- ynic-users

Door fobs plea
by Jacqueline Mayhew 21 Sep '23

21 Sep '23

Hi all If you have a YNiC door fob that you no longer require, we would appreciate them being returned so that we can reuse them. They can either be returned to YNiC directly or you could return them to Psychology reception and they can forward them to us by internal mail. Best wishes Jackie Jackie Mayhew York Diagnostic Imaging The BioCentre York Science Park Heslington York YO10 5NY

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Stimuli scripts after YNiC systems upgrade
by Richard Aveyard 21 Sep '23

21 Sep '23

Hi All, I am writing to remind everyone that, following our recent operating system upgrade,* it is important to check that your stimuli scripts are running as intended before resuming scanning*. There are testing PCs available in YNiC for this purpose, and in many cases we can help to resolve issues you might have difficulties with. *Psychopy users* Our testing has highlighted that *some psychopy scripts will be susceptible to inaccurate timing* issues with the new psychopy version (2023.2.0). We now strongly recommend that when initialising your visual window you set waitBlanking=False, or that you ensure your script runs at 120 Hz, and the monitor is adjusted accordingly using the Applications>>Settings>>Display menu. In addition, the event.getkeys() function is deprecated, an example update to fix this can be found here: https://wiki.pages.ynic.york.ac.uk/IT/summer_2023_upgrade.html#psychopy Please remember that it is your responsibility to thoroughly test your stimuli scripts and ensure that everything is working as intended. Cheers, Rich -- Dr Richard Aveyard Senior Technical Specialist York NeuroImaging Centre University of York, UK

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This Week at YNiC
by Jennifer Ashton 20 Sep '23

20 Sep '23

Hello, Please find details about Open Plan availability and the next inductions and training sessions. *Open Plan Availability* MSc inductions will be taking place at YNiC this *Friday (22nd of September) 13:00 - 15:00*. Due to the number of students attending, Open Plan will not be available to users during this time. *YNiC User Inductions* If you are aware of any new students/staff that will require access to YNiC and/or an IT account, they must attend a YNiC user induction. Our next induction will be on *Friday the 13th of October, at 13:00*. Please ask them to contact support(a)ynic.york.ac.uk to sign up. *Level 0 operator training*The next L0 training session will be held on *Friday the 20th of October, 13:00-15:00.* Please note that users requesting Level 0 training should be a PhD, RA/Postdoc, or staff, and should already have a project proposal submitted to YNiC. Please email support(a)ynic.york.ac.uk if you have any questions or wish to book on to this session. Please note that sessions are limited to 4 trainees, which will be allocated on a first-come first-served basis. *YNiC Seminar* If you would like to give a talk at our YNiC seminar, please get in touch. There are no specific requirements; presentations can include previously collected data, new data, pilot data and/or study plans and ideas. This is a great way to get feedback in a relaxed and friendly environment, please message support(a)ynic.york.ac.uk. Many thanks, Jennifer -- Jennifer Ashton, PhD Senior Research Technician York Neuroimaging Centre Working days: Monday, Tuesday and Wednesday

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Important information for everyone using YNIC
by Fiona McNab 15 Sep '23

