- ynic-users

This Week at YNiC
by Lauren Welbourne 14 Oct '19

14 Oct '19

Good morning everyone This week we have a project presentation from Frida Torkelsen on *Thursday at 4pm* in YNiC open plan, titled: "Diffusion Weighted functional brain imaging: investigating cellular swelling as a potential direct measure of neuronal activity". Talks are followed by refreshments. 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 date will be Wednesday 30th October at 2pm. Please ask them to contact support(a)ynic.york.ac.uk to sign up. Hope you have a great week! Kind regards Lauren -- Lauren Welbourne, PhD Senior Research Technician lauren.welbourne(a)york.ac.uk York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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Screening Form
by Antony Morland 14 Oct '19

14 Oct '19

Hello All, I wanted to highlight the following text that now appears on YNiC MRI safety screening forms: "It is essential that all questions on this sheet are answered truthfully. This information is essential in order to ensure your safety and will be kept completely confidential. If you do not want to answer any question(s) on this form you are free to withdraw from this scanning session without any prejudice." Please read this text to potential participants before you ask the questions on the form, some of which can be personal in nature and which some individuals may not wish to answer. Thank you Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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YNiC Seminar today 4pm
by Lauren Welbourne 10 Oct '19

10 Oct '19

Hi everyone This is a reminder that Mark Hymers will be running a seminar this afternoon at 4pm in the YNiC open plan, on how to use the YNiC cluster for processing data. It will be worthwhile for new or existing YNiC users that haven't previously used the cluster, and may need to make use of it for upcoming data analysis. We hope to see you this afternoon. Cheers Lauren -- Lauren Welbourne, PhD Senior Research Technician lauren.welbourne(a)york.ac.uk York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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This Week at YNiC
by Lauren Welbourne 07 Oct '19

07 Oct '19

Good afternoon everyone We have a few notices for you today: *Thursday Seminar - Using the Cluster:* Mark Hymers will be running a session this Thursday on how to use the cluster at YNiC. We encourage users to attend if they are unfamiliar with how to send jobs to the cluster for processing. The session will be held at *4pm on Thursday 10th October in YNiC open plan*. *Remote Desktop:* We have made some configuration changes to the remote desktop, so if you are experiencing any issues please follow these steps on the wiki: https://www.ynic.york.ac.uk/docs/ITPages/RemoteDesktop#FAQ_and_errors Please note that you must be connected to the University of York VPN, and should also have followed the latest remote desktop server setup guidelines (https://www.ynic.york.ac.uk/docs/ITPages/RemoteDesktop). *YNiC User Inductions:* Hopefully everyone that needed an induction was able to attend the two large sessions we put on last week, but if there are any other students/staff that will require an IT account for YNiC, our next induction date will be Wednesday 30th October at 2pm. Please ask them to contact support(a)ynic.york.ac.uk to sign up. Hope you all have a great week. Kind regards Lauren -- Lauren Welbourne, PhD Senior Research Technician lauren.welbourne(a)york.ac.uk York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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YNIC Science Comittee
by Jonny Smallwood 07 Oct '19

07 Oct '19

Hello everyone, Next week on Monday is the next meeting of the YNIC Science committee. Please let me know if there is any issues you would like me to raise with the other members. Thanks 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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Open plan teaching times
by Mark Hymers 30 Sep '19

30 Sep '19

Dear all, Over this term, Open plan will be used for teaching on a number of occasions. We will be asking everyone who is not taking part in the class to leave the open plan area at these times. The times for this term are: Week 1: Thursday 3rd October: 0900-1300 Friday 4th October: 0900-1300 Week 2: Tuesday 8th October: 1200-1600 Week 4: Tuesday 22nd October: 1200-1600 Week 7: Tuesday 12th November: 1200-1600 Week 9: Tuesday 26th November: 1200-1600 These times can be found on the University timetable http://www.york.ac.uk/viewtimetables by choosing YNiC as the room and clicking "View Room" Thanks, Mark

