ynic-users

ynic-users@ynic.york.ac.uk

1 participants
2786 discussions

Thursday lunchtime seminar
by Sam Johnson 12 Nov '07

12 Nov '07

Hello all, Elena Solesio has been visiting YNiC from the imaging centre in Madrid. This Thursday lunchtime, at 1:00pm, Elena will be giving a talk in YNiC open plan on some of the work she's been doing, entitled: Retroactive Interference Modulates Magnetic Brain Activity In Normal Aging: A Magnetoencephalography Study. As ever all are welcome to come along. Thanks, Sam

1 0

Connectivity seminar this spring?
by Johan Carlin 12 Nov '07

12 Nov '07

Dear All, I would really like to see a Thursday session on connectivity - dynamic causal modelling, diffusion tensor imaging, etc. Is this interesting to anyone else? Best, Johan Carlin

3 2

[Fwd: ScienceDirect Alert: Trends in Neurosciences, Vol. 30, Iss. 11, 2007]
by Tim Andrews 12 Nov '07

12 Nov '07

Paper on Bloodless MRI that might be of interest to some of you in the latest TINS -------- Original Message -------- Subject: ScienceDirect Alert: Trends in Neurosciences, Vol. 30, Iss. 11, 2007 Date: Sat, 10 Nov 2007 13:43:30 -0500 From: ScienceDirect Message Center <valert(a)prod.sciencedirect.com> To: ta505(a)york.ac.uk ScienceDirect <http://www.sciencedirect.com/science> New Volume/Issue is now available on ScienceDirect Trends in Neurosciences <http://www.sciencedirect.com/science/issue/4872-2007-999699988-673508> Trends in Neurosciences <http://www.sciencedirect.com/science/journal/01662236> Volume 30, Issue 11 <http://www.sciencedirect.com/science/issue/4872-2007-999699988-673508>, Pages 555-610 (November 2007) 1. Editorial Board <http://www.sciencedirect.com/science?_ob=GatewayURL&_method=citationSearch&…> Page i Review 2. From genes to pain: Nav1.7 and human pain disorders <http://www.sciencedirect.com/science?_ob=GatewayURL&_method=citationSearch&…> Pages 555-563 Sulayman D. Dib-Hajj, Theodore R. Cummins, Joel A. Black and Stephen G. Waxman 3. Munc18-1 in secretion: lonely Munc joins SNARE team and takes control <http://www.sciencedirect.com/science?_ob=GatewayURL&_method=citationSearch&…> Pages 564-572 Ruud F.G. Toonen and Matthijs Verhage 4. The TASK background K2P channels: chemo- and nutrient sensors <http://www.sciencedirect.com/science?_ob=GatewayURL&_method=citationSearch&…> Pages 573-580 Fabrice Duprat, Inger Lauritzen, Amanda Patel and Eric Honoré 5. Phosphatase PTEN in neuronal injury and brain disorders <http://www.sciencedirect.com/science?_ob=GatewayURL&_method=citationSearch&…> Pages 581-586 Ning Chang, Youssef H. El-Hayek, Everlyne Gomez and Qi Wan 6. The ubiquitin–proteasome pathway in health and disease of the nervous system <http://www.sciencedirect.com/science?_ob=GatewayURL&_method=citationSearch&…> Pages 587-595 Ashok N. Hegde and Sudarshan C. Upadhya 7. Neuronal ‘On’ and ‘Off’ signals control microglia <http://www.sciencedirect.com/science?_ob=GatewayURL&_method=citationSearch&…> Pages 596-602 Knut Biber, Harald Neumann, Kazuhide Inoue and Hendrikus W.G.M. Boddeke 8. Bloodless fMRI <http://www.sciencedirect.com/science?_ob=GatewayURL&_method=citationSearch&…> Pages 603-610 Alan Jasanoff Send my e-mail in plain text format <http://www.sciencedirect.com/science/account> Modify or Remove My Alerts <http://www.sciencedirect.com/science/alerts> Access the ScienceDirect Info site <http://www.info.sciencedirect.com> if you have questions about this message or other features of this service. This email has been sent to you by ScienceDirect, a division of Elsevier B.V., Radarweg 29, 1043 NX Amsterdam, The Netherlands, Tel.+31 20 485 3911. ScienceDirect respects your privacy and does not disclose, rent or sell your personal information to any non-affiliated third parties without your consent, except as may be stated in the ScienceDirect online privacy policy <http://www.sciencedirect.com/science/privacy>. By using email or alert services, you agree to comply with the ScienceDirect Terms and Conditions <http://www.sciencedirect.com/science/termsandcond>. To unsubscribe to alert services, please go to the Alerts <http://www.sciencedirect.com/science/alerts> page. Copyright © 2007 ScienceDirect. All rights reserved. Any unauthorized use, reproduction, or transfer of this message or its contents, in any medium, is strictly prohibited. ScienceDirect® is a registered trademark of Elsevier B.V. Delivery Job ID: 1929:126069537:1927:108342272 -- 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/

