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Brain Extraction
by Tom Hartley 05 Oct '06

05 Oct '06

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

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MEG planned maintenance
by Mark Hymers on behalf of YNiC 15 Sep '06

15 Sep '06

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

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[ANNOUNCEMENT] YNiC Beamformer Training Session
by Mark Hymers on behalf of YNiC 15 Sep '06

15 Sep '06

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

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Structural Scans
by a.morland＠psychology.york.ac.uk 12 Sep '06

12 Sep '06

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

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MRI Operational and Structural MRI
by a.morland＠psychology.york.ac.uk 12 Sep '06

12 Sep '06

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

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Shape/texture experiment - participants wanted
by Cristiana Pratesi 11 Sep '06

11 Sep '06

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

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Royal Society Meeting on Mental Processes in the Human Brain
by Michael Simpson 05 Sep '06

05 Sep '06

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

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Image of the Month
by Michael Simpson 05 Sep '06

05 Sep '06

Dear all, As of this email, the YNiC Image of the Month competition is live. Let me explain ... Each month YNiC is encouraging Users to submit an image of general interest, plus up to 100 words of explanatory text, into the Image of the Month contest. The best image will then be put on the web and published along with its text for a month. So, do you fancy seeing your work held up as an example of the science that is being carried out at YNiC? If so, email your images and text to: iotm(a)ynic.york.ac.uk Please send your images in .jpg (or similar format) to keep the file size small. Images will be judged by YNiC staff for both their aesthetic and scientific content. So, make your pictures pretty, but also make sure they explain something of the hypothesis which you are testing. Your 100 words will be essential in swinging this part of the vote! Good luck, 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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Image of the Month
by Michael Simpson 29 Aug '06

29 Aug '06

Dear all, there's only a few days left before September begins, could you have August's Image of the Month sitting in your homespace? If you think there is even a small possibility that this might be the case, don't hesitate to send it to iotm(a)ynic.york.ac.uk with your 100 words of descriptive text. Right, I'm eagerly awaiting a flood of jpgs ... 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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booking scanner time
by Gary Green 16 Aug '06

16 Aug '06

Dear Colleagues As The Centre is becoming busier and busier we now do have to make sure that bookings for the scanners works well for all users. We are conscious that we should be sharing time on the scanners in as equitable manner as possible. Some users have been sticking to their allocation whereas others have exceeded it by many,many hours. That was fine during the commissioning period but now with over 50 projects in progress, we do have to ensure that allocation of time is as even as possible. Given that we also need an income stream (the Centre costs nearly £1000 a day to run) we do have to give some priority to those who pay some money. We also have only a small number of operators for MEG and the fact that they have other roles as SLOs for a large number of projects, means that it is extremely difficult to respond to those users who want to make a last minute booking. At the same time, no one wants to see the scanners not being used when there is some science to be done. So.. Please can users help us by booking in the following way The scanner can only be booked by emailing Claire Fox. No one else can make the booking in the database. Please book the scanner (MEG or MRI) by Thursday of the week before you want to scan. You don't have to know the name of the participant at that stage. This helps us by allowing us to plan the diaries of the operators and the SLOs for the following week. It means that we can be more effective in supporting the wide range of projects. Please email the details of the participant to Claire by at least the day before the actual scan. This allows Claire to enter the participant's details into the database. This is essential. To access your data you will need to know the participant's ID in the database. If you do not have this the automated uploading of MEG & MRI information, the automated brain extraction, the conversion of the MEG files to be readable by Matlab or Python does not happen. Valuable scanning time is being lost when users try and get the participant ID at the time of their booking. If you have difficulty recruiting a participant then email Claire and we will place an advert on the webpage for you. This needs to be done well in advance of the scan booking of course. If you have not managed to recruit someone then please do not just go into the open plan area and ask for a volunteer. This puts undue pressure on the users doing their work there and this is unethical. We have had several complaints from students in particular that they feel that cannot say no to staff requests. If you cannot recruit someone then tell Claire to postpone your booking. If you just don't turn up you will lose that time from your allocation. If you need to book the scanner at the last minute. Please email the director to discuss your requirements. Please do not ask Claire. Claire is not in a position to judge who should get special attention and again this puts her in a difficult position if she feels that she turn down your request. We don't want to see the scanner being idle, but we do have to make sure that resource is available to provide an operator. Eventually, when we have enough paying users, we will have a full time set of operators to help all MEG requests. We are allowing teams who can operate the scanners to take advantage of 'free' time on the scanners. Why not join one of the MEG or MRI training programmes in the autumn to learn how to be an operator. If this is not clear, or you feel that there is a better way, why not email me or the ynic-users group to discuss it. Gary -- 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

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Trash
by Mark Hymers 08 Aug '06

