- ynic-users

printer at ynic
by Gary Green 11 Aug '08

11 Aug '08

The Canon printer is now back in operation. It should be used for printing documents that for some reason cannot be read on screen. Please note that it is not to be used for thesis printing. Students are responsible for the cost of printing their reports and downloaded scientific papers. Please do not use the Xerox printer. This costs more than 50p per sheet! 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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paper
by Tim Andrews 06 Aug '08

06 Aug '08

The following paper in the latest PNAS looks at how fluctuations in spontaneous activity can influence subsequent perception. http://www.pnas.org/content/105/31/10984.full.pdf+html -- 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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printer at YNiC
by Gary Green 28 Jul '08

28 Jul '08

I am sorry to have to report that the printer at YNiC (Canon) has jammed and is out of operation until an engineer can visit. I will inform you when it becomes available again 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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Interesting paper
by Michael Simpson 24 Jul '08

24 Jul '08

Dear all, an interesting and brief article on the relationship between fMRI and electrophysiology. http://dx.doi.org/10.1016/j.cub.2008.03.042 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 setup change - Mirror for visual stimuli
by Andre Gouws 24 Jul '08

24 Jul '08

Dear users TAKE HOME MESSAGE: A FRONT-SILVERED MIRROR HAS NOW BEEN MOUNTED IN MRI IMPROVING IMAGE QUALITY Many of you will be aware that the visual stimulus delivery setup in MRI relies on back-projection onto a screen which the participant then views via a mirror mounted in front of their face. We have always been aware that standard mirrors are sub-optimal for this type of setup: as soon as a standard mirror is tilted internal reflection and refraction of light causes slight blurring of the image .. sometimes this is perceived as a 'double edge' when viewing object binocularly. This effect can be minimised by using a minimum glass thickness in front of the reflective surface of the mirror. Thus, to date, we have used a 2mm thick mirror to aid image quality. Unfortuantely many of you have expressed concerns that this is still not as good as you would like. We have thus decided to fit a custom cut front-silvered mirror in place of the previous setup. These mirrors have effectively no glass thickness since it is the front surface of the mirror that is the reflective one. This (for the money) is as close as we can get to perfect reflection and should resolve your problems. Unlike standard mirrors, front-silvered ones have no protection of the reflective surface and are highly sensitive to scratching and marking. The mirror can only be cleaned of dust with special products and oily stains may be impossible to remove. As such all users / operators must avoid handling the mirror surface directly and should place the mirror array in place / store with care to avoid scratching of the mirror surface by other objects. We hope the improved quality will benefit us all. Contact me if you have any queries. Kind 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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questions about freesurfer
by Jing Kan 16 Jul '08

16 Jul '08

Dear users, Thanks for reading! I am a new user about freesurfer, after learning it a little while, I have got some problems: 1. I have used "recon-all" successfully to process the sMRI data, which generated the "lh.pial". And, I used "mris_convert lh.pial lh.pial.asc", get text mesh "lh.pial.asc". May I ask how can I view this with visible mesh associated with the vertices and triangle? 2. I have read the Manual v 0.8. It seems all of the interface has not supported in our new Freeserfer version...do you have some good suggestion about the materials for beginner to learn? I really appreciate your help!Looking forward to your reply! Kind regards, Jing

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Ole Jensen seminar TODAY
by rem 10 Jul '08

10 Jul '08

*N.B. Today's seminar will be held in A202 in Psychology and not in YNiC* Dear Users Today's seminar (Thursday 4 pm in the Venables room, A202 ) will be given by Ole Jensen from FC Donders. http://oase.uci.ru.nl/~olejen/ The title of his talk will be "How slow event-related fields are created from cognitive modulations in oscillatory brain activity". 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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Call for expertise: across session fMRI analyses
by andre＠ynic.york.ac.uk 09 Jul '08

