Hi all
If you have a YNiC door fob that you no longer require, we would
appreciate them being returned so that we can reuse them. They can
either be returned to YNiC directly or you could return them to
Psychology reception and they can forward them to us by internal mail.
Best wishes
Jackie
Jackie Mayhew
York Diagnostic Imaging
The BioCentre
York Science Park
Heslington
York
YO10 5NY
Hi All,
I am writing to remind everyone that, following our recent operating system
upgrade,* it is important to check that your stimuli scripts are running as
intended before resuming scanning*. There are testing PCs available in YNiC
for this purpose, and in many cases we can help to resolve issues you might
have difficulties with.
*Psychopy users*
Our testing has highlighted that *some psychopy scripts will be susceptible
to inaccurate timing* issues with the new psychopy version (2023.2.0).
We now strongly recommend that when initialising your visual window you set
waitBlanking=False, or that you ensure your script runs at 120 Hz, and the
monitor is adjusted accordingly using the Applications>>Settings>>Display
menu.
In addition, the event.getkeys() function is deprecated, an example update
to fix this can be found here:
https://wiki.pages.ynic.york.ac.uk/IT/summer_2023_upgrade.html#psychopy
Please remember that it is your responsibility to thoroughly test your
stimuli scripts and ensure that everything is working as intended.
Cheers,
Rich
--
Dr Richard Aveyard
Senior Technical Specialist
York NeuroImaging Centre
University of York, UK
Hello,
Please find details about Open Plan availability and the next inductions
and training sessions.
*Open Plan Availability*
MSc inductions will be taking place at YNiC this *Friday (22nd of
September) 13:00 - 15:00*. Due to the number of students attending, Open
Plan will not be available to users during this time.
*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 *Friday the 13th of October, 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 *Friday
the 20th of October, 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.
*YNiC Seminar*
If you would like to give a talk at our YNiC seminar, 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.
Many thanks,
Jennifer
--
Jennifer Ashton, PhD
Senior Research Technician
York Neuroimaging Centre
Working days: Monday, Tuesday and Wednesday
Dear All,
As you know, most of the imaging data we collect at YNIC is potentially
biometric. As well as making sure we have appropriate consent from
participants, we have to abide by certain legislative requirements relating
to collecting, storing and sharing personal data. We've put in place some
procedures to make things easier. What you need to know is summarised below
and there's a diagram attached (it contains the same information but with
boxes and arrows!) Any questions, please ask.
Please also be aware that we have a new page for YNIC forms
<https://www.york.ac.uk/psychology/research/york-neuroimaging-centre/forms/>,
where you will find new versions of the participant information sheet and
study-specific consent form (we're now on version 9 for both).
Best wishes,
Fiona and Andre
*Collecting data at YNIC and keeping it at YNIC*
- Before submitting your ethics application, you need to check whether your
study needs a separate *Data Protection Impact Assessment (DPIA)*, or
whether it is covered by DPIA_183 v2
<https://vcs.ynic.york.ac.uk/ynic-public/forms/-/raw/master/YNICDPIA183.pdf>
(found on the new YNIC forms webpage
<https://www.york.ac.uk/psychology/research/york-neuroimaging-centre/forms/>).
If it is not covered by DPIA_183 v2, there's a DPIA screening tool here
<https://www.york.ac.uk/records-management/dp/dataprivacyimpactassessments/>
.
- If it is covered by DPIA_183 v2
<https://vcs.ynic.york.ac.uk/ynic-public/forms/-/raw/master/YNICDPIA183.pdf>,
make sure you follow the procedures outlined in that document.
- Make sure everyone with access to the data has signed and submitted
the *Appropriate
Data Usage Declaration*
<https://vcs.ynic.york.ac.uk/ynic-public/forms/-/raw/master/AppropriateDataU…>
.
*Bringing into YNIC data that were collected elsewhere*
- You will need to complete and submit your own DPIA, but we have had one
of these approved already, so contact Andre and he will provide you with a
template.