1 0

registration with MRI
by Tim Andrews 01 Nov '07

01 Nov '07

Dear All, Recently, we have had some problems with registration using FSL. Some of the registrations, particularly with the standard brain appear to be quite poor. Jodie, Claire and Andre have done some work on this recently and found that the best combination of registrations in FSL is Initial Structural: 15 degree search, 6 DOF Main Structural: 15 degree search, 6 DOF Standard Brain: 15 degree search, 12 DOF If you have any views on this, could you let us know. We have also noticed that the brain extraction tool, which is set as default on FEAT has not always been removing the skull from the EPI images. If you have been doing FEAT analysis, I would be grateful if you could let us know whether BET has been working for you. If this hasn't been happening, it could affect your registrations. A related issue, is that although structural brain images are automatically skull stripped using BET, FLAIR images are not. However, I believe that BET may be automatically applied to FLAIR images in the near future. :-) Cheers, Tim -- 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/

1 0

seminar today
by Gary Green 01 Nov '07

01 Nov '07

"Off-line consolidation during sleep and wakefulness" Dr Penny Lewis Psychology Department, University of Liverpool Date: 16:00. Thursday 01 November 2007 Location: YNiC Open Plan Host: Gary Green Programme: York Neuroimaging Centre Seminars All welcome Refreshments will be served after the seminar Penny Lewis will be in YNiC this afternoon if individuals would like to meet her. We will be taking Penny out to dinner after the seminar. If you would like to join us for dinner please contact Gary Green. -- 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