09 Jul '08

Dear Users, Concatenation or higher level stats? We would value the input of any users who have experience of 'combining' fMRI data across multiple runs for more robust averaging. The issue arises when trials of an experient are acquired in different data blocks due to technical limitations of scan scquisition protocols or often to reduce the strain on participants in a single session. I have searched many available resources. There are well documented routines for (1) analysinng the sessions individually and then compring them with a higher level analysis or (2) demeaning the two timeseries and combining them into a single one .. then following the standard analysis individual subject routine. Comments would be appreciated (especially from anyone has first hand experience of doing this). Thanks Andre'

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Ole Jensen seminar
by rem 07 Jul '08

07 Jul '08

Dear Users Please note that, contrary to the email I sent this morning, this week's YNiC seminar will be held in Psychology i.e. *NOT YNIC*. Ole's talk will be in the Venables room (A202) since B020 is being used for a graduation party. 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 10th July
by rem 07 Jul '08

07 Jul '08

Dear Users This week's seminar (Thursday 4 pm at YNiC) will be given by Ole Jensen from FC Donders. http://oase.uci.ru.nl/~olejen/ The title of his talk will be "How slow event-related fields are created from cognitive modulations in oscillatory brain activity". 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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Computing service maintenance
by Gary Green 02 Jul '08

02 Jul '08

Dear Colleagues Computing Service have asked us to take our machines down for a period of three hours on Wednesday evening. This will allow us to take advantage of a change in the University network architecture and will provide more resilience in our connections to the University. Please can everyone stop submitting cluster jobs that will not be complete by 5pm on Wednesday. To be on the safe side I would suggest not submitting jobs after 3pm on Wednesday. Even then jobs may be lost if they are still running at 5. During the downtime, mail and web services will also be interrupted but for a shorter period. Thanks -- 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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Reduced Support
by Sam Johnson 27 Jun '08

27 Jun '08

Hello all, As I'm sure many of you will know there's a fairly large contingent of YNiC users and staff heading off to Barcelona in a couple of weeks for the annual 4D users meeting. This will be a very hard working trip (with not a hint of tapas or sangria, no siree) but does mean that for at least some of the week beginning 14th of July there will be very limited support available at YNiC. Some of the staff will be returning towards the end of the week but for the 14th to 16th at least, YNiC will be running with little more than a skeleton staff. We apologise for the inconvenience this may cause, but the 4D meetings have been very useful in the past and we hope will be so again this year. If you have any issues that you think may come up over that week you may well be advised to let us know as soon as possible so we can resolve them ahead of time, or put them off till the following week. Hopefully the disruption will be minimal, and worth the ideas and developments we'll bring back. Thanks, Sam

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Seminar tomorrow (Thursday)
by Gary Green 25 Jun '08

25 Jun '08

Richard Wise, from Imperial College London, will be giving the Thursday evening seminar on the 26th entitled: "So why hasn't functional imaging told us how we recover communication after an aphasic stroke" There will be the usual selection of refreshments afterwards and as always, all are welcome. The seminar will be held in YNiC at 4.30pm (note the change in time) We will be taking Richard out to dinner afterwards. Do contact me if you would like to join us, -- 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
by a.morland＠psychology.york.ac.uk 23 Jun '08

23 Jun '08

Dear All, Alex Wade, from the Smith-Kettlewell Eye Research Institute and previously Stanford, will be giving a seminar at 16:30 tomorrow (24th June) in C003, Psychology. He will be talking about recent neuroimaging work on the human visual visual. Refreshments will be available after the talk. All welcome Cheers Tony

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Next Thursday
by Sam Johnson 20 Jun '08

20 Jun '08

Hello again, Thanks to all who pointed out my deliberate mistake in nicely clashing next Thursday's seminar with an important, whole faculty psychology meeting. Oops. I'm just checking that there are no problems in moving the seminar back a bit to allow people to get across to YNiC, and once I've confirmed that I'll send another email with a slightly revised time. In the mean time, thanks again to those who let me know, and watch this space, Yours abashedly, Sam

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Fwd: two post-doc vacancies (Maguire Memory Lab) at the FIL in London
by Andy Ellis 19 Jun '08

