ynic-users July 2007

ynic-users@ynic.york.ac.uk

8 participants
16 discussions

by Sam Johnson

Hello all, This is just a heads up to let people know that there is a NAGTY group visiting the centre next Monday, the 30th. This means that Open Plan will be very busy for periods, and people may have limited access to machines. It might be a good reading day :) Thanks, Sam -- Sam Johnson Science Manager, York NeuroImaging Centre University of York http://www.ynic.york.ac.uk

17 years, 12 months

Thursday evening seminar tonight

by Michael Simpson

Dear all, Just a reminder of the Thursday evening seminar that Piers Cornelissen will be giving tonight. He'll be discussing some interesting MEG data from one of the undergraduate projects. Hope to see you all there, usual time, usual place (4pm, YNiC open plan). 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

17 years, 12 months

Thursday 2/8/07

by a.morland＠psychology.york.ac.uk

Dear All, At the Thursday evening session on 2/8 Sam Johnson and Tony Morland will provide an introduction to the new applications procedures that will be used at YNiC. This will cover: 1) Project Proposal forms 2) Project Presentations 3) Research Science and Ethics forms We have also been working on documentation concerning new arrangements for support of users. This will be introduced at a subsequent Thursday session. Tony

17 years, 12 months

Thursday Evening

by Sam Johnson

Hello all, Just a reminder that after a couple of quiet weeks this Thursday evening Piers Cornelissen will be talking. He'll be discussing some interesting MEG data from one of the undergraduate projects. Hope to see you all there, usual time, usual place (4pm, YNiC open plan). Thanks, Sam

17 years, 12 months

MEG status

by a.morland＠psychology.york.ac.uk

Dear All, The 4-D engineer has repaired the dewar positioning system. We are hopeful that the system will be up and running as normal from Monday onwards. Some final checks and testing will be performed before then. Tony

18 years

DSO arrangements

by a.morland＠psychology.york.ac.uk

Dear All, As Gary mentioned at the end of a recent Thursday evening meeting, the DSO will now occupy a desk in the open plan area so that he/she is more accessible to users. The desk is in the corner of the room and will have the name of the DSO on the desk. If the DSO is not at the desk and is working elsewhere in the centre, details of where he/she can be found will be on the desk. Please note that the DSO can be approached 10am-12pm and 2pm-4pm. Tony

