- ynic-users

Open Plan busyness
by Sam Johnson 15 Oct '08

15 Oct '08

Hello all, Just to let you know about a couple of busy periods in the open plan at YNiC next week. On the 22nd (Wednesday) there will be a group of ~10 school children at YNiC between 14:00 and 15:30 using some of the machines in open plan. They will be accompanied by a Calendar film crew so those of you who are camera shy may want to avoid the area. Alternatively of course, if you want your 5 minutes of fame as background scientition, feel free to look industrious. On the 23rd (Thursday, though you probably could have worked that out) the first of the MSc sessions will be held between 13:15 and 15:15. During this time open plan will be extremely busy, and there are unlikely to be machines available. I'd strongly advise you not to come in to YNiC in the afternoon until after they've finished, when you will of course be rushing in for the "Taking your research through to publication" seminar. Thanks, Sam

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YNiC Thursday meeting
by rem 14 Oct '08

14 Oct '08

Dear Users This week's YNiC seminar (4-5 pm) will be given by Piers Cornelissen. His talk is titled "Virtual electrodes II: an update on group level analysis of VE data" . 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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annual users' meeting
by Gary Green 08 Oct '08

08 Oct '08

Dear Colleagues The annual user meeting is tomorrow (9th October 2008) at 4pm. The meeting will be held in the Venables room in Psychology All welcome The agenda will be 1. Welcome and statements by the Director (GG) 2. News from YNiC - The New Science Committee (A. Ellis) - Ethics & Governance (A. Morland) - The new database and booking system (YNiC staff) - Operator training 2008/09 (YNiC staff) - Proposed changes to web and documentation (YNiC staff) 3. Topics raised by users - Financial situation at YNiC (GG to lead) - The proposed charging system (AM to lead) - The software programme for 08/09 (WW to lead) 4. AOB -- 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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annual users' meeting
by Gary Green 07 Oct '08

07 Oct '08

Dear colleagues Topics that have been suggested/requested for discussion at the Annual Users' Meeting, so far, include a. The financial situation at YNiC (budgets, equipment upgrades, sustainability) b. The new booking system c. Operator training for MRI and MEG (when, how) d. The proposed charging system for YNiC e. The software programme (including inclusion of dipole and minimum norm estimation in the software framework) f. Ethics and Governance (a proposal for permission to conduct work in an area rather than by project) Please do suggest other topics. We would welcome discussion on the scientific programme at YNiC if Users would like to suggest specific areas of interest or concern. 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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YNiC Thursday meeting 9th October
by Rebecca E Millman 06 Oct '08

06 Oct '08

Dear Users This week the Thursday afternoon meeting, which will be held in *Venables* (4-5 pm), is the Annual General Meeting for Users. The purpose of this meeting is for YNiC staff and Users to discuss the best way forward for research at YNiC. Please use ynic-users(a)ynic.york.ac.uk <mailto:ynic-users@ynic.york.ac.uk> to generate ideas for the agenda. The co-ordinators for this meeting will be Andy Ellis and Gary Green. Everyone is welcome to attend. *N.B. This meeting will be held in Psychology in Venables (room A202)* -- 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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Todays session
by Antony Morland 02 Oct '08

02 Oct '08

Hello All, At 4pm today we will be having an informal session on aspects of neuroimaging that folks picked up at conferences this year. Andre, Michael and Will are going to give brief talks. I will also be providing some information concerning the upgrades that will be made at YNiC next week during the scheduled closure. As is customary, some light refreshments will be available afterwards. Hope to see you there 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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Disk space
by a.morland＠psychology.york.ac.uk 30 Sep '08

30 Sep '08

Dear All, One of the disk partitions used to store analyzed data is full. As an emergency measure the disk partition is being extended so that analysis can continue. The extension of the partition will slow access time considerably this morning, so it would be wise to postpone heavy duty analysis until this afternoon. Thanks Tony

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YNiC Closure
by Antony Morland 29 Sep '08

