <http://fens.mdc-berlin.de/pens/2008/schools/lausanne/>* ** *invites student applications. The School will be held in Lausanne and Geneva, **Switzerland**, from **September 7-27, 2008** * *The deadline for application is **April 15, 2008**.* *For more* *information and application please contact*: http://fens.org/pens/2008/schools/lausanne/ ................................................................................................................................................................................................. *FENS OFFICE BERLIN* Max Delbrück Center for Molecular Medicine (MDC) Berlin-Buch, Robert-Rössle-Str. 10, D-13092 Berlin Tel.: +49 30 9406 3336, Fax: +49 30 9406 3819 e-mail: a.buchheister(a)mdc-berlin.de <mailto:a.buchheister@mdc-berlin.de>

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YNiC ASC - March 27th - Auditory fMRI
by Michael Simpson 26 Mar '08

26 Mar '08

Dear all, this is just a reminder of the YNiC ASC tomorrow, which Quentin Summerfield will be chairing, on the subject of Auditory fMRI. It will take place in Psychology B020 at 4.30pm Thursday 27th March. The agenda will be as follows: * Rebecca Millman will start the session with a presentation on Safety and Practical Issues relating to Auditory fMRI. * Quentin Summerfield will then make a presentation on his previous experiences of fMRI at Nottingham. * Andre Gouws will then make a presentation about Technical Issues relating to Auditory fMRI. * A discussion about possible ways forward in York will follow. 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: [Eeglablist] MBL Neuroinformatics 2008]
by Gary Green 19 Mar '08

19 Mar '08

Dear Colleagues FYI Gary -------- Original Message -------- Subject: [Eeglablist] MBL Neuroinformatics 2008 Date: Tue, 18 Mar 2008 17:38:06 -0700 (PDT) From: Diane Whitmer <dwhitmer(a)biomail.ucsd.edu> To: eeglablist(a)sccn.ucsd.edu ---------- Forwarded message ---------- Date: Tue, 18 Mar 2008 09:51:06 -0400 From: Catherine Hemmerdinger <catherineh(a)mbl.edu> To: catherineh(a)mbl.edu Subject: Neuroinformatics 2008 This is a gentle reminder follow-up e-mail to the e-mail copied below. Thanks for your help. We write to inform you of the opportunity for your graduate students, post-docs and colleagues to participate in the MBL special topics course "Neuroinformatics" , described at the link below, devoted to neuronal data analysis and modeling with an emphasis on signal processing and statistics. This course attracts leaders in the field to teach a unique and intensive schedule. In addition, faculty and students have numerous opportunities for informal discussion and to analyze real data sets. We believe that the educational experience and the ability to network with leading scientists from many institutions, provided by this course, is not available at any single home institution. Substantial financial aid is available to defray the cost of tuition. Neuroinformatics Course Dates: August 16 - 31, 2008 Directors: Partha Mitra, Cold Spring Harbor Laboratory David Kleinfeld. UC San Diego Location: Marine Biological Laboratory, Woods Hole MA * Application Deadline: April 11, 2008 * http://www.mbl.edu/education/courses/special_topics/neufo.html This course contains pedagogical lectures on basic statistical techniques as well as focussed mini-workshops on specific neuroscience topics where applications of these techniques are critical. Thank you in advance for passing on this information. Based on comments from alumni this educational experience has had a profound effect on their scientific career. Sincerely, Partha Mitra David Kleinfeld VISIT OUR WEB SITE: http://www.mbl.edu/education/ -- Catherine Hemmerdinger Assistant to the Director of Education Marine Biological Laboratory 7 MBL Street Woods Hole, MA 02543 tel: (508) 289-7340 fax: (508) 289-7931 e-mail: catherineh(a)mbl.edu _______________________________________________ Eeglablist page: http://sccn.ucsd.edu/eeglab/eeglabmail.html To unsubscribe, send an empty email to eeglablist-unsubscribe(a)sccn.ucsd.edu For digest mode, send an email with the subject "set digest mime" to eeglablist-request(a)sccn.ucsd.edu -- 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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Back on
by Andy Ellis 17 Mar '08

17 Mar '08

Contrary to my previous email, I will be practising my EPS talk tomorrow (Tuesday) at 4.30 in YNiC. 'The neural basis of the right visual field advantage for visual word recognition' by Ellis, Barca, Cornelissen, Simpson, Urooj and Woods. Andy -- Professor Andy Ellis Department of Psychology University of York York YO10 5DD England Tel. +44 (0)1904 433140 http://www.york.ac.uk/depts/psych/www/people/biogs/awe1.html

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Angel Nevado's leaving dinner
by Gary Green 17 Mar '08

