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2810 discussions

Bas Science link
by Michael Simpson 19 Nov '07

19 Nov '07

Dear all, Brain Imaging has reached the pages of Ben Goldacre's Guardian column, Bad Science. http://www.badscience.net/2007/11/this-is-your-brain-this-is-your-brain-on-… Thought some of you may be interested, 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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Re: Event-Related optimum schedule
by Tim Andrews 15 Nov '07

15 Nov '07

Hi Laura, Rapid event-related fMRI has many advantages for cognitive neuroscience research. However, the main problem with this technique is that the signal is very small compared to a block design. One way to increase the signal-to-noise ratio is to increase the number of trials. This typically means using a short ISI (otherwise your subjects could be in the scanner for a long time!). It is also good to vary the ISI to avoid expectation effects (i.e the subject predicting when the next event is likely to occur). However, the problem with a short ISI is that the response to one stimulus will likely overlap with the response to the next. This is not a problem if the BOLD response is linear (i.e. the response to two successive stimuli is the same as adding the response to two independent stimuli with an appropriate temporal offset). However, a number of studies have found that there are significant non-linearities when the ISI is less than ~5sec (eg Dale and Buckner, 1997; Huetell and McCarthy, 2000). So, varying ISI can have positive and negative effects on the BOLD signal. I haven't used the programs that Claire and Silvia are using, but I assume they are trying to find an optimum balance between these effects. Users - please feel free to correct or comment! Tim Laura Lee wrote: > Hi MRI-support, > > I'm struggling along trying to work out how to create a 'stochastic' > event-related design for fMRI. Claire Moody has passed on a program > that searches for the optimum stimulus schedule (she & Silvia used it > for their last project). I've read over all the bumpf but am still > quite confused by all the new concepts. I think I know roughly what I > want but then there are some parameters I am unsure about and don't > really understand the implications of the settings. I'd be really > grateful if you could give me a hand. > > This is the programme I downloaded... > http://surfer.nmr.mgh.harvard.edu/optseq > And there's a pretty comprehensive help page here... > http://surfer.nmr.mgh.harvard.edu/optseq/optseq2.help.txt > > Thanks, Laura > > > > > -- 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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Interesting (short) paper
by Michael Simpson 15 Nov '07

15 Nov '07

Dear all, there is another interesting paper in the 'Articles of interest' section of: https://www.ynic.york.ac.uk/doc/Miscellaneous This one is on combined MRI / MEG, which may or may not be of interest you. If you have any papers to add to this section, forward them to me and I'll make them globally available. 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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Seminars today
by Gary Green 15 Nov '07

15 Nov '07

Elena Solesio has been visiting YNiC from the imaging centre in Madrid. Today, 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. All are welcome to come along. ----------- At 4pm today, there is a YNiC update seminar 1. update on MEG 2. recap of MEG facilities at YNiC 3. what is new and what has changed 4. sensor space and source space 5. beamforming update 6. minimum norm and dipoles 7. Users' requests and what we can do better All welcome Refreshments will be served after the seminar -- 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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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

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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

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[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/

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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/

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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

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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

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