- ynic-users

News this week
by Antony Morland 18 Oct '17

18 Oct '17

Hello All, This weeks seminar is 'How to apply to use the centre'. This will be relevant to all newbies, but will also give an overview of updates that are in the pipeline that will affect all applicants. In other news we are continuing with our programme of training for operators of the Siemens and GE scanners. Best wishes Tony Tip of the week: At the command line you can type ls > list.txt it will generate a text file of the files and directories in the current directory (as long as you have write permissions in the current directory) ls *is the 'list' command* > *allows the output of the ls command to be redirected to a file* mylist.txt * is the file name you supply to capture the output of the ls command* Why is this useful? The generation of a file that lists directories or files can be useful when you are writing scripts to perform analysis on multiple directories or files. Note that this help with ls can be obtained by typing man ls -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Updates and news
by Antony Morland 12 Oct '17

12 Oct '17

Hello All, Quite a few things this week: 1) IMPORTANT: Our MRI screening safety screening forms have been updated. The updates are explained in our revised local rules. 2) A reminder: Our training documentation (including the local rules referred to above) is held at the following URL https://www.ynic.york.ac.uk/ docs/forms. A login in required to access the URL. 3) Last weeks seminar, which was postponed, will go ahead this week and will follow the project presentation by Shogo Kajimura entitled '*Decoding contents of mind wandering'*. The seminar series details can be found here: https://www.ynic.york.ac.uk/events/thursday-sessions#preview 4) We are currently training 14 operators at YNiC. Best wishes Tony *Tip of the week* You can control the transparency of your overlays in *fslview *by using the blue transparency slider located a the bottom right of the window - see attached -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Update - GE MRI system repair
by Andre Gouws 09 Oct '17

09 Oct '17

HI all, The GE engineer has attended and diagnosed the fault with the system. A replacement part is required for the Oxygen monitor to work correctly. This part is on express order and we hope to have it installed tomorrow, although it is unclear at what point in the day this will be. We are hoping that normal scanning service will resume by Wednesday (11th), but please keep alert for further updates which we will send once we have more information. Thanks, -- 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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GE MRI system fault
by Andre Gouws 08 Oct '17

08 Oct '17

Hi all, I am afraid to report that a sensor fault has developed on the GE system over the weekend. This sensor monitors the safe oxygen level in the MRI environment, and thus the scanner cannot be used until the fault is fixed. GE have said the will attend on Monday AM - we hope to have the scanner up and running as soon as possible. Sorry for those affected by the scanner downtime. 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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Posters
by David Coggan 06 Oct '17

06 Oct '17

Hello all, We are still looking for posters to put up around YNiC open plan. If you would like to contribute one, please get in touch or drop it off at YNiC. Best wishes, Dave

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Postponed: Today's YNiC seminar.
by Andre Gouws 05 Oct '17

05 Oct '17

Hi all, Due to some unforeseen circumstances we have to postpone today's seminar - We will reschedule and update you in next week's update bulletin. Best wishes, -- 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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Next YNIC Science Meeting
by Jonny Smallwood 03 Oct '17

03 Oct '17

Hello all, We are holding the next meeting of the YNIC Science Committee next Monday. Please send any items you would like me to raise by Thursday so I can add them to the agenda. Thanks Jonny -- 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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Disruption
by Antony Morland 03 Oct '17

03 Oct '17

Hello All, We have a Heating and Cooling contractor in attendance today. Alarms may sound. Apologies if they disrupt your work. If an alarm does and stops within 30s there is no need to act. Please be aware that staff may need to ask you to leave at short notice. Thanks Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Weekly update
by Antony Morland 02 Oct '17

