ynic-users October 2006

ynic-users@ynic.york.ac.uk

5 participants
7 discussions

trial datasets
by Michael Simpson 31 Oct '06

31 Oct '06

Dear all, when new users arrive at YNiC, some would like to practice using data analysis scripts before they record their own data. As such, we would like to document some of the paradigms that have already been recorded. We would not want to know in detail the specifics of your project, just the basics to allow for a sensible analysis. For example, the following may be enough: "In the data for project Pxxxx, responses were recorded in continuous mode to visual stimuli. There were four conditions which had the respective trigger codes 4150, 4152, 4154 and 4156. Triggers 4150 and 4152 had a group code of 2, and triggers 4154 and 4156 had group codes of 4. Participants made responses to some trials, which have a response code of 32. Suggested epochs for data analysis are 150ms pre-trigger and 900ms post-trigger. Data was recorded for participants Rxxxx, Rxxxy ... Rxyyx." With this information new Users could run a trial analysis without any necessary knowledge of your hypothesis, but enough information about your stimulus parameters to run practice analyses on your data. If you we be happy to provide this information about your data we would be most grateful. We would then put this in some shared space for all Users to access. If however you would like to give a more detailed account of your experiment, then this could contribute towards the initiative that Tony prompted in the email copied below. With 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 *_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_ Copy of mail from Tony Morland date 25th October. Dear All, Since the first beamforming course a number of people have been asking questions like; What can beamforming really do? If I do this and get that, what does it mean? Is beamoforming precise enough to distinguish between activity in brain area A and B? If I do X will it result in data that can be analysed with beamforming? Can virtual electrode traces allow latencies to be measured in brain areas A and B and do they make sense? If I filter in this frequency band rather than that band why do I get this result? The answers to many of these questions are empirical and although Will et al have been striving to test, retest and validate the methods, there will always be questions that can't quite be answered unless more data is acquired/analysed. It appears necessary therefore to start bench marking the beamforming methods that are available. The aim is to undertake a series of empirical studies that will reflect, in broad terms, the types of paradigm used by investigators. My personal preference would be for a set of basic experiments to be devised for which results are predictable and could be compared with previous research. I accept that this is a conservative aim, but the data sets acquired are likely to be the most informative about the capabilities of the beamforming analysis tools. The data acquired would also offer us an excellent resource for training any researchers wishing to undertake investigations using beamforming. Before devising new experiments it would be worth reviewing previous studies undertaken at YNiC to see whether they can be used to bench mark the beamforming methods. To this end, I would be grateful if you could provide me with details of data that you think are suitable for bench marking beamforming. The most helpful form for the information would be the following: Project Number and Title Number of participants and their registered numbers Paradigm used Relevant research (the study replicated) Predicted outcome What you want to test with beamforming Ethical concerns/limitations concerning use of the data I will review the forthcoming information and after that will arrange a brainstorming session on how best to move things forward. Thanks Tony

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MEG / MRI booking
by Michael Simpson 27 Oct '06

27 Oct '06

Dear Users, further to the email sent recently about the format of booking requests, Users may book scan time via a new on-line booking form. https://www.ynic.york.ac.uk/user-resources/booking However to cancel a booking please send the following request to bookings(a)ynic.york.ac.uk : CANCEL Date: 31st October 2006 Time: 00.00 Type of Scan: structural MRI Project ID: P0666 Participant ID: R0000 Unfortunately, verbose requests can lead to ambiguities and increase the chances of errors. Please avoid the following style of request: "This is just a request to cancel the time for one subject on Monday of this week (my subject is on holiday LOL!) and then re-book them in to another slot next Friday, for some time in the afternoon (don't mind when), with all the same information, but an amendment to the Stimulus Code from P0666et to P0666aa." Should you need to re-schedule a subject, please simply send a CANCEL request as shown above, and then re-book some new time via the website. Thanks, Michael

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Beamforming
by a.morland＠psychology.york.ac.uk 25 Oct '06

25 Oct '06

Dear All, Since the first beamforming course a number of people have been asking questions like; What can beamforming really do? If I do this and get that, what does it mean? Is beamoforming precise enough to distinguish between activity in brain area A and B? If I do X will it result in data that can be analysed with beamforming? Can virtual electrode traces allow latencies to be measured in brain areas A and B and do they make sense? If I filter in this frequency band rather than that band why do I get this result? The answers to many of these questions are empirical and although Will et al have been striving to test, retest and validate the methods, there will always be questions that can't quite be answered unless more data is acquired/analysed. It appears necessary therefore to start bench marking the beamforming methods that are available. The aim is to undertake a series of empirical studies that will reflect, in broad terms, the types of paradigm used by investigators. My personal preference would be for a set of basic experiments to be devised for which results are predictable and could be compared with previous research. I accept that this is a conservative aim, but the data sets acquired are likely to be the most informative about the capabilities of the beamforming analysis tools. The data acquired would also offer us an excellent resource for training any researchers wishing to undertake investigations using beamforming. Before devising new experiments it would be worth reviewing previous studies undertaken at YNiC to see whether they can be used to bench mark the beamforming methods. To this end, I would be grateful if you could provide me with details of data that you think are suitable for bench marking beamforming. The most helpful form for the information would be the following: Project Number and Title Number of participants and their registered numbers Paradigm used Relevant research (the study replicated) Predicted outcome What you want to test with beamforming Ethical concerns/limitations concerning use of the data I will review the forthcoming information and after that will arrange a brainstorming session on how best to move things forward. Thanks Tony

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Booking Imaging Time
by Michael Simpson 24 Oct '06

24 Oct '06

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

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Important update : ethics applications
by Gary Green 12 Oct '06

12 Oct '06

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

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YNiC system trash
by Mark Hymers 06 Oct '06

06 Oct '06

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

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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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ynic-users October 2006