29 Sep '08

Hello All, This is a reminder that YNiC will be closed from 5pm Friday 3rd October through to 9am 13th October for a major infrastructure project. Computing on the cluster will not be possible during this period and desktop access will not be available. Cluster jobs submitted on Friday will have to be complete before 5pm. At 5pm, all cluster jobs will be stopped. The new infrastructure will allow, among many other improvements, investigators to book scanner slots via a web interface. Details of the new booking procedures will appear in another email. 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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YNiC Thursday meeting 2nd October
by Rebecca E Millman 29 Sep '08

29 Sep '08

This week the Thursday afternoon meeting at YNiC (4-5 pm) will focus on Users' feedback from conferences that you have attended over the summer. Everyone is invited to talk about how their neuroimaging work was received. We would also like to hear about posters/presentations from other labs that you found particularly interesting and exciting. Tony Morland will chair this session.Please contact Tony <a.morland(a)psychology.york.ac.uk> if you would like to contribute. -- 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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YNiC Thursday afternoon schedule
by rem 22 Sep '08

22 Sep '08

Dear Users Please find below the schedule for YNiC's Thursday sessions (4-5 pm at YNiC, except where stated). Please contact me if you have any questions. Best wishes Rebecca ***************************************************************************** 2nd October: Debrief from conferences All Users are invited to talk about how their neuroimaging work was received at conferences they attended over the summer. We would also like to hear about posters/presentations from other labs that you found particularly interesting and exciting. Tony Morland will chair this session. Please contact Tony Morland <a.morland(a)psychology.york.ac.uk <mailto:a.morland@psychology.york.ac.uk>> if you would like to contribute. 9th October: Annual User Meeting A meeting for YNiC staff and Users to discuss the best way forward for research at YNiC. Please use ynic-users(a)ynic.york.ac.uk <mailto:ynic-users@ynic.york.ac.uk> to generate ideas for the agenda. The co-ordinators for this meeting will be Andy Ellis (Chair of Science Committee) and Gary Green. *N.B. This meeting will be held in Venables (A202)* 16th October: Analysis Support Colloquium (ASC) - Piers Cornelissen "Virtual electrodes II: an update on group level analysis of VE data" 23rd October: Taking your research through to publication This session will focus on problems that YNiC users may be experiencing in analyzing their data to the point where they are happy to submit it for publication, and will try to identify issues concerning the analysis tools, visualisation tools, statistics etc that could usefully be addressed. Please use ynic-users(a)ynic.york.ac.uk <mailto:ynic-users@ynic.york.ac.uk> to generate ideas for the agenda. Gary Green will co-ordinate this meeting. 30th October: External speaker - Joachim Gross "Oscillatory coupling and activity in sensorimotor areas studied with MEG" http://www.psy.gla.ac.uk/staff/index.php?id=JG001 6th November: External speaker - Stephan Moratti "Steady state visual evoked potentials/ fields: Advantages of High Signal to Noise Ratio in Basic and Clinical Psychophysiological Research" http://web.mac.com/smoratti/Stephan_Moratti,_Researcher/Stephan_Moratti_Inf… 13th November: Applying for neuroimaging grants Presentations by Sue Gathercole (and others) on strategies for successful grant applications. 20th November: TMS lab opening Silke Goebel and Beth Jeffries will open the new TMS lab. 27th November: Feedback from Annual Users Meeting Andy Ellis and Gary Green will lead a discussion on the outcomes of the Annual Users Meeting (9th October). 4th December: Analysis Support Colloquium (ASC) - Silke Goebel "Investigating Number Processing with MEG - Lost in (Source) Space" 11th December: Work in progress by Users and Staff Presentations by YNiC staff and Users on current research projects. Please contact gary.green(a)ynic.york.ac.uk <mailto:gary.green@ynic.york.ac.uk> if you would like to volunteer. 18th December: Work in progress by Users and Staff (& Christmas drinks) Presentations by YNiC staff and Users on current research projects. Please contact gary.green(a)ynic.york.ac.uk <mailto:gary.green@ynic.york.ac.uk> if you would like to volunteer. -- ************************************************************************ 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-based publications. Please respond ASAP
by a.ellis＠psych.york.ac.uk 17 Sep '08

