- ynic-users

Updates in response to issues raise at YNiC Science Committee
by Antony Morland 18 Jan '19

18 Jan '19

Hello All, Apologies for the length of this email, but issues were raised at the last Science Committee meeting that I thought would be good to share with you along with our responses to them. Thanks to those who raised the issues - they help us improve our service. Best wishes Tony YNiC issues list: 1. After the update the remote server is considerably slower, sometimes it does not connect at all. Running even simple scripts takes an inordinate amount of time. In addition, some of the software (e.g., LibreOffice) crashes often. We have deployed a new Remote Desktop system that is based on x2go broker. It has more memory and allows users to reconnect to a quieter server if they find other users are using up resources. We will be looking to add more capacity to this service this year. However, our general advice is to come to the centre and use the facilities here, which are more resilient and better specified, if you require a more efficient throughput on analysis. To be clear, we cannot offer a remote access system that works to the same performance as the systems on site. One fact that may focus the mind is a desktop at YNiC has much more memory than allocated to a remote connection. Also note that if analysis is undertaken on the remote desktop server rather than submitting jobs to the cluster, as recommended, the server(s) will allocate much of the limited resources to the analysis and that will interfere with all other users of (and connections to) the remote desktop. 1. It is also unclear why Microsoft packages have been removed, some of them (e.g., Excel) have functions superior to the Linux version. The Microsoft packages have not been removed from the machines at YNiC. We are however experiencing issues with opening files. We will work on this and update users when we have debugged the package. Libre office is working fine and can be used to open Microsoft office files and save changes in Microsoft formats. The updates to LibreOffice during the summer 2018 upgrade also fixed many compatibility issues with Microsoft Office documents. The remote desktop has been updated to have Microsoft Office package available. However, related to the point above, we had largely specified the remote access to allow investigators to run analysis jobs on the cluster when they were unable to be at YNiC. This remains our priority. So, although we have installed Office on the remote server, it should be noted that not all analysis and office software can be guaranteed to work remotely because of the configurations of these releases. 1. Scanning at 9am results in difficulties as there is not always a receptionist (to print the relevant forms) or level 3 (to sign off any issues on the information sheet). We are sorry about there sometimes being staff shortages. We were facing a challenging period as we were waiting new staff arrivals. We have only one level 3 operator. We suggest that all participants are talked through the screening form 24 hours in advance of the scan session, so the need for a countersignature from a level 3 can be identified. It should also be noted that this would be essential for any scanning that occurs outside normal hours, when a level 3 would not be available to countersign forms. We are also working on the safety form so level 3 signatures are not required for the most commonly arise advisory conditionals. This is an ongoing project and we will update operators once it is complete. This approach may require additional training for operators. 1. The air con is far too cold, making working in open plan unpleasant. We monitor the temperature in open plan (and the rest of the centre) because of historic issues of temperature fluctuations arising from failure of the York Science Park’s Building Management System. The temperature in Open Plan currently varies between 21.5 and 23 degrees. The Building Management System, which sets the temperatures, is controlled by York Science Park, not YNiC. The temperature is currently set to 22 degrees. We are happy to contact York Science Park if users alert us to an unsatisfactory temperature. 1. Making sure that operators are available for slots that are booked as operator covered (even if they come from a lab with trained operators because sometimes these people are not on hand). I think there may be a misunderstanding. If there is an YNiC operator covered slot and you need an operator, or just want them on hand, please ensure that the booking requests a YNiC operator. You are fully entitled to make that selection when you book and it helps us. If you are a qualified operator and indicate that you will operate, the default behaviour of the booking system is to mark up the time as not needing a YNiC operator. 