02 Oct '17

Hello All, Two things this week 1) The will be a seminar held in the Chemistry Department this week that may interest users: Dr Luisa Ciobanu: Functional MRI at ultra-high magnetic fields Wednesday 4th October 13.00-14.00 In room Chemistry/B101 Abstract Despite the fact that BOLD-fMRI is routinely used to map brain activity and connectivity in preclinical and clinical settings its exact relation with the underlying microscopic changes, either vascular or neuronal, is still not fully elucidated. The development of high magnetic fields promise substantial improvements in the contrast to noise ratio and the spatial resolution with which functional MRI maps are acquired possibly allowing the comparison with other, microscopic, techniques. In the first part of my talk I will review the advantages, but also the challenges, imposed by imaging at ultra-high magnetic fields. Following this, I will present recent results demonstrating that BOLD fMRI faithfully reports microvascular hyperemia, and that the detection of the smallest neuronal activation is limited only by its sensitivity. Beside improved BOLD acquisitions, high magnetic fields allow the development of other alternative ways for studying neuronal activation. In the last part of my presentation, I will describe a novel metabolic imaging approach, based on Chemical Exchange Saturation Transfer (CEST), for assessing the changes induced by neuronal stimulation in rat brains at 17.2T. Specifically, I will present images acquired under glucose-sensitizing conditions showing a significant negative contrast that highlights the same brain regions as those activated in conventional BOLD maps. 2) We are to give 'Tips of the week', hopefully, as the name suggests on a weekly basis. This will largely give advice on IT tricks and work-arounds for commonly occurring analysis tasks. Here's this week's: Scenario: You've submitted a load of jobs to the cluster which you find out will be of no use to you and you want to bring them to a halt. Solution typing: qdel -u <username> into a terminal will stop all cluster jobs submitted by that user, e.g. qdel -u ddc506 Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Important information: YNiC schedule for 2017-2018
by Andre Gouws 27 Sep '17

27 Sep '17

Dear All, We have put together a provisional schedule for the YNiC seminars for the academic year. The YNiC led seminars will occur on even weeks during the autumn and spring terms. On the odd weeks we will have seminars on an ad-hoc basis and will largely focus on project presentations or presentations arranged by the YNiC Science Committee. We have also scheduled training opportunities for scanner operators. We would really like new PhD students and postdocs who will want to operate the scanners to take these opportunities as they dovetail nicely into our workload and MSc teaching and training. With that in mind, please note that the first element of training will be held Thursday 28th September. The detailed schedule is attached. Best wishes 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 25 Sep '17

25 Sep '17

Hello All, This week we will be having induction sessions for our new intake of PhD and MSc students between 9am and 1pm on Thursday. An introduction to the IT systems will take place between 9am and 1pm on Friday. It will, therefore, be busier than usual in open plan, so please take that into account when planning your work at YNiC. We are hoping to freshen up the posters at YNiC over the next week or so. Could you bring us any spare, but relatively recent, posters that you would like to have on display at YNiC? Many thanks Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Updates
by Antony Morland 19 Sep '17

19 Sep '17

Hello All, Thanks to those of you who have reported issues arising after the IT upgrade. We have managed to deal with the majority of them. A reminder for those of you who haven't given your analysis or stimuli a spin for a while to give them a go well in advance of needing them, so we can help with any issues that arise. Next week is the start of term and therefore ynic will be busy with inductions and teaching. If you are here, please join us in welcoming our new recruits. Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Updates
by Antony Morland 11 Sep '17

11 Sep '17

Dear All, A few updates: 1) Staff changes: Ross Devlin has now left YNiC. He will be having a period of leave before taking up his new role at York Instruments. He has given YNiC many years of valuable and helpful service for which we are all very thankful. 2) A brief reminder that there will be no operator cover for any scanner on Wednesday this week. We are undertaking some training that will look at the documentation and processes we use to train operators for the Siemens scanner. 3) Project booking limits: We have a standard limit of 7 hours per week per project. We are aware however that such limits can constrain throughput on projects. We can offer some flexibility on how much time can be booked if we are given a period of time to plan. So, please get in touch should your requirements for booking be greater than 7 hours per 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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Updates
by Antony Morland 05 Sep '17

05 Sep '17

Hello All, 1) Please test stimulus code and analysis streams you rely on and feedback any errors (including the error report) through the IT system. Note that it is not a safe assumption that all code will run perfectly after an IT upgrade. 2) We will be closed from 1330 on Thursday. 3) Next Wednesday 13th September, we will be closed from midday to test out training materials for the Siemens scanner. Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Information for YNIC Science Commitee
by Jonny Smallwood 31 Aug '17

31 Aug '17

Hello everyone, Just a reminder that if anybody has any suggestions for discussion topics for the YNIC Science Committee, they should contact me to let me know. Please feel free to contact me either via email or in person to discuss any issues that you would like raised at the next meeting. Best wishes, Jonny -- 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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YNiC updates
by Andre Gouws 30 Aug '17