19 Jun '08

>Delivered-To: psychology.york.ac.uk-A.Ellis(a)PSYCH.YORK.AC.UK >X-VirusChecked: Checked >X-Env-Sender: owner-cogneuro(a)JISCMAIL.AC.UK >X-StarScan-Version: 5.5.12.14.2; banners=-,-,- >X-Originating-IP: [130.246.192.56] >X-SpamReason: No, hits=0.7 required=7.0 tests=BODY_RANDOM_LONG, > MIME_QP_LONG_LINE,ML_MATCH_3,ML_MATCH_4,UNPARSEABLE_RELAY >X-RAL-MFrom: <e.maguire(a)fil.ion.ucl.ac.uk> >X-RAL-Connect: <cream.fil.ion.ucl.ac.uk [193.62.66.20]> >X-CCLRC-SPAM-report: 0.001 : HTML_MESSAGE >Date: Thu, 19 Jun 2008 12:24:00 +0100 >Reply-To: Cognitive Neuroscience List <COGNEURO(a)JISCMAIL.AC.UK> >Sender: Cognitive Neuroscience List <COGNEURO(a)JISCMAIL.AC.UK> >From: Eleanor Maguire <e.maguire(a)FIL.ION.UCL.AC.UK> >Organization: FIL >Subject: two post-doc vacancies (Maguire Memory Lab) at the FIL in London >To: COGNEURO(a)JISCMAIL.AC.UK >List-Help: <http://jiscmail.ac.uk/cgi-bin/webadmin?LIST=COGNEURO>, > <mailto:LISTSERV@JISCMAIL.AC.UK?body=INFO COGNEURO> >List-Unsubscribe: <mailto:COGNEURO-unsubscribe-request@JISCMAIL.AC.UK> >List-Subscribe: <mailto:COGNEURO-subscribe-request@JISCMAIL.AC.UK> >List-Owner: <mailto:COGNEURO-request@JISCMAIL.AC.UK> >List-Archive: <http://jiscmail.ac.uk/cgi-bin/webadmin?LIST=COGNEURO> >X-York-MailScanner: Found to be clean >X-York-MailScanner-From: owner-cogneuro(a)jiscmail.ac.uk > >*************************************************************** >Message sent via COGNEURO listserve. N.B. >Replies to this e-mail will be directed to ALL >members of the list. >*************************************************************** > >Dear All > >I have two vacancies for post-doctoral >researchers in my Lab at the WellcomeTrust >Centre for Neuroimaging (the 'FIL'), Institute >of Neurology, University College London. I >wonder if you would be kind enough to bring >these vacancies to the attention of anyone you >think might be interested. > >Many thanks > >Eleanor Maguire > > >Vacancy1: >***Post-doctoral Research Associate: fMRI of Memory and Imagination > >*A Wellcome Trust funded Post-doctoral Research >Associateship is available under the supervision >of Professor Eleanor Maguire. The appointee will >play a key role in researching the neural basis >of episodic/autobiographical memory, scene >construction and imagination using functional >MRI and neuropsychological assessment of >patients with memory impairments. This is an >exciting opportunity to contribute to a >fast-developing field seeking to understand the >relationship between recalling the past, >imagining the future and other cognitive >functions. The appointee will benefit from >interactions with a critical mass of cognitive >neuroscience researchers, methodologists and >technologists at the Centre that contribute to >an excellent environment for conducting the >highest quality research. Applicants should have >a PhD in psychology, cognitive neuroscience or a >related discipline. They should have research >experience within the broad project area, of >programming with Matlab, and of designing, >executing and analysing experiments using >functional MRI. They should be able to >demonstrate a consistently outstanding academic >record, including publications. Excellent >organisational and