08 Aug '06

Could all users please make sure they clear their trash out regularly. This can be done by right clicking on the trash can on the dock and choosing "Empty Trash". We currently have nearly 90Gb in the Trash folders and I'd rather people did it themselves rather than have to have a system whereby files are deleted from the trash automatically. Mark -- Mark Hymers York Neuroimaging Centre

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Interview room
by Michael Simpson 07 Aug '06

07 Aug '06

Dear all, E-Prime is now installed on the computer in the Interview Room. I know this has been a concern for some MR users, but E-Prime can now be used to prep your subjects. Michael N.B. Remember, you'll not be able to use code that is expecting MR pulses on the machine in the Interview Room! -- 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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RE: Staff Cricket
by Michael Simpson 04 Aug '06

04 Aug '06

Dear all, Just to clarify some points raised by the Staff Cricket email I send recently. I'm just trying to get an idea of interest for next year because we'll probably have to contact the fixtures secretary at the end of this season if we want to enter a team. So, I'm not asking whether you'll be able to play all 10 games, I just asking whether you are keen to be involved in a joint Neuroimaging and Psychology team? Also, the standard of cricket caters for all abilities; from the novice to the pro (most teams have a mixture of the two). It's about giving staff and postgrads regular cricket throughout the summer. Enthusiasm is the only prerequisite. So, don't feel that if you haven't had a trial at County level you'll not get selected for the team. Anyone is welcome. However, that's not to say if you have had a trial at County level you won't be welcome ... absolutely not! Basically, if you can identify at least two pieces of cricket equipment from the following list you'll be more than qualified to play: BAT, BALL, racket, boomerang, wet-suit, stumps, puck, clay-pigeon, bails, jet-ski, oar, javelin, shuttlecock, cucumber sandwiches. I look forward to hearing from you, 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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Digest delivery
by Mark Hymers 03 Aug '06

03 Aug '06

Hi, Apologies to those who were signed up for digest deliveries of ynic-news or ynic-users. The cronjob which sends the digests wasn't running. It has now been enabled and you should recieve a digest either once a day, or when there are more than 30kB of mail on a particular list. Thanks, Mark -- Mark Hymers York Neuroimaging Centre

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Staff Cricket
by Michael Simpson 02 Aug '06

02 Aug '06

Dear all, A few of us from YNiC are playing in the York Staff and Postgrad Cricket league this season. We are wondering whether there would be enough interest for a joint YNiC & Psychology team for next season? The regulars from YNiC at the moment are Andre 'Danger' Gouws, Garreth 'Calypso' Prendergast, Sam 'The Apprentice' Johnson and myself. If we were to raise a team we'd really need a squad of 15 who could play relatively regularly. So, are you interested? And if so, can you bat / bowl / wicketkeep / sledge from Extra Cover? A link to the league and the typical number and dates of fixtures is here: http://www-users.york.ac.uk/~socs456/ As you can see, we'd need a pithy team name. I suggest 'Head Cases and Psychos' unless anyone can come up with an alternative. Let me know of your interest. Michael P.S. Could one of the psychologists scout for interest in Psychology please? -- 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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Research opportunities sought
by Andy Ellis 02 Aug '06

02 Aug '06

>Delivered-To: psychology.york.ac.uk-a.ellis(a)psych.york.ac.uk >From: wj3(a)york.ac.uk >To: <awy1(a)york.ac.uk>, <awe1(a)york.ac.uk>, <ta505(a)york.ac.uk> >Subject: FW: possible research vacancy >Date: Wed, 2 Aug 2006 10:44:42 +0100 >X-York-MailScanner: Found to be clean >X-York-MailScanner-From: wj3(a)york.ac.uk > >Dear All, > >Have just received the following email from a student who graduated >in July - Hui Minn Chan. Hui Minn's file shows that she received a >1st and was also nominated for the EPS and BPS prizes. > >Dont' know if any of you are able to help? > >Regards, > >Wendy > >-----Original Message----- >From: Hui Minn [mailto:huiminn@gmail.com] >Sent: 02 August 2006 10:28 >To: wj3(a)york.ac.uk >Subject: possible research vacancy > >Dear Wendy, > >I have recently graduated from the department and am now looking for >some research experience. I wonder if you know of any such vacancies >(especially in the neuroscience area) in the department which last >for about 1 year or so? I have tried searching on the departmental >website but have not come up with much. > >Thanks very much, >Minn -- Professor Andy Ellis Department of Psychology University of York York YO10 5DD UK Tel. +44 (0)1904 433140 http://www.york.ac.uk/depts/psych/www/people/biogs/awe1.html

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Testing
by Mark Hymers 12 Jul '06

12 Jul '06

Testing ynic-users list -- Mark Hymers York Neuroimaging Centre

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