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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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