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This Week at YNiC
by Richard Aveyard 23 Sep '19

23 Sep '19

Hi Everyone, As of Monday 23rd of September, *YNiC has reopened.* Following the closure *we strongly recommend that users visit YNiC to test their stimulus presentation scripts before their next scanning session.* YNiC staff will provide support in modifying scripts, but this *must* be done prior to scanning. During the closure, IT updates described in the email from the 30th of August were implemented. However, *FSL 6 will not be available* due to compatibility issues. The upgraded YNiC MEG suite is now in testing. *We are inviting informal discussions of prospective MEG studies.* During the closure the facility was re-decorated and *we welcome contributions of A0 posters for display*. The next *user inductions will take place on Thursday 3rd October* at 9am and 11am. New students will be contacted about these sessions, and any additional staff or existing PhD students that require an induction should contact us to book onto one of these sessions. There will be project *proposal presentations on Thursday the 26th of September at 15:30* in open plan: - "Pattern extraction and memory-guided decision-making" by Jamie Cockcroft - "Using intersubject correlations during movie-watching to assess the neural basis of mind wandering" by Adam Turnbull. There will be a talk by* guest speaker, Dr Ed Silson on Thursday the 26th of September at 16:00* in open plan, on the subject of: - "Scene perception, memory and the functional organisation of human medial parietal cortex." Cheers, Rich -- Richard Aveyard, Senior Research Technician York NeuroImaging Centre University of York, UK

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Posters
by Antony Morland 18 Sep '19

18 Sep '19

Hello All, We have been revamping the poster displays at YNiC during the summer closure. We are a bit short of posters showcasing areas other than vision, so would be delighted to receive any A0 (landscape or portrait) posters that we can display. A broad cross-section of topics that reflects research opportunities for the incoming MSc cohorts would be greatly appreciated. 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 Closure - IT updates
by Lauren Welbourne 30 Aug '19