15 Sep '23

Dear All, As you know, most of the imaging data we collect at YNIC is potentially biometric. As well as making sure we have appropriate consent from participants, we have to abide by certain legislative requirements relating to collecting, storing and sharing personal data. We've put in place some procedures to make things easier. What you need to know is summarised below and there's a diagram attached (it contains the same information but with boxes and arrows!) Any questions, please ask. Please also be aware that we have a new page for YNIC forms <https://www.york.ac.uk/psychology/research/york-neuroimaging-centre/forms/>, where you will find new versions of the participant information sheet and study-specific consent form (we're now on version 9 for both). Best wishes, Fiona and Andre *Collecting data at YNIC and keeping it at YNIC* - Before submitting your ethics application, you need to check whether your study needs a separate *Data Protection Impact Assessment (DPIA)*, or whether it is covered by DPIA_183 v2 <https://vcs.ynic.york.ac.uk/ynic-public/forms/-/raw/master/YNICDPIA183.pdf> (found on the new YNIC forms webpage <https://www.york.ac.uk/psychology/research/york-neuroimaging-centre/forms/>). If it is not covered by DPIA_183 v2, there's a DPIA screening tool here <https://www.york.ac.uk/records-management/dp/dataprivacyimpactassessments/> . - If it is covered by DPIA_183 v2 <https://vcs.ynic.york.ac.uk/ynic-public/forms/-/raw/master/YNICDPIA183.pdf>, make sure you follow the procedures outlined in that document. - Make sure everyone with access to the data has signed and submitted the *Appropriate Data Usage Declaration* <https://vcs.ynic.york.ac.uk/ynic-public/forms/-/raw/master/AppropriateDataU…> . *Bringing into YNIC data that were collected elsewhere* - You will need to complete and submit your own DPIA, but we have had one of these approved already, so contact Andre and he will provide you with a template. - If there are any agreements to sign, you will need to get HOD approval before signing. *Transferring data collected at YNIC to external collaborators* - You will need to complete and submit your own DPIA, but we have had one of these approved already, so contact Andre and he will provide you with a template. - You will also need an external collaborator agreement. We have had one approved already. Andre can provide a template and let you know the procedure for obtaining approval from the HOD and the contracts office. - Make sure everyone with access to the data has signed and submitted the *Appropriate Data Usage Declaration* <https://vcs.ynic.york.ac.uk/ynic-public/forms/-/raw/master/AppropriateDataU…> . *Transferring data collected at YNIC to former staff or students* - You will need to complete and submit your own DPIA, but we have had one of these approved already, so contact Andre and he will provide you with a template. (It's the same template as used for sharing data with external collaborators). - You will also need a data sharing agreement. This is not the same as the one used for external collaborators. We'll have a template soon, which Andre will be able to provide. The procedure for obtaining approval from the HOD and the contracts office will be the same. - Make sure everyone with access to the data has signed and submitted the *Appropriate Data Usage Declaration* <https://vcs.ynic.york.ac.uk/ynic-public/forms/-/raw/master/AppropriateDataU…> . *Making data collected at YNIC publicly available* (many thanks to Angela for this) - Make sure that this is covered by DPIA_183 v2 <https://vcs.ynic.york.ac.uk/ynic-public/forms/-/raw/master/YNICDPIA183.pdf> and you abide by the procedures outlined in that document. This includes making sure you use version 9 of the information sheet <https://www.york.ac.uk/psychology/research/york-neuroimaging-centre/forms/>and version 9 of the consent form <https://www.york.ac.uk/psychology/research/york-neuroimaging-centre/forms/>. There is a guidance document here <https://vcs.ynic.york.ac.uk/ynic-public/forms/-/raw/master/Open_Data_Sharin…> . - If it is not covered by DPIA_183 v2, you will need to complete and submit your own DPIA <https://www.york.ac.uk/records-management/dp/dataprivacyimpactassessments/> .

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This Week at YNiC
by Jennifer Ashton 13 Sep '23

13 Sep '23

Hello, Please find details about Open Plan availability, the next inductions and training sessions and an upcoming workshop. *Open Plan Availability* MSc inductions will be taking place at YNiC on *Friday the 22nd of September, 13:00 - 15:00*. Due to the number of students attending, Open Plan will not be available to users during this time. *YNiC User Inductions* If you are aware of any new students/staff that will require access to YNiC and/or an IT account, they must attend a YNiC user induction. Our next induction will be on *Thursday the 21st of September, at 10:00*. Please ask them to contact support(a)ynic.york.ac.uk to sign up. *Level 0 operator training*The next L0 training session will be held on *Tuesday the 19th of September, 13:00-15:00.* Please note that users requesting Level 0 training should be a PhD, RA/Postdoc, or staff, and should already have a project proposal submitted to YNiC. Please email support(a)ynic.york.ac.uk if you have any questions or wish to book on to this session. Please note that sessions are limited to 4 trainees, which will be allocated on a first-come first-served basis. *YNiC Seminar* If you would like to give a talk at our YNiC seminar, please get in touch. There are no specific requirements; presentations can include previously collected data, new data, pilot data and/or study plans and ideas. This is a great way to get feedback in a relaxed and friendly environment, please message support(a)ynic.york.ac.uk. *Upcoming Workshops* The first *Environmental Impacts of Computing in Health & Life Sciences Research workshop <https://www.eicworkshop.info/> *will be taking place on November 7th in London, and online. This will be a great opportunity to learn about the carbon footprint of high-performance computing, in neuroimaging research and beyond. Find more information on the workshop website <https://www.eicworkshop.info/>, and register for attendance here <https://www.tickettailor.com/events/universityofsussex/986909>. Many thanks, Jennifer -- Jennifer Ashton, PhD Senior Research Technician York Neuroimaging Centre Working days: Monday, Tuesday and Wednesday

