ynic-users

ynic-users@ynic.york.ac.uk

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2770 discussions

by Michael Simpson

Dear Users, Can Users who wish to book MRI / MEG please use the bookings(a)ynic.york.ac.uk email address. This address can in theory be checked by all staff, and hence always monitored. If you have made any bookings to an address other than the bookings(a)ynic.york.ac.uk email, please re-send your booking to the correct address. To make things more efficient, and enable the Operator to set up you recording preferences in advance, could your booking include the following (preferably in the following format - see example in post script): Date: Time: Type of scan: (MEG / structural MRI / fMRI) Your Name: Project ID: Participant ID: (If your participant needs to be registered on the database, please attach their registration form). Stimulus Code*: Stimulus Presentation software / apparatus*: (e.g. E-Prime, screen and etymotics) MEG position (Seated / Supine): * Contact your SLO if you don't know what a / your Stimulus Code is. with thanks, Michael P.S. Example booking - Date: 31st October 2006 Type of Scan: structural MRI Project ID: P0666 Participant ID: R0000 Stimulus Cods: P0666et Stimulus Presentation software / apparatus: Visage and Phantom MEG position (Seated / Supine): N/A -- Dr Michael Simpson Science Liaison Officer York Neuroimaging Centre Innovation Way York YO10 5DG Tel: 01904 567614 Web: http://www.ynic.york.ac.uk

18 years, 6 months

Important update : ethics applications

by Gary Green

Procedures for applying for ethical approval to conduct research at YNiC have been revised. Details of the new arrangements, along with guidance on how to prepare an application, can be downloaded from the YNiC website at: https://www.ynic.york.ac.uk/information/application/so-you-want-to-use-the-… Please could all new applications for research ethics approval conform to the revised instructions. Thank you. -- Gary Green Director York Neuroimaging Centre The Biocentre York Science Park Innovation Way Heslington York YO10 5DG tel. 01904 435349 fax 01904 435356 mobile 07986 778954

18 years, 6 months

YNiC system trash

by Mark Hymers

Due to the fact that user's Trash folders are growing in size again, we have taken the decision that we will start automatically emptying the trash directories at least once a week (initially on Friday evenings). Please note that we do not backup Trash directories at all and any file placed in there should be regarded as deleted. As from next week, we may also decide to empty Trash directories without notice should we need to (for instance we have seen 15G trash directories this week). To assist with this, please empty your Trash directory manually as often as you can (preferably as soon as you've placed anything in it). Mark -- Mark Hymers York Neuroimaging Centre

18 years, 6 months

Brain Extraction

by Tom Hartley

Dear fellow ynic-users, You may notice some difficulty removing non-brain tissue from structural MR images obtained at YNiC when using the brain extraction tool (bet - a part of FSL) with its default parameters. Symptoms are that tissue around the brainstem, mouth and throat is not removed. This might adversely affect coregistration. One workaround I know some people have used is to coregister the "unstripped" brain to the "unstripped" reference volume (which seems to work quite well). However, the FSL help strongly recommends removing non-brain tissue, so this might not be the best solution. Bet uses an estimate of the centre of the image to begin the process of finding the inner and outer scalp and brain boundaries. The default estimate doesn't seem to be right for out structural scans. I have had more success using the following from the command line: bet myinfileroot myoutfileroot -c 87 108 165 Where you replace myinfileroot and myoutfileroot with the names of your input and output files (without .hdr or .img on the end). The coordinates 87 108 165 may not be quite right for the centre of your image but the bet algorithm seems to work much better with these values. Best wishes, Tom Hartley =================================== Dr Tom Hartley Dept. of Psychology, University of York Heslington, YO10 5DD UK. t.hartley(a)psychology.york.ac.uk http://www-users.york.ac.uk/~th512 tel: +44 (0)1904 432903

18 years, 6 months

MEG planned maintenance

by Mark Hymers on behalf of YNiC

Hi again, As mentioned in the earlier email about the training session, MEG will be undergoing planned maintenance in the near future. The dates are Friday 29th September until Sunday 8th October. MEG will reopen for use on Monday 9th October. Another important announcement is that we now have a bookings(a)ynic.york.ac.uk email address. This should now be used for bookings instead of emailing Claire directly as it will allow us to cover for her when she isn't around. We'll be updating the web site and documentation to reflect this as soon as we can. Cheers, Mark (on behalf of YNiC) -- Mark Hymers York Neuroimaging Centre

18 years, 7 months

[ANNOUNCEMENT] YNiC Beamformer Training Session

by Mark Hymers on behalf of YNiC

Hi all, YNiC are pleased to announce our first formal all-day training session. This will take place on Friday 29th September at YNiC and the subject will be MEG Analysis using Beamforming. This will coincide with our general release of the YNiC Beamforming tools which some users have been beta-testing in the past few weeks. The timetable is as follows: ============================================================================= 0900-0915 Coffee and brief welcome talk 0915-1000 Talk: Introduction to Beamforming 1000-1030 Demo: How to use Beamforming at YNiC (Demonstration data) 1030-1045 Coffee break 1045-1130 Workshop: Using the Beamformer 1130-1215 Talk: Common pitfalls in MEG data analysis 1215-1300 LUNCH: (Sandwich buffet will be provided) 1300-1345 Talk and discussion: Review of results on test data 1345-1430 Talk: Why is nothing working? How to troubleshoot 1430-1445 Coffee break 1445-1530 Talk: Virtual electrodes 1530-1630 Workshop: Using virtual electrodes and examining your own data ============================================================================= To make sure that people get the most out of this training session, there will be a limit of 25 participants. Due to this training session, the YNiC Open Plan will be closed all day on the 29th to those not attending the training session. MEG will be undergoing planned maintenance that day and so will also be closed (a further announcement about this will follow soon). As this is the first YNiC training session, we will be providing lunch for the course attendees to celebrate the first of what we hope will be many such courses. To register for this course please email training(a)ynic.york.ac.uk with your name and email address. Registration will close when we have 25 people or on Friday 22nd September (although we expect places to fill up quickly). Finally, we will soon be running a poll on the YNiC website to find out the best times to run future training courses. Again, we will make an announcement about this soon. Thanks, Mark (On behalf of everyone at YNiC) -- Mark Hymers York Neuroimaging Centre