communication skills, and the >ability to work both independently and as part >of a team, are also required. This post is >available from 1^st October 2008 and is funded >for three years. Starting salary on the UCL >Grade 7 scale in the range £30,939 - £33,561 pa >inclusive, superannuable. Further details >should first be obtained from Miss Katy Brinded, >Personnel Officer, Institute of Neurology, Queen >Square, London WC1N 3BG (tel: 020 7676 2191; >email: personnel(a)ion.ucl.ac.uk ><mailto:personnel@ion.ucl.ac.uk>). Informal >enquiries welcome to: >e.maguire(a)fil.ion.ucl.ac.uk ><mailto:e.maguire@fil.ion.ucl.ac.uk>. *Closing >date for applications: >**Thursday 31^st July, 2008.* > > >Vacancy 2: >*Post-doctoral Research Associate: Decoding Memories from fMRI Signals > >*A Wellcome Trust funded Post-doctoral Research >Associateship is available under the supervision >of Professor Eleanor Maguire. The appointee will >play a key role in researching spatial and >episodic memory using multivariate analysis of >high spatial resolution functional MRI data. >Application of decoding techniques to the human >hippocampus and related brain areas offers an >exciting new avenue for exploring how memories >are coded by the neurons of the brain. The >appointee will benefit from interactions with a >critical mass of cognitive neuroscience >researchers, methodologists and technologists at >the Centre that contribute to an excellent >environment for conducting the highest quality >research. Applicants should have a PhD in >computer science, mathematics, physics, >cognitive neuroscience or a related discipline. >They should have advanced skills in programming >(e.g. Matlab, C++) combined with experience of >or an interest in applying these skills to >biological questions relating to human memory. >Experience of analysing fMRI data, and of >machine learning/multivariate analysis >techniques is also highly desirable. Applicants >should be able to demonstrate a consistently >outstanding academic record, including >publications. Excellent organisational and >communication skills, and the ability to work >both independently and as part of a team, are >also required. This post is available from 1^st >October 2008 and is funded for three years. >Starting salary on the UCL Grade 7 scale in the >range £30,939 - £36,429 pa inclusive, >superannuable. Further details should first be >obtained from Miss Katy Brinded, Personnel >Officer, Institute of Neurology, Queen Square, >London WC1N 3BG (tel: 020 7676 2191; email: >personnel(a)ion.ucl.ac.uk ><mailto:personnel@ion.ucl.ac.uk>). Informal >enquiries welcome to: >e.maguire(a)fil.ion.ucl.ac.uk ><mailto:e.maguire@fil.ion.ucl.ac.uk>*. Closing >date for applications: >**Thursday 31^st July, 2008.* >** > > > >/UCL Taking Action for Equality/ > > >--------------------------------------------- >COGNEURO archives and subscription manager can be found at >http://www.jiscmail.ac.uk/lists/COGNEURO.HTML >--------------------------------------------- >List owner's email address: COGNEURO-request(a)jiscmail.ac.uk -- 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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Thursday Afternoon Seminar
by Sam Johnson 19 Jun '08