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YNiC Cluster: now available
by Joe Lyons 13 Sep '23

13 Sep '23

Good Morning The cluster is now back up and online. The upgrade has now been completed. There are a few small changes to some software packages so please check the upgrade notes wiki page if you have any queries. https://wiki.pages.ynic.york.ac.uk/IT/summer_2023_upgrade.html Any other issues not covered in the wiki page, please email support(a)ynic.york.ac.uk. Thanks Joe -- Joe Lyons, UNIX Systems Administrator York Neuroimaging Centre (YNiC), University of York

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Update: Remote Desktops are now up
by Joe Lyons 11 Sep '23

11 Sep '23

The remote desktops are now stable. We're still waiting on a few jobs running on the cluster before it's available for use. Thanks Joe -- Joe Lyons, UNIX Systems Administrator York Neuroimaging Centre (YNiC), University of York

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Update: YNiC partially open after systems maintenance
by Joe Lyons 11 Sep '23

11 Sep '23

Good Morning. We're still having some issues from the upgrade last week. The desktops in Openplan are up and running. The cluster is currently down as we're debugging an issue with the new OS. The remote desktops are also down as we're seeing problems with some of the nodes. Thanks Joe -- Joe Lyons, UNIX Systems Administrator York Neuroimaging Centre (YNiC), University of York

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Reminder: YNiC Closed for systems maintenance
by Joe Lyons 05 Sep '23

05 Sep '23

YNiC is closed for the week while we perform some essential systems maintenance. All remote desktops and cluster services will be down. We'll update you once services are back up and running. Thanks Joe -- Joe Lyons, UNIX Systems Administrator York Neuroimaging Centre (YNiC), University of York

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Test your stimuli on new PC in YNiC
by Rebecca Lowndes 30 Aug '23

30 Aug '23

Hi all Just reminding you all that there is a new stim PC with new software available in OpenPlan to test scripts/stimuli. All the desktops will move over to this software when we are closed next week Thanks Becky -- Rebecca Lowndes Research Technician York Neuroimaging Centre

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YNiC Desktop Upgrades
by Joe Lyons 23 Aug '23

23 Aug '23

Hello As mentioned in the "This Week at YNiC" email, we'll be doing our annual software upgrades on the YNiC desktops w/c 4th September. The centre will be closed while we undertake the upgrades. A wiki page has been setup with details of the changes. https://wiki.pages.ynic.york.ac.uk/IT/summer_2023_upgrade.html A desktop with the new software is available in OpenPlan to test scripts/stimuli. Please email support if you have any questions. Thanks Joe -- Joe Lyons, UNIX Systems Administrator York Neuroimaging Centre (YNiC), University of York

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IT closure this weekend
by Rebecca Lowndes 18 Aug '23

18 Aug '23

Hi all, Due to emergency power testing at the Science Park, the remote desktop may not be accessible or reliable on Saturday and Sunday. While the remote desktop machines may be intermittently available they may shut down without notice, so we strongly advise you do not attempt to work on the remote desktop this weekend. Open Plan will also be unavailable. Thanks Becky -- Rebecca Lowndes Research Technician York Neuroimaging Centre

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This Week at YNiC
by Richard Aveyard 17 Aug '23