18 years

Fwd: BrainVoyager QX advanced course July 19 & 20 2007

by a.morland＠psychology.york.ac.uk

>Sorry for the late notice: >This may be of interest to AVA members; we are running an advanced training >course on Brain Voyager (see schedule attached) on July 19th and 20th at the >Birmingham University Imaging Centre. Basic knowledge of the software is >necessary, as the course will be covering only advanced topics. > >Please contact Zoe Kourtzi directly if you are interested. > >Zoe Kourtzi, PhD >Chair of Brain Imaging >Behavioural and Brain Sciences >School of Psychology >University of Birmingham >Edgbaston, Birmingham >B15 2TT UK > >tel: 121 414 8509 >fax: 121 414 4897 >e-mail: z.kourtzi(a)bham.ac.uk >web: http://psg275.bham.ac.uk/cnil/ > > >BrainVoyager QX advanced course > >Birmingham, July 19 & 20, 2007 > >Program > >Day 1 Analysis and visualization of structural MRI data > > >09:00 10:00 Overview - Tools and methods: Image enhancement, Region >Growing, Edge detection, Image matching and averaging >10:00 - 10:45 Demonstration: Contrast, intensity, inhomogeneity correction, >filtering. Automatic/ semi-automatic segmentation of structural data >10:45 - 11:00 Demonstration: Coregistration/ averaging of structural data >11:00 - 11:15 - Tea break - >11:15 - 12:15 Exercise: Data preprocessing, automatic/ semi-automatic >segmentation >12:15 - 13:00 Cortex-based inter-subject alignment > >13:00 14:00 - Lunch break - > >14:00 15:00 Exercise: A) Cortex-based alignment B) Transfer of Broadman >areas >15:00 15:30 Cortical thickness analysis >15:30 16:30 Exercise: Cortical thickness analysis >16:30 - 16:45 - Tea break - >16:45 17:15 DTI data analysis and visualization >17:15 18:15 Exercise: DTI data analysis and visualization > > > >BrainVoyager QX advanced course > >Birmingham, July 19 & 20, 2007 > >Program > >Day 2 Analysis of functional MRI data > > >09:00 09:30 Overview: Tools and methods, concepts, VTC/MTC, ROI/POI >09:30 11:00 Multi-subjects/ multi-study statistics in BVQX: Fixed and >random effects group analysis (GLM, RFX ANCOVA) >11:00 11:15 - Tea break - >11:15 12:15 Volume-based/ cortex-based single-subject and group ICA >12:15 12:45 Granger causality mapping >12:45 13:00 Exercise: Coregistration - fMRI data with structural 3d data > patient data with deformed brains > >13:00 14:00 - Lunch break - > >14:00 15:00 Exercise: A) Volume-based and cortex-based ICAB) RFX ANCOVA, >C) GLM analysis on aligned cortices >15:00 15:30 Mapping: Localizer and follow up >data analysis (VOI, MSK, POI) >15:30 16:30 Demonstration: Mapping visual areas field sign maps as >preparation for VOI/ POI data analysis >16:30 16:45 - Tea break - >16:45 17:15 Future Tools 1: Combined fMRI/MRI and EEG analysis >17:15 17:45 Future Tools 2: Simulation of brain processes >17:45 18:00 Discussion Dr Peter Thompson, Executive Editor, Perception National Teaching Fellow British Association - Royal Society Millennium Fellow Department of Psychology, University of York, YO10 5DD, UK P.Thompson(a)psych.york.ac.uk tel: +44 1904 433150 fax +44 1904 433181 Creator of the solar system: www.solar.york.ac.uk Try www.viperlib.com your one-stop visual perception image site

18 years

MRI and MEG

by a.morland＠psychology.york.ac.uk

Dear All, The MEG scanner has a problem with the dewar, as has been previously reported. Until further notice, no scanning. The radiographer is off sick this week and currently Andre is assisting with as much MRI scanning as he can. It will be necessary however to cancel or shorten some scanning sessions. Please do not book any more MRI sessions this week. Tony

18 years

IMPORTANT - VALIDATING BEAMFORMING OUTPUTS

by Andre Gouws

We have always stressed the importance of checking a few of the manual steps in the beamforming processing stream where possible. These include the outputs generated by the co-registration routines which co-register your MEG headshape to your structural MRI for each subject, and simultaneously calculate the local sphere sources for each channel in the MEG sensor array. This information, calculated early in the processing tree is obviously vital for all post-processing steps. You should be routinely checking that the co-registration itself is accurate and that the spheres generated make are 'sensible' for each sensor. If you are not doing this you are STRONGLY ENCOURAGED to do so. Whilst there have been very few instances of the outputs failing (only 2 in the last year!) they have had significant effects on results for both individuals and groups. These errors are easily resolved if detected. Please see the following page for more information: https://www.ynic.york.ac.uk/doc/BeamformerUsage and see "/STEP 3 - Visually check that the co-registration is reasonable for each subject and associated MEG run/" (Thanks to those who brought this to our attention!) -- ************************************************************************ Andre Gouws User Support Manager York Neuroimaging Centre The Biocentre York Science Park Heslington YO10 5DG Tel: +44 (0) 1904 435328 Fax: +44 (0) 1904 435356

18 years

Thursday Evening

by Sam Johnson

Hello all, Due to the rearranging of sessions there's a bit of a hole in the schedule and the next Thursday evening will be the 26th, when Piers will talk. Unless of course we have any volunteers, or (without making any promises) requests for more training biased sessions. Thanks, Sam

18 years

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ynic-users July 2007