30 Aug '19

Hi everyone During the YNiC closure the following updates and changes will be made to the available software: *FSLView* - This will be the last YNiC desktop build which contains FSLView. It is deprecated and we are already pulling various tricks to make it work. We had initially scheduled its removal for Summer 2018 but we have managed to keep it going. We now intend to remove it in Summer 2020. This really is the end of fslview, so please migrate to FSLeyes. *FSL* - FSL 5 has been updated from 5.0.9 to 5.0.11 with all new tools also added (bianca, mist, surface-based tools, film_cifti). - FSL 6 is now installed (version 6.0.1) but version 5 will remain the default. - We will review the default FSL version in Summer 2020 and decide whether to switch the default to FSL-6 at this time. *Freesurfer*. - This will be the last YNiC desktop build which contains Freesurfer 5.3. All projects should now be using 6.0. Please let us know if you are still using 5.3. *AFNI* - AFNI is being reintroduced after a several year absence. We will be using the latest stable release (20190220), but will configure AFNI in such a way that multiple versions can be supported at once. Details of how to use AFNI at YNiC will be added to the documentation pages. *MATLAB* - The available versions of Matlab will be 8.5 and 9.6 - Matlab 9.0, 9.2 and 9.4 are no longer available. - Note that we will not retain 8.5 beyond Summer 2021, so if you are still using it, you need to migrate your tools as soon as possible. Please let us know if you are still using 8.5 for some reason. *SPM* - SPM 12 has been updated to the latest patch release. - SPMs 5 and 8 have been removed from the system. These versions are over a decade old, are not supported upstream, and building them is becoming harder as compilers become more pedantic about code quality. - We have retained SPM 2 as it is still buildable and has historically been used by a couple of other packages (for co-registration etc). SPM 2 will be removed in Summer 2021. If you still have a real need for SPM 2, 5 or 8, please get in touch as soon as possible. - All new projects should be using SPM 12. *Connectome Workbench* - This has been upgraded from 1.2.3 to 1.3.2 *Python 2 / 3* - This will be last build of the YNIC desktop where Python 2 is fully supported as it is now deprecated upstream. - All new code should be written using Python 3. We plan to run a workshop in the first weeks of term to assist people in migrating code from Python 2 to 3; this will be especially relevant for those who use Psychopy. - Python 3.7.3 is now installed, upgraded from 3.5.3. - We are aware of the following modules used under Python 2 which are not currently available for python 3: *python-mvpa2:* Upstream are working on porting this; we will make it available as soon as possible. *python-pymc: *We are currently working on python3 compatible packages for this Major module updates: - numpy 1.16.2 (from 1.12.1) - scipy 1.1.0 (from 0.18.1) - matplotlib 3.0.2 (from 2.0.0) - h5py 2.8 (from 2.7) - mdp is no longer available: you should use sklearn instead - mpi4py 3.0.2 (from 2.0.0); note that this is a newer version than in Debian Buster by default - nibabel 2.3.2 (from 2.1.0) - nifti -> this is a python 2 module and is deprecated; use nibabel instead - pil 5.4.1 (from 4.0) - pyglet 1.4.1 (from 1.1.4); note that this is a newer version than in Debian Buster by default - scikits.audiolab is replaced by soundfile 0.10.1 - sounddevice 0.3.13 is the supported sound presentation module - vtk: version 7 for Python 3; version 6 for Python 2 - wxpython 4.0 (from 3.0); note that this is a major version change - Psychopy has been updated to 3.1.5 (from 1.90.0). This involves changing from Python 2 to Python 3. We recommend that people attend the Python 2 to 3 migration workshop which will provide a good opportunity for people to get assistance in updating scripts (where necessary). *Mathematica* - Version 10 is no longer available; you should use Mathematica 11. *Shutter (the screenshot app)* - This application is no longer available. We recommend Flameshot as the replacement. YNiC will be closed from 5pm today (Friday 30th Aug), and will re-open on Monday 23rd September. Please note that there will be no access to YNiC open plan, remote desktops, or support, during the closure period. I hope you all have a pleasant YNiC break, and we'll see you again in a few weeks! Kind regards Lauren -- Lauren Welbourne, PhD Senior Research Technician lauren.welbourne(a)york.ac.uk York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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This Week at YNiC
by Lauren Welbourne 27 Aug '19

27 Aug '19

Hi everybody I hope you all enjoyed the record-breaking temperatures this weekend! This is the final week that YNiC is open before the closure; we will send out a separate email to let you know exactly what IT upgrades will be happening during the closure period. YNiC will be closed from Monday 2nd until Friday 20th September, there will be no remote access or support during this period. Please be aware that on Wednesday 28th August, PAT testing will be carried out in open plan. Each PC will need to be turned off for approximately 10 minutes for the testing to be done - if you are in open plan during the time the testing occurs you will be given advanced warning of when we'll need to turn off your PC. We apologise for any inconvenience this will cause. Hope you all have a great week. Kind regards Lauren -- Lauren Welbourne, PhD Senior Research Technician lauren.welbourne(a)york.ac.uk York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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This Week at YNiC
by Lauren Welbourne 20 Aug '19

20 Aug '19

Hi everyone There's nothing new to report this week, so here's a reminder of the upcoming closures again: - Monday 26th August (Bank Holiday) - Monday 2nd September - Friday 20th September (YNiC Closure) Don't forget that during the YNiC Closure in September we will be performing essential IT upgrades and maintenance, and therefore there will be no access to the centre (including remotely), and no support will be provided over this period. Hope you have a great week! Kind regards Lauren -- Lauren Welbourne, PhD Senior Research Technician lauren.welbourne(a)york.ac.uk York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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This Week at YNiC
by Lauren Welbourne 12 Aug '19