- If there are any agreements to sign, you will need to get HOD approval
before signing.
*Transferring data collected at YNIC to external collaborators*
- You will need to complete and submit your own DPIA, but we have had one
of these approved already, so contact Andre and he will provide you with a
template.
- You will also need an external collaborator agreement. We have had one
approved already. Andre can provide a template and let you know the
procedure for obtaining approval from the HOD and the contracts office.
- Make sure everyone with access to the data has signed and submitted
the *Appropriate
Data Usage Declaration*
<https://vcs.ynic.york.ac.uk/ynic-public/forms/-/raw/master/AppropriateDataU…>
.
*Transferring data collected at YNIC to former staff or students*
- You will need to complete and submit your own DPIA, but we have had one
of these approved already, so contact Andre and he will provide you with a
template. (It's the same template as used for sharing data with external
collaborators).
- You will also need a data sharing agreement. This is not the same as the
one used for external collaborators. We'll have a template soon, which
Andre will be able to provide. The procedure for obtaining approval from
the HOD and the contracts office will be the same.
- Make sure everyone with access to the data has signed and submitted
the *Appropriate
Data Usage Declaration*
<https://vcs.ynic.york.ac.uk/ynic-public/forms/-/raw/master/AppropriateDataU…>
.
*Making data collected at YNIC publicly available* (many thanks to Angela
for this)
- Make sure that this is covered by DPIA_183 v2
<https://vcs.ynic.york.ac.uk/ynic-public/forms/-/raw/master/YNICDPIA183.pdf>
and you abide by the procedures outlined in that document. This includes
making sure you use version 9 of the information sheet
<https://www.york.ac.uk/psychology/research/york-neuroimaging-centre/forms/>and
version 9 of the consent form
<https://www.york.ac.uk/psychology/research/york-neuroimaging-centre/forms/>.
There is a guidance document here
<https://vcs.ynic.york.ac.uk/ynic-public/forms/-/raw/master/Open_Data_Sharin…>
.
- If it is not covered by DPIA_183 v2, you will need to complete and submit
your own DPIA
<https://www.york.ac.uk/records-management/dp/dataprivacyimpactassessments/>
.
Hello,
Please find details about Open Plan availability, the next inductions and
training sessions and an upcoming workshop.
*Open Plan Availability*
MSc inductions will be taking place at YNiC on *Friday the 22nd of
September, 13:00 - 15:00*. Due to the number of students attending, Open
Plan will not be available to users during this time.
*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 21st of September, at 10:00*. 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 *Tuesday
the 19th 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.
*YNiC Seminar*
If you would like to give a talk at our YNiC seminar, 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.
*Upcoming Workshops*
The first *Environmental Impacts of Computing in Health & Life Sciences
Research workshop <https://www.eicworkshop.info/> *will be taking place on
November 7th in London, and online. This will be a great opportunity to
learn about the carbon footprint of high-performance computing, in
neuroimaging research and beyond. Find more information on the workshop
website <https://www.eicworkshop.info/>, and register for attendance here
<https://www.tickettailor.com/events/universityofsussex/986909>.
Many thanks,
Jennifer
--
Jennifer Ashton, PhD
Senior Research Technician
York Neuroimaging Centre
Working days: Monday, Tuesday and Wednesday
Good Morning
The cluster is now back up and online.
The upgrade has now been completed. There are a few small changes to some
software packages so please check the upgrade notes wiki page if you have
any queries.
https://wiki.pages.ynic.york.ac.uk/IT/summer_2023_upgrade.html
Any other issues not covered in the wiki page, please email
support(a)ynic.york.ac.uk.
Thanks
Joe
--
Joe Lyons, UNIX Systems Administrator
York Neuroimaging Centre (YNiC), University of York
The remote desktops are now stable. We're still waiting on a few jobs
running on the cluster before it's available for use.
