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
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
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
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
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
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
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/
=======================================================
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
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.
--
Beth Jefferies
Department of Psychology, University of York, UK
+44 01904 324368
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
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