17 Aug '23

Hello, Please find details about a change to the YNiC phone system, an upcoming summer closure, and the next scheduled induction and training sessions below. *YNiC phone number change* Due to an update to phone systems throughout the science park, unfortunately YNiC can no longer be contacted using our long-standing number. *You can now reach us on 01904 325940. *Please update our contact details anywhere you hold them, and in particular,* please update any material provided to participants.* As part of the upgrade to the science park phone system, we have new phone hardware. As these phones serve an important part of our safety procedures,* we encourage all operators to familiarise themselves with the new phones.* *YNiC summer closure* *YNiC will be closed to users for the week commencing Monday the 4th of September. *This is necessary for us to undertake vital updates to our computing systems. More details will be provided by email shortly. We apologise for any inconvenience this may cause. Please let us know if there are any mitigations we may be able to provide. *YNiC User Inductions* If you are aware of any new students/staff that will require access to YNiC and/or an IT account, they must attend a YNiC user induction. Our next induction will be on *Thursday the 14th of September, at 13:00*. Please ask them to contact support(a)ynic.york.ac.uk to sign up. *Level 0 operator training* *The next L0 training session will be held on Monday the 11th of September, 13:00-15:00. *Please note that users requesting Level 0 training should be a PhD, RA/Postdoc, or staff, and should already have a project proposal submitted to YNiC. Please email support(a)ynic.york.ac.uk if you have any questions or wish to book on to this session. Please note that sessions are limited to 4 trainees, which will be allocated on a first-come first-served basis. Training must be booked at least a week before the session date, in order to reserve the scanner booking. *YNiC Seminar* If you would like to give a talk next term, please get in touch, there are no specific requirements; presentations can include previously collected data, new data, pilot data and/or study plans and ideas. This is a great way to get feedback in a relaxed and friendly environment. Please message support(a)ynic.york.ac.uk. Cheers, Rich -- Dr Richard Aveyard Senior Technical Specialist York NeuroImaging Centre University of York, UK

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Useful dataset
by Aidan Horner 16 Aug '23

16 Aug '23

Hi all, A big new data set has just been published that could be useful for many of us, particularly for those interested in hippocampal subfields (who isn't?!): https://www.nature.com/articles/s41597-023-02449-9 Best wishes, Aidan -- *I work 0.8FTE and my working days are Monday-Wednesday and Friday* ======================================================= Dr Aidan J Horner Associate Professor (Senior Lecturer) in Psychology Department of Psychology University of York York YO10 5DD Mastodon: @aidanhorner@fediscience.org Twitter: @aidanhorner Lab website: http://www.aidanhorner.org/ =======================================================

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Fwd: Green Computing Paper
by Beth Jefferies 08 Aug '23

08 Aug '23

Here's an interesting paper from Nick about how we can reduce the carbon footprint of fMRI analysis. https://osf.io/7q5mh/ Let me know what you think :) Cheers Beth ---------- Forwarded message --------- From: Nick Souter <nes522(a)york.ac.uk> Date: Tue, 8 Aug 2023 at 17:00 Subject: Green Computing Paper To: FLEXSEM <flexsem-group(a)york.ac.uk> Hi all, Hope you're all doing well :) I've just released the preprint for my first post-doc paper <https://osf.io/7q5mh/>! It's a short perspective piece focusing on 10 steps neuroimagers can take to reduce the carbon footprint of their research computing (preprocessing and analysis). Thought I would share here in case there is anything actionable you could take away from it. In particular, there is stuff about long term data storage and data cleaning which might be relevant to issues with freeing up space on the FLEXSEM drive at YNiC. As part of this, we've developed a tool called fMRIPrepCleanup <https://github.com/NickESouter/fMRIPrepCleanup> specifically designed to comb over fMRIPrep output and delete all the junk files (although take caution using it, as covered in the readme!!). Thanks! Nick Nick Souter, PhD Department of Psychology University of York nes522(a)york.ac.uk -- You received this message because you are subscribed to the Google Groups "FLEXSEM" group. To unsubscribe from this group and stop receiving emails from it, send an email to flexsem-group+unsubscribe(a)york.ac.uk. To view this discussion on the web, visit https://groups.google.com/a/york.ac.uk/d/msgid/flexsem-group/CACz3qpZwiMMdG… <https://groups.google.com/a/york.ac.uk/d/msgid/flexsem-group/CACz3qpZwiMMdG…> . -- Beth Jefferies Department of Psychology, University of York, UK +44 01904 324368

