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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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