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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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