Dear All,
We have put together a provisional schedule for the YNiC seminars for
the academic year. The YNiC led seminars will occur on even weeks
during the autumn and spring terms. On the odd weeks we will have
seminars on an ad-hoc basis and will largely focus on project
presentations or presentations arranged by the YNiC Science Committee.
We have also scheduled training opportunities for scanner operators. We
would really like new PhD students and postdocs who will want to operate
the scanners to take these opportunities as they dovetail nicely into
our workload and MSc teaching and training. With that in mind, please
note that the first element of training will be held Thursday 28th
September.
The detailed schedule is attached.
Best wishes
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Hello All,
This week we will be having induction sessions for our new intake of PhD
and MSc students between 9am and 1pm on Thursday. An introduction to the
IT systems will take place between 9am and 1pm on Friday. It will,
therefore, be busier than usual in open plan, so please take that into
account when planning your work at YNiC.
We are hoping to freshen up the posters at YNiC over the next week or so.
Could you bring us any spare, but relatively recent, posters that you would
like to have on display at YNiC?
Many thanks
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Hello All,
Thanks to those of you who have reported issues arising after the IT
upgrade. We have managed to deal with the majority of them. A reminder
for those of you who haven't given your analysis or stimuli a spin for a
while to give them a go well in advance of needing them, so we can help
with any issues that arise.
Next week is the start of term and therefore ynic will be busy with
inductions and teaching. If you are here, please join us in welcoming our
new recruits.
Best wishes
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Dear All,
A few updates:
1) Staff changes: Ross Devlin has now left YNiC. He will be having a
period of leave before taking up his new role at York Instruments. He has
given YNiC many years of valuable and helpful service for which we are all
very thankful.
2) A brief reminder that there will be no operator cover for any scanner on
Wednesday this week. We are undertaking some training that will look at
the documentation and processes we use to train operators for the Siemens
scanner.
3) Project booking limits: We have a standard limit of 7 hours per week per
project. We are aware however that such limits can constrain throughput on
projects. We can offer some flexibility on how much time can be booked if
we are given a period of time to plan. So, please get in touch should your
requirements for booking be greater than 7 hours per week.
Best wishes
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Hello All,
1) Please test stimulus code and analysis streams you rely on and feedback
any errors (including the error report) through the IT system. Note that
it is not a safe assumption that all code will run perfectly after an IT
upgrade.
2) We will be closed from 1330 on Thursday.
3) Next Wednesday 13th September, we will be closed from midday to test out
training materials for the Siemens scanner.
Best wishes
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Hello everyone,
Just a reminder that if anybody has any suggestions for discussion topics
for the YNIC Science Committee, they should contact me to let me know.
Please feel free to contact me either via email or in person to discuss any
issues that you would like raised at the next meeting.
Best wishes,
Jonny
--
Jonathan Smallwood, Reader in Psychology / Cognitive Neuroscience
Room C023, Department of Psychology, University of York, England. YO10 4PH.
Telephone: 01904 324651
Hi all
* IT upgrade and centre maintenance:
We have completed the IT upgrade and centre maintenance works.
We have done our best to ensure a smooth transition for you across the
IT infrastructure - please do let us know if you experience any issues
or "odd behaviour" on the IT systems and we will attempt to fix them as
soon as possible. For a summary of software changes, please see the list
at the end of this email.
* Reception reorganisation:
The works on our new reception area are now complete and bring
us in line with the best practices outlined by the CQC (Care Quality
Commission) - essentially we have made the reception more professional,
more welcoming and crucially more secure. If you need help from the
reception staff, or are picking up / dropping off forms, please do so by
speaking to reception staff at the glass service hatch - access to the
reception office is restricted
Andre'.
Summary of software changes at YNiC in Summer 2017
---------------------------------------
FSL:
* FSL 5.0 has been updated to 5.0.9
* FSL 4.1 is no longer available
* FSLView is only available as a backwards compatibility option and
will be removed next summer. FSLEyes is the replacement for FSLView.
Python:
* Python 2 and 3 are now both supported at YNiC as far as is possible
* Ensure that you are using the correct version of Python for the
script you are running.
* iPython installs for Python 2 and 3 are both now available
* Spyder installs for Python 2 and 3 are both now available
* numpy -> 1.12
* scipy -> 0.18
* matplotlib -> 2.0.0
* mvpa2 -> 2.6.0
* most other modules have been updated to their latest stable revisions
* psychopy remains at version 1.84.1 and is Python 2 only
MATLAB:
* Version R2017a (9.2) is now available and is the default version.
* Version 8.5 and 9.0 remain available. 9.0 will be removed when
R2018a is released.
SPM:
* SPM 8 has been updated to the latest revision r6313
* SPM 12 has been updated to the latest revision r6906
* SPM 2 and 5 have been updated to their final releases
Freesurfer:
* Both Freesurfer 5.3 and 6.0 are now available.
* See the documentation pages (TODO) on how to use each version
R:
* The version of R installed is now 3.3.3
* rstudio has been updated to 1.0.153
* We have added the latest revisions of all of the `tidyverse`
packages, removing the need to install these per-user
Generic software:
* Connectome Workbench 1.2.3 is now installed by default
* Libreoffice has been upgraded to 5.2.7
* Mathematica 11 is now available alongside Mathematica 10
* Maple 2016 replaces Maple 18
* SPSS 23 replaces SPSS 20
* The Iceweasel (Firefox) and Icedove (Thunderbird) aliases are no
longer available - you may need to update any desktop shortcuts.
Stimulus PC-specific:
* Presentation (NBS) stimulus delivery package has been removed
Known issues:
* There are known problems with hdfview - these are due to an upstream
bug, we are preparing a workaround for this
--
André
************************************************************************
André Gouws PhD
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 all,
As of lunchtime today, the centre will be closed to allow us to perform
our annual IT systems upgrades. We have done our best to minimise
disruptions but following these upgrades please do keep a close eye on
your data processing and acquisition streams and let us know if there
are any issues.
Please note that we also use this opportunity to perform a number of
other "housekeeping" jobs that include moving furniture and some minor
building & decorating work - thus please consider the centre as *closed*.
We will let you all know once everything is up and running again.
--
André
************************************************************************
André Gouws PhD
York Neuroimaging Centre
University of York
The Biocentre
York Science Park
Heslington
YO10 5NY
Tel: +44 (0) 1904 435327
Fax: +44 (0) 1904 435356
As there has been practically no use of the Presentation stimulus
delivery software package at YNiC over the past 12 months, we are not
intending to renew the five licenses we currently purchase annually.
As such, Presentation will no longer be available for use on the
stimulus delivery PCs at YNiC after the centre IT upgrade next week.
Please contact me if you have any queries.
Thanks,
--
André
************************************************************************
André Gouws PhD
York Neuroimaging Centre
University of York
The Biocentre
York Science Park
Heslington
YO10 5NY
Tel: +44 (0) 1904 435327
Fax: +44 (0) 1904 435356