12 Aug '19

Hi everyone Our final YNiC user induction for the summer will take place this *Thursday 15th August at 2pm*. If you are aware of any students/staff that will require an IT account for YNiC, they must complete a User Induction first. Please ask them to contact support(a)ynic.york.ac.uk to sign up for this next induction date. Any new staff or students that start after this final summer induction can join the group induction sessions for new MSc and PhD students. These will take place on Thursday 3rd October at 9am and 11am. New students will be contacted about these sessions, and any additional staff or existing PhD students that require an induction should contact us to book onto one of these sessions. Finally, please note the upcoming closures: - Monday 26th August (Bank Holiday) - Monday 2nd September - Friday 20th September (YNiC Closure) Hope you have a great week, Kind regards Lauren -- Lauren Welbourne, PhD Senior Research Technician lauren.welbourne(a)york.ac.uk York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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This Week at YNiC
by Lauren Welbourne 05 Aug '19

05 Aug '19

Hi everyone *YNiC Closures* I wanted to remind you all of the upcoming bank holiday and the YNiC closure dates. The Centre will be closed on the following: - Monday 26th August (Bank Holiday) - Monday 2nd September - Friday 20th September (YNiC Closure) During the YNiC closure we will perform essential IT upgrades and maintenance. There will be no access to the centre (including remotely), and no support will be provided over this period. *User Inductions* Our final YNiC user induction for the summer will take place on *Thursday 15th August at 2pm*. If you are aware of any students/staff that will require an IT account for YNiC, they must complete a User Induction first. Please ask them to contact support(a)ynic.york.ac.uk to sign up for the next induction date. Any new staff or students that start after the final summer induction can join the group induction sessions for new MSc and PhD students. These will take place on Thursday 3rd October at 9am and 11am. New students will be contacted about these sessions, and any additional staff or existing PhD students that require an induction should contact us to book onto one of these sessions. Hope you have a great week! Kind regards Lauren -- Lauren Welbourne, PhD Senior Research Technician lauren.welbourne(a)york.ac.uk York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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Request for example Psychopy stimulus presentation scripts
by Mark Hymers 29 Jul '19

29 Jul '19

Hi all, We are currently preparing a large software update for YNiC. This update will be applied during YNiC's closure in September. To assist us in our testing, we would like to request that labs provide us with example stimulus code which you have used at YNiC. This will help us build up a repository of stimulus code for regression test purposes. Please email me directly (mark.hymers(a)ynic.york.ac.uk). The easiest way to do this is for you to send a path to your code on the YNiC system along with a note that you are happy for us to copy the code and us it in our tests. More details about the upgrade work will follow over the next few weeks. 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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This Week at YNiC
by Lauren Welbourne 29 Jul '19

29 Jul '19

Hi all The only update I have for you this week is to remind you that our next YNiC user induction is provisionally planned for this *Thursday 1st August *(time TBC). If you are aware of any students/staff that will require an IT account for YNiC, they must complete a User Induction first. Please ask them to contact support(a)ynic.york.ac.uk to sign up for the next induction date. Hope you have a great week! Kind regards Lauren -- Lauren Welbourne, PhD Senior Research Technician lauren.welbourne(a)york.ac.uk York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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Siemens scanner - normal service resumed
by Andre Gouws 23 Jul '19

23 Jul '19

Hi all, You will be glad to hear that we have the Siemens scanner back up and running. The transmit box in the scanner was the guilty party and the part took several hours to replace. Quality assurance tests have been run and the machine appears to be in spec. Normal service will resume as of tomorrow morning. Sorry again for anyone affected by the down time. 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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This Week at YNiC
by Lauren Welbourne 22 Jul '19

22 Jul '19

Hi everyone *Summer Closure and Bank Holiday* In addition to our September Closure (2nd to 20th September), please be aware that there is also a Bank Holiday on Monday 26th August, and therefore the centre will be closed to users on this day. *YNiC User Inductions* Our next YNiC user induction is provisionally planned for *Thursday 1st August *(time TBC). If you are aware of any students/staff that will require an IT account for YNiC, they must complete a User Induction first. Please ask them to contact support(a)ynic.york.ac.uk to sign up for the next induction date. *Siemens Scanner* Please be advised that the Siemens scanner is currently down; we are awaiting new parts and the Siemens engineer should be completing the necessary fixes early this week. We will keep you informed once the scanner is available to book again. *Remote Desktop* The remote desktop is up and running again (as per my email last week), thanks to the hard work of Mark and Joe! Hope you have a good week. Kind regards Lauren -- Lauren Welbourne, PhD Senior Research Technician lauren.welbourne(a)york.ac.uk York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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Remote Desktop
by Lauren Welbourne 16 Jul '19