1 0

brainstorming session and beamforming
by Gary Green 25 Oct '07

25 Oct '07

Dear Users Yesterday we had an extremely useful brainstorming session. The discussion brought to light some issues about using beamforming which have not been reported in the literature yet. As these observations might affect other users we thought it would be of interest to bring them to the attention of all users. Uzma Urooj, supervised by Andy Ellis with Michael Simpson as SLO, had identified two particular puzzling issues when using the beamforming approach to (a) localise time locked activity and (b) create virtual electrodes. (a) the first observation is that if one constructs a NAI map from a beamformer, the statistically significant blobs do not necessarily align with the largest amplitude averaged response seen with virtual electrodes. What the user has done was to perform a standard beamforming analysis of some data and localised the most significant blob. They then placed virtual electrodes at this point and around it. At each of these virtual electrode positions they calculated the average response across epochs. The largest amplitude evoked response was not at the location of the beamformer blob. This observation has also been replicated in simulation studies by Mark Hymers where he has placed dipoles at known locations in a model brain which had realistic background noise. The reason this occurs is because of the way the beamformer works. The beamformer is a set of spatial filters which are designed to measure the brain activity (the NAI) from each brain location in turn. The filters are constructed to ensure that activity only comes from one location at a time. All other locations are suppressed. This is done by computing the power within the MEG signal and ensuring that this is measured with a gain of one from a specified location and that it is zero from all other positions. This is the key point - the beamformer is specified in terms of MEG power. The power in an MEG signal can come from two forms of oscillation, those that are time locked to the stimulus and those power changes that produced by a stimulus but are not time locked in terms of the oscillatory phase (often called the stimulus induced power). Thus the blobs created by the application of the beamformer programme are in terms of total power (time locked and induced). When the average virtual electrodes were computed, these measures were only of time locked activity. The user that brought this to our attention has made an important observation, within a specific region, brain responses that are time locked maybe at a different location to induced power changes. As we do not know the relationship between fMRI haemodynamic changes and MEG oscillations (time locked vs induced), it may be that beamformer results will not always align with fMRI results either. This does not mean that the beamformer is wrong in some way. In means that we have to be very careful in how we interpret beamformer output in terms of blobs and virtual electrodes. There clearly is a need to be able to distinguish between time locked and induced responses. To this end, Will Woods has been working on a 'evoked' beamformer. implications for users of the beamformer NAI statistical maps reflect total power changes within a band and can contain both induced and time locked responses, just induced power changes or just time locked responses. In the latter case the virtual electrode averages will align with the NAI maps. In the other two cases, NAI maps may not align with VE maps. The issue for users is what form of response should be used to test a specific hypothesis. This will be down to the individual user who will have a specified model for their particular experiment in terms of how stimuli may be encoded. NAI maps are estimates of statistical changes in total power, these maps are related to the mean and variance of the power in the oscillations produced by both induced and time locked responses Averages of VEs provide estimates of the average time locked response, only. (b) the second interesting observation made by Uzma related to the construction of time series of virtual electrode activity for every epoch. Uzma has used a specific time window (say 200 milliseconds) to estimate weights for a beamformer. Uzma then used these weights to estimate the virtual electrode time series for a much longer time window beyond that of the original 200 milliseconds for every epoch. The virtual electrode output (three orthogonal components) was manipulated to create an estimate of power as a function of time. This was done by taking the squares of each VE component and summing them. This gives a measure of the power as a function of time for each epoch. Uzma then averaged these power time series, producing the average power changes as a function of time. Uzma made an observation that has not been reported before. Beyond the end of the original 200milliseconds, a large slow change in power was observed. If this was all repeated for a window that was 1000 milliseconds long, the slow change in power was now observed if the power was estimated for times greater than 1 second. This is a very important observation. The current thoughts about this are that this is a property of the beamformer. It might arise as follows. The beamformer weights are estimated from the covariance matrix of the original MEG data within the specified window (say 200 milliseconds). Covariance is related to power within a signal, that is why it is stated that a set of beamformer weights is about detecting the power from a specific location and not any other. If a window is only 200 milliseconds long, a very poor estimate will be made of power below 5Hz (1/0.2). Thus this beamformer will not be able to correctly deal with slow changes in power and estimates beyond the original window may be inaccurate. implications for users of the beamformer When using a beamformer to estimate changes in power (especially induced power) with time, observations are only reliable when made within the time contraints of the original window length that was used to construct the beamformer. The problem with this is that a beamformer works best if the window length matches the duration of the induced power change, especially if performing a statistical comparison between two conditions. If long windows are used and the induced power changes are fractional proportions of the length of the window, then statistical power will be lost. In this case it would be best to use moving windows as in the Pammer and Cornelissen paper. ---------------- I believe this demonstrates that brainstorming sessions are quite important activities. Some people might be concerned about bringing problems to the attention of other users, but as the above demonstrates, it can be invaluable as it can highlight problems that are not fully appreciated. Many thanks to the user who brought this to our attention. -- 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

1 0

Re : YNiC Seminar this week]
by Gary Green 22 Oct '07

22 Oct '07

October 25th 4pm YNiC Open Plan 1. Project presentation: Michael Simpson 2. Project presentation: Laura Lee 3. Work in progress - a look at an ongoing project All welcome. Refreshments will be available. -- 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

1 0

potentially interesting talk
by Silvia Gennari 19 Oct '07

19 Oct '07

I thought I would circulate the following talk to YNiC users as it could be potentially interesting to many users. This is talk presenting results of an fmri experiment after extensive training with different kinds of sounds. Speech-like processing of nonspeech sounds following extensive categorization training. Dr James Keidel, University of Manchester Monday, Oct 22nd, 2007, 12.30pm, C108, Dept of Psychology Silvia Silvia Gennari Department of Psychology University of York Heslington, York YO10 5DD United Kingdom

1 0

Fixation-contingent presentation of stimuli in MEG
by a.ellis＠psych.york.ac.uk 19 Oct '07