17 Sep '08

Dear all University Research Committee has delivered its report on YNiC following the review that was conducted in June. The report compliments YNiC on having reached the point it has, notes (inevitably) the need for more external grant income, and makes a variety of points about the relationship between Psychology and YNiC, the committee structure etc. that are prefectly acceptable and already being addressed. The department is required to make a formal response to the review. It would be good to include in that response the growing list of the publications that are now emerging from YNiC, along with the conference presentations. I attach the most up-to-date list I have. Please could you let me know of any changes or additions. A response by the end of Friday would be very helpful. With thanks Andy

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Late notice of seminar
by Gary Green 15 Sep '08

15 Sep '08

Simon Duckett and I have organised a chemistry/YNiC hyperpolarisation team meeting this morning where we are discussing MRI/NMR theory. As the numbers attending are more than can be housed in my office we are moving the seminar into the open plan area of YNiC. All are welcome and the talk will start at 9.30 A presentation on the mathematical background to NMR and MRI will be presented. The talk will be mainly on Density matrices, Product operators and the theory behind double quantum states selection in polarised molecules. Sorry for the late notice 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 Downtime.
by Sam Johnson 10 Sep '08

10 Sep '08

Hello All, For the start of the new academic year we're making changes that will require some downtime on the systems here at YNiC. The reason for this downtime is that we will be implementing some major changes to the software that helps us run and administer the Centre. Hopefully many of these changes will go unnoticed, but there will be one or two things that we hope will make your lives easier. The most significant change will be the introduction of a new booking system that can be accessed off site and will allow users to make their own bookings for MRI, TMS and MEG. This will be part of a new and improved database that will also allow investigators to track their projects' progress and help us ensure that the right projects get the appropriate support at the appropriate time. The upgrades will also include a uniform login and security system across all the computers (this will be invisible to most users but does have some major advantages) and a better, more equitable use of quotas on the filesystems. We will also add more disc space to help with the current overloading of the existing systems. To do all this we need to change the servers that run the whole system. As a result, YNiC will be closed from 5:00 p.m. on Friday the 3rd of October and will reopen at 9:00 a.m. on Monday the 13th of October. This version of the database will be released as v0.9, and we already have some ideas about what will be going into v0.95 and v1.0, but early next term, when people have had a chance to play with it, we'll be asking for your input on additional functionality that you'd find useful. Look out for the Annual Users' Meeting that will provide an opportunity for users to contribute to planning the next stages of development. We will need some additional information for some projects to allow investigators to take advantage of the new booking procedure, and in the next couple of days principal investigators will be getting an email requesting those details. It is very important that we get this information by the end of the month or some projects will no longer be able to book time on the scanners. One unfortunate side effect of some of the changes is that all passwords will have to be reset. First thing on Monday the 13th when we reopen, new passwords will be provided which will enable you to login and reset you password to something more memorable. Hopefully though, that will be the only disruption and from the 13th normal (and improved) service will resume. So, to reiterate, YNiC will be closed between: 17:00 Friday 3rd October and 09:00 Monday 13th October. If you have any questions about these changes, please contact Sam Johnson <sam.johnson(a)ynic.york.ac.uk> or Mark Hymers <mark.hymers(a)ynic.york.ac.uk>. Thanks, and sorry for any inconvenience, Sam

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MEG down
by Gary Green 27 Aug '08

27 Aug '08

Dear colleagues I am sorry to have to report that MEG is not available due to another, different, fault. 4D Neuroimaging will be on site tomorrow (Thursday) and will replace a set of electronics. I will report when it is available again. -- 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 down
by Gary Green 15 Aug '08

15 Aug '08

Dear Users I am sorry to have to tell you that MEG is down. We have an intermittent fault that causes the system to fail such that either the coil information cannot be captured and/or the channels all flat line. We have worked with 4D all week to try and isolate the cause of the fault but it appears that whatever it is creates a variety of different fault conditions depending on where in the process stream one has reached. It is likely that it is due to a processor board problem in the DAS rack. 4D will be arriving early next week to rectify the matter and will be replacing a number of cards in the main acquisition rack (the DAS). I am very sorry for the serious disruption this is causing some of you at such a critical time in your research studies. As soon as MEG is available again I will email you. 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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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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