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
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
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
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
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.
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.
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
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
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
Hello All,
Please be aware that participants, who are pregnant should not be scanned.
I know this is standard practice, but I thought it would be a timely
reminder because of the following.
We are in the process of having a risk assessment about pregnancy and MRI
operators. While this risk assessment is being performed MRI operators who
are pregnant should no longer enter the scanner room.
I will update you on any changes resulting from the risk assessment.
Best wishes
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Hi everyone
This week Ryan Elson will be giving two project presentations in YNiC open
plan at *4pm on Thursday 11th*, followed by refreshments. The titles of
these talks are:
- "Investigating motor feedback in the STS and SC during expression
recognition."
- "Investigating 'within' and 'between' expression processing in the STS
using combined TMS and psychophysics."
Please also 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.
We hope to see you at the talks on Thursday.
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
This Tuesday 2nd July at 1pm we will have a site visit by the Chair of the
Wellcome Trust, Eliza Manningham-Buller. If you are in open plan or
scanning during this time, please behave professionally.
Our next YNiC user induction is provisionally planned for *Wednesday 10th
July *(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 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
Hi everyone
We have a few announcements for you this week:
*Summer Closure*
We would like to give you advanced notice of our summer closure period,
which will take place between the 2nd and 20th September. During this
period 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.
*Screening Participants*
We know that we have had to turn away participants on the day that they
attend for scanning. We also know that this is very frustrating for
researchers. The situation can occur for all participant groups, but is
more frequent in special or elderly populations. Our existing advice is to
ensure that you speak with your participant *before* the day of their scan
to go through the screening form, and obtained any Level 3 signatures
required. We know that this is done routinely, but we have a couple of
further suggestions:
- First, be absolutely clear that the questions you will be asking are
vital to ensure participant safety, and that each participant should answer
fully and take time to consider their answers.
- Second, make the participant aware that having participated in a scan
before does not mean that they will be clear for an upcoming scan; they
need to consider each question carefully and identify anything that they
may have previously had approved by an operator
- Finally, and related to the previous point, knowing that a participant
has been scanned before is not a guarantee that that same participant will
be eligible for an upcoming scan, because of any potential change in their
status or indeed changes in safety regulations governing who may be scanned.
*YNiC User Inductions*
We are running our next YNiC user induction this *Wednesday 26th June* at
the updated time of *4pm*. 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 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
Hi everyone
- We will be running our next *YNiC user induction on Wednesday 26th June
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.
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
Just one notice this week, there will be no support at YNiC on Wednesday
12th June, due to staff attending the Yorkshire Vision Network meeting.
The centre will still be open for use.
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
Hi everyone
Please be aware that the majority of YNiC staff will be unavailable on 12th
June for the Yorkshire Vision Network meeting. Therefore, there will be no
support or operator cover on this day, but the centre will still be open.
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
Please be aware that next week (w/c 3rd June) we have very limited Level 3
availability for signing off safety forms. If you have any participants
being scanned next week that will need a signature you must get these
signed-off no later than Monday afternoon.
You can get the participant safety form printed at reception, and you can
also hand these back to reception once the forms are signed if you have
nowhere safe to store them before the scan. Reception will attach the
signed form to the general consent sheet, which you can collect as normal
on the day of the scan.
It should be noted that it is standard procedure to obtain signatures in
advance of the scan day - we cannot guarantee that booked scans will go
ahead if a signature is not obtained in advance.
We appreciate your understanding in this process, and in the importance of
participant safety over research.
Please let me know if you have any questions.
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