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MEG at YNIC - only 2 weeks remaining (with current system)
by Andre Gouws 31 Jul '23

31 Jul '23

Hi all, We are coming to the end of an era. The "4D / York Instruments / Aveyard Industries" hybrid MEG scanner that was originally commissioned in 2004 will be allowed to warm up (and thus stop working) as we reach the end of our allocated liquid helium supply in 2 weeks time. Firstly, this is a last call for anyone currently using the system to wrap up ASAP. Contact us if you need support. Second, for those interested in using MEG at YNiC in the future, the replacement MEG system (Optical pump magnetometers; no liquid Helium so more sustainable [and affordable]) has been funded through the University's Capital Investment Scheme is being ordered and commissioned as we speak - we hope to have it up and running from Q2 2024. Best wishes, -- André ************************************************************************ André Gouws PhD Lead Technical Specialist York Neuroimaging Centre and York Diagnostic Imaging Departmental Safety Advisor - Dept. of Psychology University of York The Biocentre York Science Park Heslington YO10 5NY

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Siemens scanner back up and running
by Rebecca Lowndes 20 Jul '23

20 Jul '23

Dear users, Following downtime earlier this week, the Siemens scanner is running and available for use again. Please fill out your scan reimbursement forms if you were affected by the downtime. Also note, it will be out of action next Thursday (27th) for further preventative maintenance. Thank you Becky -- Rebecca Lowndes Research Technician York Neuroimaging Centre

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Micah Murray talk TODAY 12 noon
by Rebecca Lowndes 19 Jul '23

19 Jul '23

Hi all, Don't forget to come down to YNiC for our seminar presented by Professor Micah Murray. Micah is the Scientific and Academic Director of the Sense Innovation and Research Center, Lausanne, Switzerland and section head, EEG CHUV-UNIL at the Center for Biomedical Imaging. At noon he will be giving a talk on recent work he has been doing on high spatial- and temporal-resolution fMRI and also on recent advances in EEG. *12 Noon, Weds 19th July, at YNiC* *Title: "From old dogs to new tricks in human EEG and fMRI"* Some links are provided to give you more background: Micah Murray ( https://www.unil.ch/line/en/home/menuinst/people/micah-m-murray.html) Rapid fMRI ( https://www.biorxiv.org/content/10.1101/2023.05.13.540663v2.abstract) EEG (https://link.springer.com/article/10.1007/s10548-021-00882-w). It would be really great if you could come over to YNiC to attend the talk. Many thanks, Becky -- Rebecca Lowndes Research Technician York Neuroimaging Centre

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YNiC Seminar Tomorrow (Wednesday 12pm)
by Jennifer Ashton 18 Jul '23

18 Jul '23

Hi Everyone, Tomorrow we are fortunate to be hosting Professor Micah Murray at YNiC. Micah is the Scientific and Academic Director of the Sense Innovation and Research Center, Lausanne, Switzerland and section head, EEG CHUV-UNIL at the Center for Biomedical Imaging. At noon he will be giving a talk on recent work he has been doing on high spatial- and temporal-resolution fMRI and also on recent advances in EEG. *12 Noon, Weds 19th July, at YNiC* *Title: "From old dogs to new tricks in human EEG and fMRI"* Some links are provided to give you more background: Micah Murray ( https://www.unil.ch/line/en/home/menuinst/people/micah-m-murray.html) Rapid fMRI ( https://www.biorxiv.org/content/10.1101/2023.05.13.540663v2.abstract) EEG (https://link.springer.com/article/10.1007/s10548-021-00882-w). It would be really great if you could come over to YNiC to attend the talk. We look forward to seeing you then! Many thanks, Jennifer -- Jennifer Ashton, PhD Senior Research Technician York Neuroimaging Centre Working days: Monday, Tuesday and Wednesday

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MRI Scanner Fault
by Jennifer Ashton 17 Jul '23

17 Jul '23

Dear Users, Unfortunately there has been a fault with the Siemens MRI scanner over the weekend. We are working to get this fixed as soon as possible, but will be unable to run any scans in the meantime. We will keep you updated. Many thanks, Jennifer -- Jennifer Ashton, PhD Senior Research Technician York Neuroimaging Centre Working days: Monday, Tuesday and Wednesday

