- ynic-users

This week at YNiC
by Andre Gouws 24 Jul '17

24 Jul '17

Hi all, * Please join us at YNiC this Thursday at 4pm where there will at least 2 project presentations from the Smallwood / Jefferies Labs: "Understanding the gridlike encoding of associative information" - Deniz Vatansever "Understanding the neural basis of spontaneous thought" - Charlotte Murphy "TBC" - Jonny Smallwood * * Work on the YNiC reception continues this week, and we hope to resume service as usual ASAP. We will keep you updated but, for now, please continue to use the Biocentre entrance. -- André ************************************************************************ André Gouws PhD York Neuroimaging Centre University of York The Biocentre York Science Park Heslington YO10 5NY Tel: +44 (0) 1904 435327 Fax: +44 (0) 1904 435356

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Works at YNiC
by Antony Morland 17 Jul '17

17 Jul '17

Hello All, The work at YNiC has started this morning. Today's work will create a considerable amount of noise. I'll update you on when we anticipate other disruptions through the week. Sorry for any inconvenience. Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Matlab licenses in YNiC
by Joe Lyons 14 Jul '17

14 Jul '17

Hi We're still seeing issue with the Matlab license in YNiC. We're waiting to hear from IT Services and will update when we get more information. Thanks Joe

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Project rpoposal
by Antony Morland 13 Jul '17

13 Jul '17

Hello all, Apologies for the late notice - there will be a project proposal at 1030 today, not 4pm. This is due to a clash with a meeting in Psychology. Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Closures
by Antony Morland 11 Jul '17

11 Jul '17

Dear All, We are planning some refurbishments to the YNiC reception. We are currently booked in for the start of the works 17th July. This work will mean that reception is not available and that entry to YNiC should be through the Biocentre doors. We hope to be able to honour scans booked, but please allow additional time to obtain the appropriate forms for your participants during the closure of reception as temporary arrangements will be in place that may cause delays. We also have a training course 18th July and will not be able to perform any scanning that day. Open plan will be open as usual, however. Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Project presentation postponed to next week
by Antony Morland 06 Jul '17

06 Jul '17

Dear All, Apologies, I in a previous email I indicated a presentation would be made this week, which is, in fact, going to be held next week - 13th July at 4pm. Best wishes tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Potential closures and project presentations
by Antony Morland 04 Jul '17

04 Jul '17

Dear All, We are upgrading the reception area this month. The current date penciled in is the week commencing 17th July. Open plan will be accessible from the Biocentre entrance. Further announcements about potential interruption of scanning may be forthcoming, but at the moment research scanning can continue. We have a project presentation by Becca Kitching this week. Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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mrVista - Population Receptive Field Mapping Workshop
by Marc Himmelberg 27 Jun '17

27 Jun '17

Hi All, I'd like to gather expressions of interest for those those who would be interested in attending a 'MrVista - Population Receptive Field Mapping' workshop at YNiC. For those of you not familiar with mrVista, it is a MATLAB interface for analysing functional and anatomical MRI data, based on the Vistasoft toolbox developed by Stanford University, whilst population receptive field (pRF) mapping is a form of retinotopic mapping, where we compute a model of pRFs and visual field maps within the visual cortex (Dumoulin, S. O., & Wandell, B. A. (2008). Population receptive field estimates in human visual cortex. *NeuroImage*, *39*(2), 647–660. https://www.ncbi.nlm. nih.gov/pmc/articles/PMC3073038/). The aim of the workshop is to familiarise yourself with fMRI analysis using mrVista and learn how to conduct visual field mapping using the pRF method - including data collection/running stimuli, structural processing and segmentation, pre-processing, running the model, localising visual field maps, and plotting data. The workshop will run over 3 days at YNiC open plan and each session will cover both theory and practical. All required data and software will be supplied. Dates scheduled are: *Monday 31st July* 9:30am - 5pm *Tuesday 1st August* 9:30am - 5pm *Monday 7th August* 9:30am - 5pm Please let me know if you are interested in attending or have any questions. Thanks. Best, Marc -- Marc Himmelberg PhD Student | ESR within NextGenVis ITN PS/C018, Department of Psychology University of York York, YO10 5DD UK