17 Mar '08

Dear Colleagues Angel Nevado will be leaving soon to take up a position in Madrid. To celebrate his success in obtaining his prestigious new position and to thank him for all of his contributions whilst he has been working in York, there will be celebratory drinks and a dinner on Wednesday evening. Drinks will be served at YNiC from 5pm on Wednesday. The dinner will be at the ASK restaurant at about 8pm that same evening. If you wish to attend, please email me Gary -- 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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seminar today at YNiC
by Gary Green 13 Mar '08

13 Mar '08

Dear colleagues Today there will be a new project presentation by Cindy Hagan on 'Crossmodal Integration of Tone of Voice' 4pm, YNiC Open Plan area New project proposal seminars are an opportunity to contribute to the design and implementation of the science programme at YNiC. Users are required to make a presentation as part of the application process. All welcome Refreshments wil be provided ------------- The next seminar will be 'The neural basis of the right visual field advantage for word recognition' by Andy Ellis, Laura Barca, Piers Cornelissen, Michael Simpson, Uzma Urooj & Will Woods on Tuesday the 18th of March at 4.30pm in the YNiC open plan area All welcome Refreshments will be provided -- 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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[Fwd: CVPR group seminar on 12th March, Wednesday in Computer Science Dept.]
by Gary Green 11 Mar '08

11 Mar '08

Dear colleagues, We will have a seminar on next wednesday, 12th March about medical image analysis by Dr. Lee Harrison, UCL. We would like to invite you and your group members to join the seminar. The detail of the seminar is as follows. Please could you circulate this email to your group members, and we welcome every one to join the seminar. Best regards, Fan Zhang Computer Vision and Pattern Recognition Group, Computer Science Department, University of York, UK ----------------------------------------------------------------------------------------------------------------------------- Lee Harrison (University College London) Title: "Spatial models of functional magnetic resonance images" 11:15AM - 12:30AM, 12th March, Wednesday in Room CS103, Computer Science Building ----------------------------------------------------------------------------------------------------------------------------- "I will talk about Bayesian spatial models of fMRI time-series data. In particular, we use a weighted graph Laplacian (WGL) to partition a brain volume into computationally manageable segments, using an isoperimetric partitioning algorithm (Grady 2006). Data from each segment is then entered into a 2-level general linear model (GLM) with matrix-variate normal densities over likelihood and prior at the 1st and 2nd levels. The spatial covariance matrix of the prior over voxels is given by the heat kernel of a WGL and all parameters and hyperparameters e.g. controlling dispersion of the heat kernel, are optimized using an EM algorithm with Fisher-Scoring ascent scheme. The benefits of this approach are that GLM parameters have an explicit and (generally) non-stationary spatial model. This allows formal model comparison of different hypotheses about how data are generated, e.g. from a stationary or non-stationary spatial process." -- 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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ASK - AUDITORY fMRI at YNiC - 27th of March
by Andre Gouws 10 Mar '08

10 Mar '08

Dear colleagues, _Auditory stimulus delivery in fMRI._ This ASK session will be held at 4:30 pm on Thursday the 27th of March. This is a change from the original scheduling of Wednesday the 19th of March. We will confirm the venue, but hope to host the session in B020 as before. Remember that these sessions are intended to be a forum where you can air your concerns, share your expertise and request a wish list for solutions to be provided at (not necessarily by!) YNiC. We hope to see you there. Regards, Andre' ************************************************************************ 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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Brain awareness week
by Gary Green 10 Mar '08

10 Mar '08

Welcome to 'Brain Awareness Week 2008'! - an annual opportunity for neuroscientists across the globe to focus on celebrating and communicating progress in brain science to the public. Coordinated in the UK by the European Dana Alliance for the Brain (www.edab.net <http://www.edab.net/> ), one of the events is... ---- National Brain Science Writing Prize 2008. In collaboration with EDAB, At-Bristol and Focus magazine, the BNA is launching a competition this week to find the best brain communicators. Could you write a newspaper-style article celebrating the amazing world of brain science? To find out more, contact: www.youramazingbrain.org <http://www.youramazingbrain.org/> . Closing date for entries: 30th June, 2008. -- Gary Green York Neuroimaging Centre The Biocentre York Science Park York YO10 5DG tel (+44) (0) 1904 435349 fax (+44) (0) 1904 435356 mobile 07986778954

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YNiC today
by Gary Green 06 Mar '08