18 years, 7 months

Structural Scans

by a.morland＠psychology.york.ac.uk

Dear All, Thanks to some work from Andre, it has now been determined that the current structurals are fit for purpose. Although the scalp identification is a little noisy, the fits to the scalp information derived in MEG do not appear to be unduly compromised. So, structural scans can be acquired for the use with MEG data. Although Andre has checked the registration of the MRI and MEG scalp information on a few data sets, it really would be helpful if all users who acquire such data could visually inspect their registrations (the docwiki has information on how this can be done). Please alert us to any discrepant registrations and proceed with caution. Sorry for the rapid turn around on this issue. I am loath to recommend scanning when the images are clearly not of the quality that we have previously obtained, but in this case I think we can proceed (with caution). The change in the image quality will still be pursued with GE. Happy scanning! Tony

18 years, 7 months

MRI Operational and Structural MRI

by a.morland＠psychology.york.ac.uk

Dear All, As some of you may be aware, the recent MRI upgrade has introduced an undesirable effect on the acquisition of structural anatomy scans, which are routinely used in MEG analysis. The problem is subtle, but the code that automatically identifies the skull runs less smoothly on the recently acquired data. GE have been informed. As of now, structured MRIs for the use with MEG will not be acquired, unless there are some exceptional circumstances. MEG data can be acquired, but participants will have to be rescheduled for their structural MRIs. Please note however, that self-contained MRI studies will not be affected in the same way because they are not so critically dependent on identification of the skull surface. Thus, acquisition of functional data and structurals (for registration) can proceed. On a more positive note, the MRI scanner is up and running today. Tony

18 years, 7 months

Shape/texture experiment - participants wanted

by Cristiana Pratesi

Researchers at the University of Durham are seeking healthy volunteers to participate in neuroimaging experiments using functional magnetic resonance imaging. The experiments will be performed at the York Neuroimaging Center using a 3Tesla magnet. We will start a new experiment in the next couple of weeks and participants will be asked to discriminate visual objects on the basis of their geometrical (shape) or surface (texture) features. Visual stimuli are images of 3D objects, and behavioural responses will be collected via button press. Typical sessions last for 1-2 hours, and involve lying still in the scanner while brain images are recorded. For detailed information about the experiment see attached file. The experiment is part of a research project based at the University of Durham. The experimenter is Dr. Cristiana Cavina-Pratesi and the main investigators are Prof. D. Milner; Prof. C. Heywood and Prof. R. Kentridge. If you are interested, read the information below and if you think to be eligible for participating, please fell free to contact Dr. Cristiana Cavina-Pratesi cristiana.cavina-pratesi(a)durham.ac.uk for further information. Your name will be entered in a database. You can decide to remove your name from the database at any time and you are always free to decline when an experimenter contacts you. To be eligible to participate, you must: a.. have no metal in your body (fillings are okay) b.. not be claustrophobic c.. be able to remain relatively still for periods of 5-8 minutes d.. be in good health and have no history of neurological disorders (e.g., epileptic seizures, head injuries) e.. be able to see without glasses (contacts are okay) at arms' length (for vision experiments); Thanks in advance for your attention Cristiana Cavina-Pratesi

18 years, 7 months

Royal Society Meeting on Mental Processes in the Human Brain

by Michael Simpson

Dear all, this may be of interest to you ... > A Royal Society discussion meeting on "Mental Processes in the Human Brain" has > been organised by Jon Driver, Patrick Haggard and Tim Shallice from the UCL > Institute of Cognitive Neuroscience, for Oct 16-17 2006, at the Royal Society > in London. > The programme and flyer are available on: > http://www.royalsoc.ac.uk/downloaddoc.asp?id=2835 > This Royal Society meeting is free to attend, but on-line pre-registration is > *essential*. To register, please click on www.royalsoc.ac.uk/events Then under the > "Choose month to view" box, click on Oct 2006 from the drop-down selection and > then click "go". If you then click on the title of the event (Mental Processes > in the Human Brain) you will get the option to "Register for this Event".Please > note the overlap of dates with the rescheduled Society for Neurosciences > meeting in the USA. Despite this unfortunate timetable clash, the Royal Society > meeting is still expected to be heavily oversubscribed; hence early > registration as above is strongly recommended > Rosalyn Lawrence, ICN Secretary, for the Organisers > John Draper > Departmental Administrator > Psychology Department > UCL > Gower Street > London WC1E 6BT > tel: 020 7679 5338 > fax: 020 7436 4276 j.draper(a)ucl.ac.uk http://www.psychol.ucl.ac.uk/john.draper/john.html -- Dr Michael Simpson Science Liaison Officer York Neuroimaging Centre Innovation Way York YO10 5DG Tel: 01904 567614 Web: http://www.ynic.york.ac.uk

18 years, 7 months

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