1. Training needs to be more regular to afford more projects to begin in a timely fashion. We struggle to meet demand for training, particularly as it has grown over the last three years. The training also has multiple levels. We attempt to run level 0 training frequently and it can be done in small groups. Level 1 training is more challenging insofar as it cannot always be done in groups and we need a large number of scan hours to ‘offer’ the trainee to become safe and effective at operating the scanner before we sign them off. We set up training for the Autumn term and when possible we try to meet requests for training at other times too, but this can be a challenge. We also try to use both the MSci and MSc reserved slots as training opportunities, which means that in addition to the Autumn term, we also have the potential to run efficient training in the Summer term. That said, I think we found last year that there was little demand at that time of year. We hope that our new appointees will help alleviate the pressure on our other staff to provide training. We also anticipate that more operator covered slots will be made available in 2019 as we train up our new appointees. 1. YNiC wiki contains outdated information and is difficult to navigate. It would be very useful if specific issues can be submitted to RT so we can make appropriate updates. 1. Poor communication i.e. informing users of status of the scanner, or the status of unresolved RT tickets. We endeavour to keep people informed about the status of the scanners. This is done via messages to ynic-users(a)ynic.york.ac.uk. The loss of service is unpredictable and re-establishing service can sometimes depend on many factors outside our control. I have checked the messages sent to the email list and found that we have, in general, kept users of the centre up-to-date with the scanner outages. We will continue to send messages concerning scanner status to ynic-users(a)ynic.york.ac.uk and will strive to improve comms in general. RT remains the best way to communicate with us. Yes, it does seem impersonal and there can be delays, but it is the only way that we can manage and prioritise requests. It is also a system similar to those used the Department of Psychology and some University services. When we were short staffed, so some things took longer than usual to resolve. Please be patient and please don’t ask staff to do things in person to try to accelerate resolution of your issue – I know it is human nature to try, but it simply delays the resolution of everyone else’s issues. We now review tickets at our weekly staff meeting to ensure outstanding tickets are resolved. 1. Variation in the times of operator covered activity would help recruitment because it would allow participants with a broader range of availability to be tested. We have considered this before and when we have a full staff complement we will re-engage with the issue. At present however we need to arrange staff meetings and undertake other tasks (e.g. Training, Helium fills, Quality Assurance, Scanner Cleaning) to ensure the centre runs safely and effectively. The best way to manage these tasks is to do them at fixed times during the week. Indeed diary conflicts often mean that only a limited number of slots are available to arrange meetings and activities even when we have a fixed pattern of operator slots. At the moment varying the operator cover pattern will make arranging our activities impossible. We can frequently accommodate special requests, however, and have done so particularly when participants come from special populations that are a challenge to recruit and their availability may therefore limit recruitment opportunities. Moreover, if your requirement is known well in advance we can be more flexible. I suggest those who have specific needs get in touch with us. 1. Cleanliness around the coffee machine and in the open plan more generally. The coffee area is cleaned by a member of YNiC staff at least once a day. We usually wipe the area down in the period that we are waiting for the kettle to boil or the coffee machine to fill our cups. There are wet wipes (in a white, blue-lidded tub) that can be used if you would also like to wipe the area down if it appears unclean. The contract cleaners do not clean this area, so it is up to us (those who use the area) to clean it. During the closure periods (in the summer 2018 and over Christmas) we cleaned the open plan area carefully, including the computer screens and all desks. The open plan area is cleaned by contract cleaning staff daily. We will encourage those who use the Open Plan Areas to keep it clean. We have now cleaned keyboards and hope that enhances the user experience of the centre. We are in the process of arranging a carpet clean this term. -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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YNiC Project Presentation 4pm
by Lauren Welbourne 17 Jan '19