16 Jul '19

Hi all You'll be pleased to hear that the remote desktop service is now back up and running again. Big thanks to Joe and Mark for their work on this! Cheers Lauren -- Lauren Welbourne, PhD Senior Research Technician lauren.welbourne(a)york.ac.uk York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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Congratulations to Dr Karapanagiotidis
by Jonny Smallwood 16 Jul '19

16 Jul '19

Hello everyone,Theo has just passed his defence. Come and celebrate with us in the ground floor of E-block reception. 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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This Week at YNiC
by Lauren Welbourne 15 Jul '19

15 Jul '19

Hi everyone Further to the IT issues we experienced last week, please be advised that we are still working on getting the remote services up and running. You may also experience other technical glitches while everything is restored to normal service, if so, please can you report the issue to us at it-support(a)ynic.york.ac.uk. We are running a *YNiC user induction tomorrow *(Tuesday 16th) at *9:30am*, as a replacement to the induction that was cancelled last week during the unplanned closure. If you are aware of any students/staff that will require an IT account for YNiC, they must complete a User Induction first. Please ask them to contact support(a)ynic.york.ac.uk to sign up for tomorrows induction. Finally, as I mentioned last week, please be aware that due to staff annual leave over the summer, there will be a limited number of operator covered slots across the two scanners. I hope you have a good week! Kind regards Lauren -- Lauren Welbourne, PhD Senior Research Technician lauren.welbourne(a)york.ac.uk York Neuroimaging Centre University of York Innovation Way Heslington York YO10 5NY

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Essential services back up
by Antony Morland 10 Jul '19

10 Jul '19

Hello All, We are now up and running essential services, so Open Plan is ready for business. Remote services are still a work in progress and are unlikely to return until later in the week. The speedy return to services is a result of Mark Hymers and Joe Lyons working overnight. Huge thanks to them for their work. 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 recovery
by Antony Morland 10 Jul '19

10 Jul '19

Hello All, Progress is being made and we hope to be able to have essential services up and running from 1pm. Initially, we are concentrating on on site services and remote services will looked at later. The 1pm time is based on things running smoothly between now and then. More news soon. Thanks for your patience Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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YNiC IT issues today
by Joe Lyons 09 Jul '19

09 Jul '19

Dear all Last night we had a disk failure in our of our storage arrays which caused some issues with a few servers and some of the file shares. We restarted the servers affected which included the remote desktops this morning. The cluster was then rebooted and a file system check was performed on /scratch/home at 12:00 to check for any errors. All systems we back to normal from 1pm. Apologies for any inconvenience caused. Thanks Joe -- Joe Lyons, UNIX Systems Administrator York Neuroimaging Centre (YNiC), University of York

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YNiC IT issues
by Joe Lyons 09 Jul '19

09 Jul '19

Unfortunately, we're experiencing more issues with our storage system and so we've closed the centre for the day so we can restore service and check the file systems. All remote desktop systems will be unavailable for the rest of the day. Thanks Joe -- Joe Lyons, UNIX Systems Administrator York Neuroimaging Centre (YNiC), University of York

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Important: YNiC Desktops reboot
by Joe Lyons 09 Jul '19

09 Jul '19

Hello Due to some hardware issues over night, we're going to be rebooting the file server that provides /home and /scratch/home to all the YNiC desktops (including remote desktops) at *12:00 midday today*. Please log out of your desktop session before 12 to prevent any work from being lost. Thanks Joe -- Joe Lyons, UNIX Systems Administrator York Neuroimaging Centre (YNiC), University of York

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