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.
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
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
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
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
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
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
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
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
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