17 Jan '19

Hi all Today MiaoMiao Yu will present her project proposal. The talk will be at 4pm in YNiC open plan. Hope to see you all there, Lauren -- Lauren Welbourne, PhD Senior Research Technician York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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YNIC Science Issues
by Jonny Smallwood 15 Jan '19

15 Jan '19

Hello everyone, We are holding the next meeting of the YNIC Science Committee on Monday the 21st at 2.30. If you have an issues that you would like me to raise for the committee please let me know. Jonny -- Jonathan Smallwood, Professor in Psychology / Cognitive Neuroscience Room E008, Department of Psychology, University of York, England. YO10 4PH. Telephone: 01904 324651

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Teaching at YNiC
by Mark Hymers 10 Jan '19

10 Jan '19

Dear all, As usual, there will be teaching in the YNiC Open plan area during the spring term. During these times, the area will be closed to anybody not involved in the teaching. Times for the Spring term are: Week 2: Tuesday 15th January: 1200-1600 Friday 18th January: 1200-1600 Week 3: Friday 25th January: 1200-1600 Week 4: Tuesday 29th January: 1200-1600 Friday 1st February: 1200-1600 Week 5: Friday 8th February 1200-1600 Week 7: Tuesday 19th February: 1200-1600 Friday 22nd February 1200-1600 Week 8: Friday 1st March: 1200-1600 Week 9: Tuesday 5th March: 1200-1600 Friday 8th March: 1200-1600 Week 10: [NB: Different to all other weeks] *Wednesday* 13th March: 0900-1300 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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YNiC Closures
by Lauren Welbourne 14 Dec '18

14 Dec '18

Hi All Please be aware of the following closure dates over the Christmas period: 1) On Monday 17th and Tuesday 18th December there will be a soft close - the centre will be open for use but there will be no support or operator cover provided 2) From Wednesday 19th December to Tuesday 1st January the centre will be closed. There will be no access to the centre and no support will be provided over this period. Please note that there may be periods where remote access is unavailable, however we will aim to notify all users prior to any downtime occurring. 3) YNiC will be open as usual from Wednesday 2nd January. Kind regards Lauren -- Lauren Welbourne, PhD Senior Research Technician York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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Congratulations to Dr Hao-ting Wang
by Jonny Smallwood 28 Nov '18

28 Nov '18

Who has successfully defended her PhD thesis. Come to E block on the ground floor to congratulate her. -- Jonathan Smallwood, Professor in Psychology / Cognitive Neuroscience Room E008, Department of Psychology, University of York, England. YO10 4PH. Telephone: 01904 324651

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Talk: Rod Braga Dec 17th 4pm C003
by Jonny Smallwood 27 Nov '18

27 Nov '18

Hello everyone, Rod Braga (http://www.rodbraga.com/neuroscience) will be visiting York in December and has agreed to give a talk on his ongoing work looking in great detail at the organisation of large scale networks at the level of an individual. I though this might be of general interest to people in the Department and at YNIC so I booked C003. Please do attend if you are interested. Afterwards we will head into York for dinner and drinks. Let me know if you would like to be involved in any of the post talk activities. -- Jonathan Smallwood, Professor in Psychology / Cognitive Neuroscience Room E008, Department of Psychology, University of York, England. YO10 4PH. Telephone: 01904 324651

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YNiC Project presentation today @ 4pm
by Andre Gouws 15 Nov '18

15 Nov '18

Hello All, Just a reminder that we will be hosting a project presentation by Amelia Gully (Department of Electronic Engineering) today at 4pm. These will be project presentations that offer everyone the chance to learn about approaches investigators using the centre employ to do their research. All welcome and refreshments will be provided. -- André ************************************************************************ André Gouws PhD Manager of Imaging Services 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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New member of staff
by Antony Morland 08 Nov '18

08 Nov '18

Dear All, I am delighted to report that Lauren Welbourne has joined us at YNiC and will be working to support research at the centre. Lauren did her PhD at York so may be known to many of you. Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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IT issues
by Antony Morland 08 Nov '18

08 Nov '18

Hello All, We are having some issues with our file system. This will limit the way in which you can access IT on site and remotely. More to follow. Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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At YNiC this week.. (including important info for MRI operators)
by Andre Gouws 31 Oct '18

31 Oct '18

There are a few things to bring to your attention this week: *Final metal screening (with the aid of a metal detector)* There will be a training session in place of the seminar tomorrow @ 4pm (Thursday the 1st of Nov). All MRI operators are invited to attend to learn our new policy on final subject metal screening and to train in the use of the metal detectors we will use to aid this final screening. Please note: * Operators already trained with the metal detector do not need to attend. * We will be temporarily suspending all operators on the database and will only reinstate operator status once this training has been completed - a register will be taken tomorrow so that is your chance to keep your operator status live. *Activity at YNiC* The MScI (m-sci) scanning has begun this week and places a significant load on YNiC operators. Further to a previous email, additional operator-covered slots have been added to the booking system to facilitate ongoing research scanning. Please note that during this period we use every opportunity to train new operators and this may mean us training an operator during your scanning session. Thanks in advance for your cooperation. Best wishes, -- André ************************************************************************ André Gouws PhD Manager of Imaging Services 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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YNiC Remote Desktop
by Joe Lyons 26 Oct '18

