- ynic-users

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

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MEG and MRI
by Gary Green 17 Oct '07

17 Oct '07

You will probably be pleased to hear that MEG is now fully operational again. We have also taken time to get the system recalibrated, eye trackers installed and a complete overhaul of the mechanics of the bed. The noise level is lower as the source of the small electrical pulse artefacts has been identified and removed. All MEG channels are working. The original problem was due to a faulty interface between the fibre optics taking data out of the shielded room into the data acquisition rack. The board has been replaced. Bookings can now be taken for MEG. You may also be pleased to hear that MRI has had a routine maintenance and all is well. happy scanning! -- 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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Fwd: Visual Dysfunction and Cognition in Childhood
by Andy Ellis 08 Oct '07

08 Oct '07

> > >Please bring this conference to the attention of colleagues who may >be interested- > >BPS Division of Neuropsychology > > >Visual Dysfunction and Cognition in Childhood > >This day conference will increase knowledge on psychological, >neurological and neurobiological systems involved in vision and >visual defects of brain and peripheral optic pathways. it will also >increase knowledge on brain:cognition relationships and cognitive >patterns associated with visual defects, including spatial >cognition, and severe visual impairment. The conference introduces >the latest theory and practice in these areas, including clinical >assessment and interpretation of cognitive development and disorders >in children with severe visual impairment. > >Date: 30 October 2007 > > >Who should attend? > >This event is open to clinical or educational practitioners or >researchers in child neuropsychology, clinical child psychology, >paediatric, neurology, occupational therapists and related >neuroscience disciplines. Relevant to practitioners and researchers. > > >Programme > >09:30 Registration & Refreshments > >10:00 Two visual systems: agnosia, optic ataxia & neglect > >Professor David Milner (Professor of Cognitive Neuroscience, >University of Durham): Co-author of Sight Unseen (winner of the BPS >Book Award) > >11:15 Refreshments > >11:30 Neurobiological models of visual-spatial deficits in childhood > >Professor Janette Atkinson (Director of Visual Development Unit: >University College London/ Oxford University): Author of The >Developing Visual Brain > >12:45 Lunch > >14:00 Visual impairment and cognition: neurodevelopmental issues > >Dr Naomi Dale (Head of Psychology (Neurodisability), Great Ormond >Street Hospital/ UCL Institute of Child Health): Co-lead in >developing the governmental Early Support Developmental Journal for >parents and children with VI > >14:45 Refreshments > >15:00 Visual impairment and cognition: clinical assessment and >interpretation > >Dr Naomi Dale (Head of Psychology (Neurodisability), Great Ormond >Street Hospital/ UCL Institute of Child Health): Co-lead in >developing the governmental Early Support Developmental Journal for >parents and children with VI > >15:45 Concluding Remarks > > >Speakers > >Professor David Milner (University of Durham): Co-author of Sight >Unseen (winner of the BPS Book Award) > >Professor Janette Atkinson (University College London/ Oxford >University): Author of The Developing Visual Brain > >Dr Naomi Dale (Great Ormond Street Hospital/ UCL Institute of Child >Health): Co-lead in developing the governmental Early Support >Developmental Journal for parents and children with VI. >Location Directions >UCL Institute of Child Health, London > >For further details click here- >http://www.ich.ucl.ac.uk/education/short_courses/courses/2S18 > >--------------------------------------------- >COGNEURO archives and subscription manager can be found at >http://www.jiscmail.ac.uk/lists/COGNEURO.HTML >--------------------------------------------- >List owner's email address: COGNEURO-request(a)jiscmail.ac.uk -- Professor Andy Ellis Department of Psychology University of York York YO10 5DD England Tel. +44 (0)1904 433140 http://www.york.ac.uk/depts/psych/www/people/biogs/awe1.html

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Draft programme for Thursdays at YNiC
by Gary Green 21 Sep '07

21 Sep '07

Attached is the 'draft' programme for YNiC Thursday evening seminars for the autumn and early winter. The current plan is that after Christmas the seminars would mainly consist of invited speakers, internal speakers and journal club. The third term would be devoted to people giving talks about work that has been or is about to be published from YNiC projects. ALL comments are welcome. Your ideas are absolutely essential to running a Centre that will make imaging research possible and fun for all. Please send your comments to me, Sam Johnson (science.manager(a)ynic.york.ac.uk) or Tony Morland (a.morland(a)psych.york.ac.uk) Gary -- 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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[Re : Project presentations : Today
by Gary Green 20 Sep '07

20 Sep '07

Today we have two new project presentations (Thursday the 20th at 4pm in YNiC Open Plan) Project presentations will be made by Professor P. O'Higgins. HYMS. Scalp and head reconstruction from MRI. Dr. T. Jellema, University of Hull, Department of Psychology. Imaging in Autism. We will also announce what is being discussed for YNiC for the autumn term. Do come along and discuss training requirements, seminars and any other issues you would like to see scheduled for a Thursday afternoon. 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

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Thursday Evening Sessions this autumn
by Gary Green 18 Sep '07

18 Sep '07

We are currently planning the Thursday evening sessions and other training sessions for next term. If you have any thoughts or ideas we would be keen to hear your views. The main sessions will start on the 18th of October. This week though we have two new project presentations (Thursday the 20th at 4pm in YNiC Open Plan) Project presentations will be made by Professor P. O'Higgins. HYMS. Scalp and head reconstruction from MRI. Dr. T. Jellema, University of Hull, Department of Psychology. Imaging in Autism. We will also announce what is being discussed for YNiC for the autumn term. Do come along and discuss training requirements, seminars and any other issues you would like to see scheduled for a Thursday afternoon. We will circulate the draft timetable and ask for comments by email as well. 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