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Extra YNiC Seminar!
by Rebecca Lowndes 12 Jul '23

12 Jul '23

Dear all, Next Wednesday (19th July) we are fortunate to be hosting Professor Micah Murray at YNiC. Micah is the Scientific and Academic Director of the Sense Innovation and Research Center, Lausanne, Switzerland and section head, EEG CHUV-UNIL at the Center for Biomedical Imaging. At noon he will be giving a talk on recent work he has been doing on high spatial- and temporal-resolution fMRI and also on recent advances in EEG. 12 Noon, Weds 19th July, at YNiC Title: "From old dogs to new tricks in human EEG and fMRI" Some links are provided to give you more background: Micah Murray ( https://www.unil.ch/line/en/home/menuinst/people/micah-m-murray.html) Rapid fMRI ( https://www.biorxiv.org/content/10.1101/2023.05.13.540663v2.abstract) EEG (https://link.springer.com/article/10.1007/s10548-021-00882-w). All are welcome to come along Thanks, Becky -- Rebecca Lowndes Research Technician York Neuroimaging Centre

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Siemens Scanner next week
by Rebecca Lowndes 06 Jul '23

06 Jul '23

Hi all, As many of you will have noticed, the Siemens scanner was blocked out for use next week for the removal of GE. This work has now been postponed, so we have released the scanner for booking next week. We are not able to provide operator cover, as we have already committed to covering MEG, but if you are able to operate yourselves, please go ahead and book. Apologies for the late notice and any inconvenience caused Thanks Becky -- Rebecca Lowndes Research Technician York Neuroimaging Centre

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MEG-UKI Poster Abstracts
by Jennifer Ashton 03 Jul '23

03 Jul '23

Hello, Please find details about submitting poster abstracts to this year's MEG-UKI meeting below. You can find more information about the meeting here https://meguk.ac.uk/meg-uki-2023-conference/ Many thanks, Jennifer -- Jennifer Ashton, PhD Senior Research Technician York Neuroimaging Centre Working days: Monday, Tuesday and Wednesday ---------- Forwarded message --------- From: Redmond O'Connell <REOCONNE(a)tcd.ie> Date: Fri, Jun 23, 2023 at 2:54 PM Subject: poster abstracts for MEG-UKI Hi all, Just a very quick word. Places are filling up nicely for the MEG-UKI meeting but we haven't had a lot of poster abstract submissions as yet. Please do encourage your labs and colleagues to submit something (not obligatory that there be MEG data involved specifically). We understand that some are not ready to commit to an abstract just yet so please note that *we're happy for people to register now and submit a poster abstract later on* through the conference e-mail address (meguki2023(a)gmail.com) with the deadline for the abstracts being 1st August. All the best Redmond

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Siemens MRI scanner down
by Andre Gouws 20 Jun '23

20 Jun '23

Hi all, I am sorry to report that due to coolant leak the MRI scanner is offline for the rest of today, all day tomorrow (Tues 20th) and possibly Wed 21st. We have diagnosed the problem but it will take a while to ship the parts for repair from Germany - this could happen today but may only happen tomorrow. If you have the scanner booked on tomorrow Tues 20th you will need to reschedule. If you have the scanner booked on Wed / Thu you may want to let your participants know that there may be a cancellation, but we are hopeful to be back online. We will update you as soon as we have any further information. Best wishes, -- André ************************************************************************ André Gouws PhD Lead Technical Specialist York Neuroimaging Centre and York Diagnostic Imaging Departmental Safety Advisor - Dept. of Psychology University of York The Biocentre York Science Park Heslington YO10 5NY

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YNiC - MRI Scanner Fault
by Jennifer Ashton 19 Jun '23

19 Jun '23

Dear Users, We have a system fault with the Siemens MRI scanner at YNiC, as such the scanner will be down for the rest of the day. We are working to get this fixed and we will keep you updated on our progress. Many thanks, Jennifer -- Jennifer Ashton, PhD Senior Research Technician York Neuroimaging Centre Working days: Monday, Tuesday and Wednesday

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