26 Oct '18

Hello We have a new remote desktop cluster available for existing users of the remote desktop service at YNiC. This new setup has a group of desktops and will connect you to the whichever is the least used at that time. Details on how to connect are available on the wiki, https://www.ynic.york.ac.uk/docs/ITPages/NewRemoteDesktop. If you would like to use this, please email support(a)ynic.york.ac.uk. This service is only available to Psychology staff, PhD students, Postdoctoral Researchers and PIs. Thanks Joe Joe Lyons, UNIX Systems Administrator York Neuroimaging Centre (YNiC), University of York

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MRI Operator cover on scanners for the next 5 weeks
by Andre Gouws 25 Oct '18

25 Oct '18

Hello All, We are about to start a period of scanning for MSci projects. These slots (16 hours per week) are covered by YNiC operators. In addition to the 7.5 hours we need to staff our clinical scanning, we are adding more operator covered slots (18 hours) to allow PIs to undertake their research. Given the amount of operator covered slots we are using them as level 1 training opportunities as much as possible. During this period, YNiC staff will have less time to help with other issues, so please keep that in mind. Many thanks Tony, Mark and André -- André ************************************************************************ André Gouws PhD Manager of Imaging Services 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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Care Quality Commission Inspection
by Antony Morland 08 Oct '18

08 Oct '18

Hello All, Our clinical service will be inspected on a Monday occurring in the remainder of this month or all of next month. The inspectors come without any notice. The outcome of the inspection is a rating, which, depending on the the level we achieve, will allow is continue with the service effectively. We want to be rated as highly as possible. We anticipate that the inspectors will attend between 10am and 6pm. If you are at the centre during these hours, please be aware that many of the staff here may be busy cooperating with the inspectors. It would also be very much appreciated if during your time here you could use the reception area minimally and as always recognise the needs of the patients, who will be waiting for their scan in reception. Thank you Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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TMS
by Antony Morland 05 Oct '18

05 Oct '18

Hi All, Just to let you know the TMS gear will be unavailable 10th October. Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Reboot of remote.ynic.york.ac.uk
by Joe Lyons 04 Oct '18

04 Oct '18

Hello We're seeing some NFS issues on the remote desktop server and so will be rebooting the server at 4pm today. Please save any work and log off before this time. Thanks Joe -- Joe Lyons, UNIX Systems Administrator York Neuroimaging Centre (YNiC), University of York

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Ethics applications
by Gareth Gaskell 01 Oct '18

01 Oct '18

Dear all, just a quick reminder to anyone planning to put in a new YNiC ethics application that the forms at the full application stage have changed, including the application form, the consent form and the participant information sheet. This means that it's much better to start afresh from the templates provided here <https://www.ynic.york.ac.uk/forms> than to rework an older outdated application. For users who are new to the system, the procedure for applying to run a study at YNiC is given here <https://www.ynic.york.ac.uk/information/application>. Many thanks, Gareth YNiC REC Chair -- Gareth Gaskell Department of Psychology University of York Heslington, York YO10 5DD UK Office: Psychology, E209 Phone: +44-1904-323187 Email: gareth.gaskell(a)york.ac.uk Home page: https://www.york.ac.uk/psychology/staff/academicstaff/mgg5/ Research group: https://www.york.ac.uk/psychology/research/facilities/slam/

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YNIC Science Committee
by Jonny Smallwood 01 Oct '18

01 Oct '18

Hello The next meeting of the YSC is on the 8th of October. Please could any users that have issues they would like raised at this meeting, send them to me by the end of play on Friday? 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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YNiC Project presentation Thursday 27th @ 4pm.
by Andre Gouws 26 Sep '18

26 Sep '18

Hi all, We will be hosting a project presentation by Bardur Joensen (Berens, Horner) at YNiC tomorrow (Thurs 27th) at 4pm: “ Tracking the retrieval of episodic events over time ”. Please join us for the presentation and discussion to be followed by light refreshments. Best wishes (and sorry for the late notice), -- André ************************************************************************ André Gouws PhD Manager of Imaging Services 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 scanner update
by Antony Morland 25 Sep '18

25 Sep '18

Hello All, I am happy to report that the GE scanner is now up and running. Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Teaching at YNiC
by Mark Hymers 24 Sep '18