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project presentations
by Antony Morland 26 Jun '17

26 Jun '17

Hello All, We will have Rachel Woodall give a presentation about two upcoming projects this week (4pm Thursday 29th June). Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Large scale data sets
by Jonny Smallwood 04 Jun '17

04 Jun '17

Hello YNIC users, We are trying to gauge interest in the use of large scale data sets by users of the imaging centre. There are a growing number of open access data sets that contain data from large samples of participants with phenotypical data and a range of brain imaging measures (often resting state as well as task data). I have added links to two of these data sets that I have had experience using and publishing data from. It would be very helpful if users who thought that this kind of data would be beneficial to their ongoing work could get in contact with me. This would allow the centre to get a sense of how many people would be interested in using these types of data. Thanks, Jonny http://www.humanconnectomeproject.org/ http://fcon_1000.projects.nitrc.org/indi/enhanced/ -- Jonathan Smallwood, Reader in Psychology / Cognitive Neuroscience Room C023, Department of Psychology, University of York, England. YO10 4PH. Telephone: 01904 324651

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Updates
by Antony Morland 31 May '17

31 May '17

Hello All, As many of you will already know, our GE scanner is back in action. Thank you for your patience. Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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GE update
by Antony Morland 22 May '17

22 May '17

Sorry, All, the GE scanner is still poorly. Progress on its diagnosis is being made, however, and we hope GE will get it fixed tomorrow. Best wishes Tony

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Important: Immediate change to booking slot release
by Mark Hymers 19 May '17

19 May '17

Dear all, As many of you will be aware, for around a decade the YNiC booking system has released slots at midnight each day. How far ahead slots are released depends on the project and the nature of its funding source. We have just made an immediate change to the booking system such that slots will now be released at MIDDAY rather than midnight. This change takes effect immediately. We believe that this change should be reflected in the appearance of the web booking system as well as the internal YNiC booking tools used by staff. If anyone spots any issues with the booking system as a result of this change, please email me directly with details and I will investigate. Many thanks, Mark -- Mark Hymers, Lecturer in Neuroimaging Methods York NeuroImaging Centre and Department of Psychology University of York, UK Please note that my email address is: mark.hymers(a)ynic.york.ac.uk Responses to messages sent to other addresses may be delayed

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GE Update
by Mark Hymers 19 May '17

19 May '17

Hi all, Another update on the GE scanner. Although the GE scanner looks more like an MRI scanner again, it is still not functional. Diagnostic work carried out today means that we believe that the two parts likely to be responsible have been identified. One part arrived at YNiC this evening and the other is due to be delivered first thing on Monday morning. GE Engineers will be on site on Monday to fit the parts and, hopefully, resolve the issue. Scanning on Monday has been cancelled. Another update should be sent around Monday lunchtime. Thanks, Mark -- Mark Hymers, Lecturer in Neuroimaging Methods York NeuroImaging Centre and Department of Psychology University of York, UK Please note that my email address is: mark.hymers(a)ynic.york.ac.uk Responses to messages sent to other addresses may be delayed

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GE Scanner update
by Mark Hymers 18 May '17

18 May '17

Hi all, The attached picture shows the GE scanner just after 5pm. Unsurprisingly, this means that we will not be scanning tomorrow. We are awaiting a part (arriving later this evening) and engineers will be on-site this evening and tomorrow continuing to work on the problem. We are currently discussing the effect that this has had on MSc scanning and will write to students and supervisors once the scanner is available again to let them know what arrangements we are making to make sure we get all of the scanning done. More updates tomorrow. Thanks, Mark -- Mark Hymers, Lecturer in Neuroimaging Methods York NeuroImaging Centre and Department of Psychology University of York, UK Please note that my email address is: mark.hymers(a)ynic.york.ac.uk Responses to messages sent to other addresses may be delayed

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Scanner update
by Antony Morland 17 May '17

17 May '17

Apologies, All, another day, another update. The GE engineers replaced a number of parts today, but have still to fix the problem. They return tomorrow to do more work to remedy our problem. I hope to be able to relay more positive news soon. Best wishes Toby