19 Oct '07

FIXATION-CONTINGENT PRESENTATION OF STIMULI IN MEG Laura Barca and I ran an MEG experiment in which participants were instructed to fixate on a central point on a screen positioned 1 metre in front of them. A stimulus (e.g. a word) was then presented very briefly to the left or right of the fixation point. The aim was to track the processing through the brain of words presented in the right visual field, projecting directly to the left (language) hemisphere, or in the left visual field, projecting first to the left (non-language) hemisphere and presumably needing to be transferred across to the left hemisphere via the corpus callosum for processing. In the absence of eye movement monitoring we had to trust our participants to fixate centrally, and to rely on the brief presentations to assert that they could not have re-fixated in the time that the stimulus was on the screen. We can also point to differences in the patterns of brain activation we observed as indicating that we were successful on most trials of the experiment in controlling presentation as we wanted to. There are, however, people out there who could end up reviewing grant applications for further work who get very animated about the need for accurate fixation control in this kind of experiment. There are also two strands of future research that may need more accurate monitoring. One is work I would like to do following up Lisa Henderson's MSc project comparing the responses of dyslexic and non-dyslexic students to words presented in the left and right visual fields. The other is a project by a PhD student of Richard Wise at Imperial College London , Zoe Woodhead (a former undergraduate of ours), who want to use the York MEG system to look at word recognition in patients with hemianopias following occipital strokes. Both dyslexic and hemianopic participants may be assumed to have greater difficulty controlling their fixation than 'normal' participants, and good fixation control would be especially helpful for those studies. It would also help with studies I would like to do in which words will be presented centrally on the assumption that certain letters fall to the left of fixation while other letters fall to the right. What would be nice to have, then, is a way of ensuring that stimuli are only displayed on the screen when a participant is fixating on, or close to, a central fixation point. We normally offset the inner edge of our stimuli by 1.5 degrees, so it would be good to define a central fixation sphere with a radius of 0.5 degrees at 1 m distant from the participant, and only to present the stimulus on a given trial when fixation is within that sphere. So: 1. Would the resolution of the system allow us to know when someone is fixating within a sphere that has a diameter of 1 degree at 1 metre distance? Is a smaller resolution possible? 2. What would be the minimum time between registering that fixation is within the defined region and a stimulus appearing on the screen? I want to avoid suggestions that participants may have moved their eyes in the interval between fixation being registered and the stimulus being presented. It might help to present the stimulus after fixation has been within the central sphere for a certain period of time in order to exclude the possibility that participants were sweeping their eyes through the sphere when presentation was triggered. 3. Richard Wise and Zoe Woodhead would be interested in a variant of this procedure where a stimulus remains on the screen for as long as fixation remains within the central region. This would allow more prolonger presentation of stimuli to, for example, patients with hemianopias whose processing of visual inputs may be relatively slow. I know that Richard and Zoe have toyed with presenting "sentences" in one or other visual field by displaying one word after another at the same position. That would be OK to do if we could know that fixation remained central throughout. 4. Finally, I gather from the meeting last night that only one eye is monitored. There is quite a lot of discussion in the literature about how often the two eyes focus on the same point, and how often there is either 'crossed' or 'uncrossed' fixation. We would need to think about this, and whether we should, for example, put a patch over the unmonitored eye. I am posting this on ynic-users because we were encouraged to do so. I am hoping for a sober response from YNiC which is realistic about what could and could not be done, any difficulties we may run into, and the time that would be required to implement a system like this (assuming that it is do-able). At the moment all I need to know is what could or could not be achieved so that I can write that in confidence into grant applications. Other people with an interest in vision and MEG (Silvia, Piers, Andy Y etc) may want to chip in so that YNiC can get a fuller understanding of what people would like to have in the way of intergrated fixation monitoring and stimulus presentation. Andy Ellis 19 Oct 2007

4 3

YNiC Seminar this week
by Gary Green 17 Oct '07

17 Oct '07

October 18th 4pm YNiC Open Plan 1. This autumn in YNiC - the programme 2. What is new and what has changed 3. Booking and the database 4. Ethics and governance 5. new tools 6. The support system explained 7. What is happening in YNiC - a look at the future 8. A discussion about users' needs and a new forum for getting users involved All welcome. Refreshments will be available. -- 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

1 0

Jump to page:

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

ynic-users