19 Jun '08

Hello All, Richard Wise will be giving the Thursday evening seminar on the 26th (next week), entitled: "So why hasn't functional imaging told us how we recover communication after an aphasic stroke" There will be the usual selection of refreshments afterwards and as always, all are welcome. There is no seminar this afternoon. Thanks, Sam

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Bookings
by Antony Morland 19 Jun '08

19 Jun '08

Dear All, Please be aware that when you submit bookings for scanning there is a limit of 7 hours per week per scanner for your project. Also note, that requests for bookings after 4pm may not be possible to arrange because it involves additional radiographer cover. Thanks Tony Antony Morland PhD Deputy Director York Neuroimaging Centre Professor of Visual Neuroscience Department of Psychology University of York York YO10 5DD UK Tel +44 (0) 1904 432 860 Email a.morland(a)psychology.york.ac.uk

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Etiquette
by a.morland＠psychology.york.ac.uk 12 Jun '08

12 Jun '08

Dear All, I just wanted to pass on some advice with regard to accessing the MRI corridor, when you are about to scan participants. I am communicating this information because over recent days, quite consistently, investigators together with their participants have been milling around in the MRI corridor in advance of their booked slot. I know that this reflects enthusiasm and an effort on the investigators part to be well prepared for their scan session and make good use of time. However, the presence of people in the MRI corridor also runs the risk of disquieting patients who have been scanned for health reasons. I want to try and strike a balance between optimising the use of the scanner and maximising privacy for patients and research participants, who change clothes in the cubicles on the MRI corridor. Heres the plan then: (1) A maximum of two investigators, but preferably just one investigator, may accompany the research participant into the MRI corridor. (2) The investigator(s) can stay in the corridor only for the time it takes to explain the procedure for changing into scrubs to the participant. (3) The investigator(s) must then enter the interview room and wait for the participant to join them. (4) The MRI operator with then come to the interview room to invite the investigator(s) and participant through to the scanner suite. It is very likely that a patient will be changing back into their clothes at this time, so please keep conversation professional and to a minimum. (5) If other investigators wish to join the scan session, they may do so only at the discretion of the MRI operator, who will be able to determine whether patients privacy will be compromised by the presence of addition people and will be able to advise when investigators should leave to ensure privacy is maintained. If you find that the interview room has already been reserved, participants may change into scrubs, but must return to and wait in reception with the investigators until they are invited through to the scanner suite by the MRI operator. If investigators are found not to be conforming to this procedure, one of their scan sessions will be used as a training session on how to prepare participants for scanning. Thanks for your help with this. Tony

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Booking Changes
by Mark Hymers 09 Jun '08

09 Jun '08

Hi, As of today, there is a small change to the booking system for MEG and MRI at YNiC. Whilst previously, bookings were made on 10-minute intervals, in order to fit the clinical and research booking together more easily, this has now changed, for future bookings, to 15-minute intervals (i.e bookings start and end at 00, 15, 30 and 45 minutes past the hour). The bookings page (https://www.ynic.york.ac.uk/bookings/) has also been changed to show the timings of existing bookings more clearly. Thanks, Mark -- Mark Hymers York Neuroimaging Centre

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Beamformer Software Update
by Mark Hymers 01 Jun '08

01 Jun '08

Hi, Please be aware that the default behaviour of the beamformer has changed as of 01/06/2008. An artifact has been identified which has now been compensated for. As such, if you have run any beamforming studies prior to 01/06/2008, it is vitally important that you familiarise yourself with the issue of FilterPadding found at: https://www.ynic.york.ac.uk/doc/FilterPadding Any questions should be directed to analysis-support(a)ynic.york.ac.uk Thanks, Mark (on behalf of the YNiC Staff) -- Mark Hymers York Neuroimaging Centre

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YNiC open plan Wed 4th June
by rem 30 May '08

30 May '08

Dear Users We have some visitors coming to YNiC on Wednesday 4th June from 4.30-7.30 pm. We will be talking to the visitors in Open Plan and they will need access to at least half of the iMacs. If you intend to work in Open Plan on Wednesday afternoon, please could you move to a computer towards the back of the room (i.e. away from the projector) as we approach 4.30 pm. Thank you 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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Tuesday 3rd June
by Gary Green 30 May '08

30 May '08

Dear colleagues On Tuesday the 3rd of June from 2pm onwards, YNiC will be reviewed by the University. A committee will be investigating how we operate, talking to users & staff and reviewing our space. If you are thinking of working at YNiC that day, it would help us to have users in the open plan area in case the Committee Members wish to talk about User experiences/research. Of course I cannot guarantee that they will want to do this as we have only been sent a general outline about what they wish to cover in the two and half hour visitation 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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YNiC seminar TODAY
by rem 29 May '08

29 May '08

Jonathan Peirce will be speaking from 4-5 pm at YNiC on "PsychoPy - Psychology and neuroscience stimuli in python". http://www.nottingham.ac.uk/neuroscience/contact/a-z/M-R/peirce_jon.phtml 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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YNiC seminar 29th May
by rem 23 May '08

23 May '08

Dear Users Next week's seminar (Thursday 4 pm at YNiC) will be given by Jonathan Peirce from the University of Nottingham. http://www.nottingham.ac.uk/neuroscience/contact/a-z/M-R/peirce_jon.phtml The title of his talk will be "PsychoPy - Psychology and neuroscience stimuli in python". Tim Andrews will be hosting this visit. 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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