30 Aug '17

Hi all * IT upgrade and centre maintenance: We have completed the IT upgrade and centre maintenance works. We have done our best to ensure a smooth transition for you across the IT infrastructure - please do let us know if you experience any issues or "odd behaviour" on the IT systems and we will attempt to fix them as soon as possible. For a summary of software changes, please see the list at the end of this email. * Reception reorganisation: The works on our new reception area are now complete and bring us in line with the best practices outlined by the CQC (Care Quality Commission) - essentially we have made the reception more professional, more welcoming and crucially more secure. If you need help from the reception staff, or are picking up / dropping off forms, please do so by speaking to reception staff at the glass service hatch - access to the reception office is restricted Andre'. Summary of software changes at YNiC in Summer 2017 --------------------------------------- FSL: * FSL 5.0 has been updated to 5.0.9 * FSL 4.1 is no longer available * FSLView is only available as a backwards compatibility option and will be removed next summer. FSLEyes is the replacement for FSLView. Python: * Python 2 and 3 are now both supported at YNiC as far as is possible * Ensure that you are using the correct version of Python for the script you are running. * iPython installs for Python 2 and 3 are both now available * Spyder installs for Python 2 and 3 are both now available * numpy -> 1.12 * scipy -> 0.18 * matplotlib -> 2.0.0 * mvpa2 -> 2.6.0 * most other modules have been updated to their latest stable revisions * psychopy remains at version 1.84.1 and is Python 2 only MATLAB: * Version R2017a (9.2) is now available and is the default version. * Version 8.5 and 9.0 remain available. 9.0 will be removed when R2018a is released. SPM: * SPM 8 has been updated to the latest revision r6313 * SPM 12 has been updated to the latest revision r6906 * SPM 2 and 5 have been updated to their final releases Freesurfer: * Both Freesurfer 5.3 and 6.0 are now available. * See the documentation pages (TODO) on how to use each version R: * The version of R installed is now 3.3.3 * rstudio has been updated to 1.0.153 * We have added the latest revisions of all of the `tidyverse` packages, removing the need to install these per-user Generic software: * Connectome Workbench 1.2.3 is now installed by default * Libreoffice has been upgraded to 5.2.7 * Mathematica 11 is now available alongside Mathematica 10 * Maple 2016 replaces Maple 18 * SPSS 23 replaces SPSS 20 * The Iceweasel (Firefox) and Icedove (Thunderbird) aliases are no longer available - you may need to update any desktop shortcuts. Stimulus PC-specific: * Presentation (NBS) stimulus delivery package has been removed Known issues: * There are known problems with hdfview - these are due to an upstream bug, we are preparing a workaround for this -- 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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Fwd: Park Central - Now open
by Claire Fox 25 Aug '17

25 Aug '17

Email not displaying correctly? View it in your browser <http://mailchi.mp/yorksciencepark/park-central-now-open?e=6b12080e27>. Heading 1 Heading 1 Park Central has re-opened with some amazing new menu items. Come along and try their freshly baked homemade cakes, delicious pastries and hearty breakfast sandwiches! Park Central will be open Monday to Friday 08.00 to 15.00 hours. (Closed Monday 28 August!) Quesadillas, paninis, baguettes, ready made sandwiches, fresh soup and many more tantalising goodies await! If you would like to pre-order *breakfast sandwiches*, Park Central will take orders - please call *01904 325120*. Unfortunately, no other food orders can be accepted. We hope you enjoy the new offerings in Park Central - please take the time to complete the feedback forms or send us an email at enquiries(a)yorksciencepark.co.uk <javascript:_e(%7B%7D,'cvml','enquiries(a)yorksciencepark.co.uk');> - we gladly welcome your feedback! Please see the full menu <http://yorksciencepark.us5.list-manage.com/track/click?u=be60566cfd55403b74…> on our website! For Residents, we are delighted to offer promotions and below is the first offer. *29 August to 8 September - 8am to 11am* *Breakfast Buttie promotion* Bacon or sausage sandwich with 12oz hot beverage for £3.00 (saving up to £1.75) [image: YSPL Facebook] <http://yorksciencepark.us5.list-manage1.com/track/click?u=be60566cfd55403b7…> [image: YSPL Twitter] <http://yorksciencepark.us5.list-manage2.com/track/click?u=be60566cfd55403b7…> *Copyright © 2017 York Science Park Ltd, All rights reserved.* Innovation Centre, Innovation Way, Heslington, York, YO10 5DG F: 01904 435135 Company No. 2939132 | Registered address: Heslington Hall, Heslington, York, YO10 5DD VAT No. 647 2055 41 unsubscribe from this list <http://yorksciencepark.us5.list-manage1.com/unsubscribe?u=be60566cfd55403b7…> | update subscription preferences <http://yorksciencepark.us5.list-manage.com/profile?u=be60566cfd55403b7452a6…> -- Claire Fox Centre Administrator York Neuroimaging Centre The Bio Centre York Science Park Heslington York YO10 5NY Tel: +44 (0)1904 435329 Fax: +44 (0)1904 435356 <%2B44%20%280%291904%20325805> Email: claire.fox(a)york.ac.uk Web: https://www.ynic.york.ac.uk/ Available Monday, Tuesday, Thursday and Friday. Email disclaimer: http://www.york.ac.uk/docs/disclaimer/email.htm