24 Sep '18

Dear all, As usual, there will be teaching in the YNiC Open plan area during the autumn and spring terms. During these times, the area will be closed to anybody not involved in the teaching. Times for the Autumn term are: Week 1: Thursday 27th September 0900-1300 Friday 28th September 0900-1300 Week 2: Tuesday 2nd October: 1200-1400 Week 4: Tuesday 16th October: 1200-1400 Week 7: Tuesday 6th November: 1200-1400 Week 9: Tuesday 20th November: 1200-1400 Times for the Spring term will be sent out during the Christmas vacation period. 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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Upgrades and changes
by Antony Morland 24 Sep '18

24 Sep '18

Hello All, We are now open after our summer closure for upgrades and maintenance. As always, please let us know if there is anything that no longer functions as it did and we will try to rectify the situation. Here is a summary of what has been updated/upgraded during the closure: *Software*: FSLeyes upgraded to most recent version (0.26.1) Psychopy upgraded to 1.90.3 including changes to video handling (addition of moviepy and sounddevice) Matlab 9.4 added; no Matlab versions removed; 9.0 will be removed in January. Libreoffice upgraded to 6.1 Crossover Office upgraded to 17.5 Mendeley upgraded to latest release SPM 12 upgraded to latest patch (r7219) Windows is no longer supported on the Stimulus PCs *Hardware changes:*New cabling of offices Networking improvements Telephony updated New chiller installed for GE system - this should be completed by tomorrow *Estate:* The Chemistry areas have been reconfigured and rationalized Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Email addresses
by Antony Morland 24 Sep '18

24 Sep '18

Hello All, We have received (indirectly) some emails asking for help. They were posted to rec-submission(a)ynic.york.ac This is the address to send ethics applications, not a email queue that we monitor for general issues. To avoid undue delays please send requests for help etc to support(a)ynic.york.ac.uk Many thanks Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Fwd: REMINDER - SEMINAR INFO: JEOL Postdoc Competition Winners' Seminar & refreshments, TOMORROW, 13:00, C/A/101
by Antony Morland 20 Sep '18

20 Sep '18

The second talk described below may be of interest *JEOL Postdoc Competition Winners’ Seminar * *Thursday 20th September * *13.00-15.00* *C/A101* *13.00 Dr. Aggie Lawer* *"Synthesis of functionalised peptides/macrocycles and medium-size **rings via stereoselective fluorination and SuRE/NICE chemistry"* Insertion of fluorine into organic molecules is well-known to affect the molecules’ electronic distribution and conformation in ways that can be beneficial in drug development. However, the effects of fluorination have not been widely investigated in the context of peptides, which limits the development of peptide-based drugs. In the first part of the talk, I will discuss how stereoselective fluorination was used to control the conformations of peptides and enhance the potency of a peptide-based enzyme inhibitor. While peptides/macrocycles and medium-size rings have recently gained noteworthy interest in the area of medicinal chemistry, their synthesis is mostly limited to the traditional end-to-end macrocyclisations which suffer from unfavourable thermodynamic factors, and oftentimes require the use of high dilution conditions. In the second part of my talk, I’ll describe how Successive Ring Expansion (SuRE) and N-acyl Iminium ion mediated Cyclisation/Expansion (NICE) reactions developed in Unsworth group could be employed to overcome these limitations, providing an efficient, scalable and practical route to make diverse macrocycles and medium-size rings. *13.45 Dr. Peter Rayner * *"Tunable Hyperpolarisation by Synthetic Design"* NMR and MRI are two of the most popular techniques to study molecules and materials. However, both of these approaches are insensitive and hyperpolarization methods to increase signal size are needed in order to access new applications. This talk will describe how rational synthetic design of both the contrast agents and N-heterocyclic carbene catalysts utilized in the Signal Amplification by Reversible Exchange process, have led to signals that are up to 120,000 times larger than those achieved on a typical hospital scanner and can be observed many minutes after their creation. These improvements have allowed the observation of hyperpolarized molecules by in vivo MRI techniques. *The seminar will be followed at 14.30 by refreshments* -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Remote desktop
by Antony Morland 17 Sep '18

17 Sep '18

Hello All, The Remote Desktop is now up and running. We are still closed for maintenance and upgrades so while we hope the service will run uninterrupted, there may be unplanned outages. Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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