06 Mar '08

Dear colleagues Last week we held a YNiC Thursday seminar on using Unix on the Macs. The attendance was quite low suggesting that Users probably had enough knowledge on this topic for them to be able to do what they needed at that level of computing. The original idea was that the session would continue this week but as we have had apologies even from those who had attended last week, it seems that we should not hold today's seminar. So, NO seminar today. Next week there will be a new project presentation, 4pm, Thursday the 13th, YNiC open plan. All welcome Gary -- 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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URGENT : Scratch space
by Gary Green 05 Mar '08

05 Mar '08

Dear colleagues As you know we have been encouraging users to use their 'scratch' disc space for temporary files and as a workspace for intermediate analysis. We monitor the total usage of this space daily and it is growing very rapidly. We predict that this space will run out in a few days if we do not act. The majority of the usage is by just a few users but, please, if you have a large amount of data/information in scratch, can you look at it and endeavour to delete anything that is redundant. If we do not do this then the systems will fail. One way of getting around these problems is to use a group space for your project. Group scratch is not used much and is an efficient way of sharing information without it having to be duplicated by each user, within a group, in their own scratch space. If your project does not have a group scratch directory then please email it-support(a)ynic.york.ac.uk thanks Gary -- 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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MEG now available
by Gary Green 05 Mar '08

05 Mar '08

Dear Colleagues MEG is now up and running again. You can now book your MEG sessions again through Claire. It looks as though the Polhemus failed due to a fault in an serial line isolator. So the whole system failed due to a £5 component. Sorry! While we were waiting for a delivery of a new Polhemus system and the engineeer, the YNiC team took the opportunity to reorganise the MEG equipment room. The equipment and cables have been tidied, labelled and organised. Please do not change anything in the equipment room as there is now actually no need to change cables or equipment. The camera has also been moved in the MSR (magnetically shielded room) and it is now possible to monitor your subjects during an experiment even if you are using the large screen. Please remember to tell your subjects that they are being monitored. Happy MEGing Gary -- 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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Today at YNiC
by Gary Green 04 Mar '08

04 Mar '08

Dear colleagues Today we are being visited by the VC, the pro-VC for research and Sir David Cooksey. David Cooksey wrote the recent government report on medical research which has resulted in the setting up of the National Institute of Medical Research and the integration of the NHS R&D programme with the MRC. His current main interests are concerned with translational research. If ...., you were thinking of visiting YNiC yourself today then it would help us if you happened to be present in open plan between 1.30 and 2.15 with some interesting images on the screen. If anyone is doing experiments within MRI or MEG then please be prepared to have visitors ask some questions about what you are doing. Of course I cannot predict if they will visit, whether they will be on time or whether they will actually stop as we walk through open plan. thank you Gary -- Gary Green York Neuroimaging Centre The Biocentre York Science Park York YO10 5DG tel (+44) (0) 1904 435349 fax (+44) (0) 1904 435356 mobile 07986778954

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[Fwd: [SPM] UCLA Advanced Neuroimaging Summer School]
by Gary Green 29 Feb '08

29 Feb '08

FYI We are now accepting applications for the 2008 UCLA Advanced Neuroimaging Summer School, to be help July 14-25, 2008 in Los Angeles, CA. For more information and to apply for the course, please visit: http://www.poldracklab.org/nitp2008 Cheers, Russ --- Russell A. Poldrack, Ph.d. Associate Professor Wendell Jeffrey and Bernice Wenzel Term Chair in Behavioral Neuroscience UCLA Department of Psychology Franz Hall, Box 951563 Los Angeles, CA 90095-1563 phone: 310-794-1224 fax: 310-206-5895 email: poldrack(a)ucla.edu web: www.poldracklab.org

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YNiC ASC - March 19th - Auditory fMRI
by Michael Simpson 28 Feb '08

28 Feb '08

Dear all, this is just a quick mailing to advertise a YNiC ASC on March 19th. It will be on the subject of Auditory fMRI, and will be chaired by Quentin Summerfield. Should you want to contribute anything to the agenda, please email Quentin in advance <aqs1(a)york.ac.uk>. Otherwise, simply come along and join in the discussion. As before, a short digest of the YNiC ASC will be emailed to ynic-users a few days after the session. Nearer the time, Quentin will forward an agenda (i.e. once it has been established). And as before, the session will take place in Psychology B020, at 4pm. 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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Thursday Seminar
by Sam Johnson 27 Feb '08

27 Feb '08

Hello all, Just a reminder and a little more information about this Thursday's Seminar at YNiC. Mark has prepared an introduction to Unix that I will do my very best to translate into something we mere mortals can understand. This week we'll be covering some of the generic basics, including the permissions problem I know has been an issue of late. There'll also be information on some simple command line tools and the basics of scripting. Next week we'll be looking at YNiC specific information, including some useful hints and tips that will hopefully help to save you time and blood pressure. Thanks, Sam

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