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This week at YNiC
by Andre Gouws 21 Aug '17

21 Aug '17

Hi all, As of lunchtime today, the centre will be closed to allow us to perform our annual IT systems upgrades. We have done our best to minimise disruptions but following these upgrades please do keep a close eye on your data processing and acquisition streams and let us know if there are any issues. Please note that we also use this opportunity to perform a number of other "housekeeping" jobs that include moving furniture and some minor building & decorating work - thus please consider the centre as *closed*. We will let you all know once everything is up and running again. -- 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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Stimulus delivery - PRESENTATION will be removed from stim PCs
by Andre Gouws 17 Aug '17

17 Aug '17

As there has been practically no use of the Presentation stimulus delivery software package at YNiC over the past 12 months, we are not intending to renew the five licenses we currently purchase annually. As such, Presentation will no longer be available for use on the stimulus delivery PCs at YNiC after the centre IT upgrade next week. Please contact me if you have any queries. Thanks, -- 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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This week at YNiC
by Andre Gouws 14 Aug '17

14 Aug '17

Hi all, No presentations this week, but the centre will be busy with the MSc CN project hand in deadline looming. Please note: * CENTRE CLOSURE Tuesday 21st - Friday 24th August. - A reminder that we are closed for part of next week for system upgrades. * RETURN OF SCREENING/CONSENT FORMS: With the reception works complete, please return all signed screening / general consent forms to the gray postbox next to the reception office door if the office is closed. * CENTRE ACCESS AND ALARMS: Keyholders should be aware that the main reception alarm will now be set when the centre is closed. If you are the first to enter, you will need to deactivate the alarm before opening the main shutter to the reception area. This alarm is in the cupboard immediately next to the key that opens the shutter. The alarm code is the same for all areas. -- If you have any queries please see a member of the team. -- 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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This week at YNiC
by Andre Gouws 07 Aug '17

07 Aug '17

Hi, No project presentations this week, so just a couple of reminders: * Reception services are back to normal at YNiC - please use the normal YNiC entrance again. * The servicing of the GE scanner was successful so we should be back up to "full speed" now. * ** DATES FOR YOUR DIARY ** - a reminder that the YNiC IT systems upgrade is scheduled for the week commencing Monday the 21st of August. There will be no scanning or access to computing facilities during that week. We will let you know if anything changes. -- 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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Entering YNiC - reception refurbishment completed
by Andre Gouws 04 Aug '17

04 Aug '17

Hi all, Thank you for your patience and cooperation during the remodeling of the YNiC reception area. A few minor cosmetic issues aside, the work is now completed and we can start to use the reception area as just that! Please enter and leave YNiC via this area from now on rather than the Biocentre entrance, and instruct anyone taking part in your studies to do so too. Best wishes, -- 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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Project presentation today at YNiC
by Andre Gouws 03 Aug '17

03 Aug '17

A reminder that Richard Vernon will be giving a project presentation at 4pm today: "Curvature and angular-position shape manipulations". -- 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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This week at YNiC
by Andre Gouws 31 Jul '17

31 Jul '17

Hi all, * Please join us at YNiC this Thursday at 4pm where there will be a project presentation by Richard Vernon entitled "Curvature and angular-position shape manipulations". * Thank you for you patience as the improvement works on the new reception area continue - we are awaiting the installation of some glass panels and then normal service will resume. Until further notice, please do continue to use the Biocentre entrance. * GE Scanner service: Some components of the image reconstruction hardware on the GE scanner are showing a fault and will need to be replaced on Thursday afternoon - the scanner is still in use and should perform normally for most users - just be aware that there may be a slightly longer delay between scans as the images are processed. Best wishes, -- 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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Brief Closure
by Antony Morland 25 Jul '17

25 Jul '17

Hi All, Pleas note the centre will be closed for all research scanning and analysis from 5pm, Monday 21st August until the end of the week. This is to upgrade our IT provision and perform annual maintenance. Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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