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GE update
by Antony Morland 16 May '17

16 May '17

Hello All, Sorry, still no good news to report. Tomorrow, GE will attend again to replace parts and see if that resolves the issues we are encountering. Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Update
by Antony Morland 16 May '17

16 May '17

Apologies, All, the GE engineer was unable to fully resolve the scanner issues yesterday. GE will be at ynic again today to investigate and hopefully resolve the issue. Updates to follow. Best wishes Tony

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Updates
by Antony Morland 15 May '17

15 May '17

Hello All, As some of you may already know, we have had some issues with the GE scanner. GE attended Friday and today. They have made some progress. We are running tests this afternoon to check that data collection can resume from tomorrow. We are resuming testing the MEG scanner in collaboration with York Instruments. More news on this should emerge through June. Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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YNiC talk this afternoon
by Alex Wade 11 May '17

11 May '17

Dear YNiC users Our talk today is from a visiting speaker: Marko Nardini from Durham will be talking about "Perceptual inference in the developing brain". Marko has keen interest in perceptual development and his work will be of interest both to our imaging community and to vision and developmental scientists. https://www.dur.ac.uk/psychology/staff/?id=11704 4pm at YNiC open plan. Best Alex

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Closure 12th May
by Antony Morland 05 May '17

05 May '17

Dear All, We are having some work done in the MRI suite 12th May, which means the centre will be closed for scanning. Open Plan will be Open, however. YNiC staff will be attending a training event, so there will be no reception or staff cover 12th May. Sorry for the short notice - the contractor only gave us this lead period for the work. Thanks Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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This week at YNiC
by Antony Morland 02 May '17

02 May '17

Hello All, This week we will be hosting two project presentations; Lucilla Lanzoni (from Beth Jefferies's Lab) will talk about 'Effect of cues on semantic retrieval' Xiuyi Wang (from Jonny Smallwood's Lab) will talk about 'Graded constraints in semantic cognition: how do we retrieve knowledge in a flexible way' As usual the seminar will be on Thursday at 4pm (4th May) and refreshments will be provided after the presentations. Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK. For support issues email: support(a)ynic.york.ac.uk

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MRI projection screen upgrade
by Andre Gouws 28 Apr '17

28 Apr '17

We have now upgraded the projection screen material in MRI and this will be the default screen in the scanner moving forward. Many of the existing projects that use "lower-level" calibration routines or are dependent on the use of the polarizer HAVE ALREADY BEEN USING THIS "NEW" SCREEN MATERIAL. Note that the "old" screens are still available for use by existing projects that have already acquired data - just remember that these screens will no longer be pre-loaded into the scanner by default and you will need to load them yourselves. As usual, if you have any queries, please drop me a line. -- André ************************************************************************ André Gouws York Neuroimaging Centre University of York The Biocentre York Science Park Heslington YO10 5NY Tel: +44 (0) 1904 435327 Fax: +44 (0) 1904 435356

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Updates
by Antony Morland 25 Apr '17

25 Apr '17

Dear All, Some upcoming events and news from YNiC. The current week marks the start of the MSc project scanning period. This week pilot scans will be performed to check all groups are ready to acquire data starting the week commencing 1st May. The summer terms seminar programme is flexible and will accommodate visiting speakers and project presentations. Two project presentations will take place 4th May and Marko Nardini (Durham) will give the seminar 11th May. Details on both to follow nearer the time. If you would like to present some of your work at YNiC over the coming weeks, please let me or Jonny Smallwood know. We had a successful visit from the Deputy Vice Chancellor, Saul Tendler, on Thursday 20th April. Thanks to all who attended and to those who presented their work. Saul left with an excellent impression of the centre. Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK. For queries regarding support at YNiC email: support(a)ynic.york.ac.uk

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Essential IT Maintenance - Thursday 13th April
by Joe Lyons 13 Apr '17

13 Apr '17

Dear users, Please note that during our soft closure next week, the centre will be closed for the afternoon of Thursday 13th April so we can carry out essential maintenance on our IT systems. Computers in open plan will be available up to 11am. Thanks Joe Lyons Unix Systems Administrator York Neuroimaging Centre

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