Hi all
This is a reminder that we have a project presentation from Frida
Torkelsen *Today
at 4pm* in YNiC open plan, titled: "Diffusion Weighted functional brain
imaging: investigating cellular swelling as a potential direct measure of
neuronal activity". Talks are followed by refreshments.
We hope to see you there.
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
Good morning everyone
This week we have a project presentation from Frida Torkelsen on *Thursday
at 4pm* in YNiC open plan, titled: "Diffusion Weighted functional brain
imaging: investigating cellular swelling as a potential direct measure of
neuronal activity". Talks are followed by refreshments.
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 date will be Wednesday 30th October at 2pm. Please ask them to
contact support(a)ynic.york.ac.uk to sign up.
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
Hello All,
I wanted to highlight the following text that now appears on YNiC MRI
safety screening forms:
"It is essential that all questions on this sheet are
answered truthfully. This information is essential in order to ensure
your safety and will be kept completely confidential. If you do not want
to answer any question(s) on this form you are free to withdraw from
this scanning session without any prejudice."
Please read this text to potential participants before you ask the
questions on the form, some of which can be personal in nature and which
some individuals may not wish to answer.
Thank you
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Hi everyone
This is a reminder that Mark Hymers will be running a seminar this
afternoon at 4pm in the YNiC open plan, on how to use the YNiC cluster for
processing data.
It will be worthwhile for new or existing YNiC users that haven't
previously used the cluster, and may need to make use of it for upcoming
data analysis.
We hope to see you this afternoon.
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
Good afternoon everyone
We have a few notices for you today:
*Thursday Seminar - Using the Cluster:*
Mark Hymers will be running a session this Thursday on how to use the
cluster at YNiC. We encourage users to attend if they are unfamiliar with
how to send jobs to the cluster for processing. The session will be held
at *4pm on Thursday 10th October in YNiC open plan*.
*Remote Desktop:*
We have made some configuration changes to the remote desktop, so if you
are experiencing any issues please follow these steps on the wiki:
https://www.ynic.york.ac.uk/docs/ITPages/RemoteDesktop#FAQ_and_errors
Please note that you must be connected to the University of York VPN, and
should also have followed the latest remote desktop server setup guidelines
(https://www.ynic.york.ac.uk/docs/ITPages/RemoteDesktop).
*YNiC User Inductions:*
Hopefully everyone that needed an induction was able to attend the two
large sessions we put on last week, but if there are any other
students/staff that will require an IT account for YNiC, our next induction
date will be Wednesday 30th October at 2pm. Please ask them to contact
support(a)ynic.york.ac.uk to sign up.
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
Hello everyone,
Next week on Monday is the next meeting of the YNIC Science committee.
Please let me know if there is any issues you would like me to raise with
the other members.
Thanks
Jonny
--
Jonathan Smallwood, Professor in Psychology / Cognitive Neuroscience
Room E008, Department of Psychology, University of York, England. YO10 4PH.
Telephone: 01904 324651
Dear all,
Over this term, Open plan will be used for teaching on a number of
occasions. We will be asking everyone who is not taking part in the
class to leave the open plan area at these times.
The times for this term are:
Week 1:
Thursday 3rd October: 0900-1300
Friday 4th October: 0900-1300
Week 2:
Tuesday 8th October: 1200-1600
Week 4:
Tuesday 22nd October: 1200-1600
Week 7:
Tuesday 12th November: 1200-1600
Week 9:
Tuesday 26th November: 1200-1600
These times can be found on the University timetable
http://www.york.ac.uk/viewtimetables
by choosing YNiC as the room and clicking "View Room"
Thanks,
Mark
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
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