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Update on MEG
by Gary Green 17 Sep '07

17 Sep '07

I am sorry to say that MEG is still unavailable. 4D are working on the problem and believe that they have determined the cause. We expect an engineer to visit this week and ti make adjustments to the main power supplies to the system. As soon as MEG is available I will let you know. MRI is working fine Gary -- 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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MEG unavailable
by Gary Green 13 Sep '07

13 Sep '07

I am sorry to have to report that MEG is currently unavailable. An electronics board that is the interface between the scanner and the main computer rack has failed. 4D have been informed and are trying to get a board to us as fast as possible. Unfortunately this may take more than a week as the new board will need substantial testing before it can be installed. I will keep you informed as to when MEG will be available again. I know this will cause some inconvenience and I apologise for the problems that this will undoubtedly bring to some projects. -- 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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Stimulus Delivery at YNiC - Presentation licenses
by Andre Gouws 28 Aug '07

28 Aug '07

The Presentation licenses at YNiC have now been renewed for another year. If any users experience problems with the stimulus delivery PCs (especially if there are prompts for license files) please contact the DSO and / or email it-support(a)ynic.york.ac.uk Thanks -- ************************************************************************ 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

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Thursday Seminars
by Sam Johnson 09 Aug '07

09 Aug '07

Hello all, Due to the inevitable summer lull, and the long awaited arrival of some sunny weather, the Thursday evening sessions are being put on hold till the beginning of September. So those of you who are around can make the most of the balmy summer's evenings and we'll recommence in a month or so by which time normal weather service will no doubt be resumed, the winter evenings will be drawing in and a YNiC seminar will be a welcome respite from the rain and snow. Thanks, Sam

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Interesting MRI
by Michael Simpson 01 Aug '07

01 Aug '07

Sorry, the link should be: https://www.ynic.york.ac.uk/doc/Miscellaneous apologies. 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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Interesting MRI
by Michael Simpson 01 Aug '07

01 Aug '07

Dear all, The .pdf named WhiteCollarBrain, located here: https://www.ynic.york.ac.uk/docwiki/Miscellaneous may be of interest to you. Download it and have a look. It received a 'That's amazing!' from Prof. Morland when he saw it on my screen earlier! 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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Thursday evening seminar 2nd August.
by Michael Simpson 01 Aug '07

01 Aug '07

Dear all, just a reminder that at this weeks Thursday evening seminar, Sam and Tony will be presenting the new streamlined Science and Ethics applications procedure. It will be beneficial to attend this if you are interested in carrying out any studies at YNiC. Also, for the oenologists in YNiC, you'll be pleased to know that this weeks refreshments have already been procured from the York Beer and Wine shop. Usual time, usual place (4pm, YNiC open plan). 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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NAGTY at YNiC
by Sam Johnson 27 Jul '07

27 Jul '07

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

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Thursday evening seminar tonight
by Michael Simpson 26 Jul '07

26 Jul '07

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

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Thursday 2/8/07
by a.morland＠psychology.york.ac.uk 24 Jul '07

24 Jul '07

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

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Thursday Evening
by Sam Johnson 24 Jul '07

24 Jul '07

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

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MEG status
by a.morland＠psychology.york.ac.uk 20 Jul '07

20 Jul '07

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

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DSO arrangements
by a.morland＠psychology.york.ac.uk 18 Jul '07

18 Jul '07

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

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Fwd: BrainVoyager QX advanced course July 19 & 20 2007
by a.morland＠psychology.york.ac.uk 17 Jul '07

17 Jul '07

>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

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MRI and MEG
by a.morland＠psychology.york.ac.uk 17 Jul '07

17 Jul '07

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

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IMPORTANT - VALIDATING BEAMFORMING OUTPUTS
by Andre Gouws 13 Jul '07

13 Jul '07

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

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Thursday Evening
by Sam Johnson 09 Jul '07

09 Jul '07

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

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re: use of fridge, kitchen and toilets
by Gary Green 05 Jul '07

05 Jul '07

Dear users and staff Just a gentle reminder. Please, please do not use the fridge in ynic reception for food. I have just had to do archeology on someone's lunch. It is not very good for public relations when people try and get some milk but are faced with fungal blooms. Also, please can everyone use the kitchen in the link corridor between the biocentre and the innovation centre rather than the one near biocentre reception. This is because the reception kitchen is for the use of the biocentre team rather than tenants. The other kitchen does have a fridge for your lunches, etc. Last, and sorry to keep on, please can you use the toilets by the biocentre reception rather than the toilet in the mri corridor. The toilet in the mri corridor is really for patients and participants rather than users. The problem is that the mri toilet is not keeping up with demand! thanks Gary ps Good news. Work starts very soon on the new cafeteria at the Biocentre. Details are on the notice board in the Open Plan office. It should be available in the autumn. -- 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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re: Today YNiC Thursday evening seminar. 5th July, 4pm.]
by Gary Green 05 Jul '07

05 Jul '07

Dear all, just a reminder that tonight's seminar features Gary and Tim reviving their 'good-cop bad-cop' style interrogation of a journal article and the associated correspondence. Continuing with the face processing theme, they will be looking at the following paper relating to the N170 response. Article http://www.nature.com/neuro/journal/v10/n4/full/nn1864.html And then they will discuss the following correspondence and replies. Correspondence http://www.nature.com/neuro/journal/v10/n7/full/nn0707-801.html Reply http://www.nature.com/neuro/journal/v10/n7/full/nn0707-802.html Supplementary Figures http://www.nature.com/neuro/journal/v10/n7/suppinfo/nn0707-801_S1.html Please read the above in advance if you get the chance. Usual time 4pm, usual place, YNiC Open Plan. Refreshments will be provided afterwards.

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