Thanks
Joe
--
Joe Lyons, UNIX Systems Administrator
York Neuroimaging Centre (YNiC), University of York
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
--
You received this message because you are subscribed to the Google Groups
"FLEXSEM" group.
To unsubscribe from this group and stop receiving emails from it, send an
email to flexsem-group+unsubscribe(a)york.ac.uk.
To view this discussion on the web, visit
https://groups.google.com/a/york.ac.uk/d/msgid/flexsem-group/CACz3qpZwiMMdG…
<https://groups.google.com/a/york.ac.uk/d/msgid/flexsem-group/CACz3qpZwiMMdG…>
.
--
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
Hi all,
Don't forget to come down to YNiC for our seminar presented by Professor
Micah Murray.
Micah is the Scientific and Academic Director of the Sense Innovation and
Research Center, Lausanne, Switzerland and section head, EEG CHUV-UNIL at
the Center for Biomedical Imaging. At noon he will be giving a talk on
recent work he has been doing on high spatial- and temporal-resolution fMRI
and also on recent advances in EEG.
*12 Noon, Weds 19th July, at YNiC*
*Title: "From old dogs to new tricks in human EEG and fMRI"*
Some links are provided to give you more background:
Micah Murray (
https://www.unil.ch/line/en/home/menuinst/people/micah-m-murray.html)
Rapid fMRI (
https://www.biorxiv.org/content/10.1101/2023.05.13.540663v2.abstract)
EEG (https://link.springer.com/article/10.1007/s10548-021-00882-w).
It would be really great if you could come over to YNiC to attend the talk.
Many thanks,
Becky
--
Rebecca Lowndes
Research Technician
York Neuroimaging Centre
Hi Everyone,
Tomorrow we are fortunate to be hosting Professor Micah Murray at YNiC.
Micah is the Scientific and Academic Director of the Sense Innovation and
Research Center, Lausanne, Switzerland and section head, EEG CHUV-UNIL at
the Center for Biomedical Imaging. At noon he will be giving a talk on
recent work he has been doing on high spatial- and temporal-resolution fMRI
and also on recent advances in EEG.
*12 Noon, Weds 19th July, at YNiC*
*Title: "From old dogs to new tricks in human EEG and fMRI"*
Some links are provided to give you more background:
Micah Murray (
https://www.unil.ch/line/en/home/menuinst/people/micah-m-murray.html)
Rapid fMRI (
https://www.biorxiv.org/content/10.1101/2023.05.13.540663v2.abstract)
EEG (https://link.springer.com/article/10.1007/s10548-021-00882-w).
It would be really great if you could come over to YNiC to attend the talk.
We look forward to seeing you then!
Many thanks,
Jennifer
--
Jennifer Ashton, PhD
Senior Research Technician
York Neuroimaging Centre
Working days: Monday, Tuesday and Wednesday
Dear Users,
Unfortunately there has been a fault with the Siemens MRI scanner over the
weekend. We are working to get this fixed as soon as possible, but will be
unable to run any scans in the meantime.
We will keep you updated.
Many thanks,
Jennifer
--
Jennifer Ashton, PhD
Senior Research Technician
York Neuroimaging Centre
Working days: Monday, Tuesday and Wednesday
Dear all,
Next Wednesday (19th July) we are fortunate to be hosting Professor Micah
Murray at YNiC. Micah is the Scientific and Academic Director of the Sense
Innovation and Research Center, Lausanne, Switzerland and section head, EEG
CHUV-UNIL at the Center for Biomedical Imaging. At noon he will be giving a
talk on recent work he has been doing on high spatial- and
temporal-resolution fMRI and also on recent advances in EEG.
12 Noon, Weds 19th July, at YNiC
Title: "From old dogs to new tricks in human EEG and fMRI"
Some links are provided to give you more background:
Micah Murray (
https://www.unil.ch/line/en/home/menuinst/people/micah-m-murray.html)
Rapid fMRI (
https://www.biorxiv.org/content/10.1101/2023.05.13.540663v2.abstract)
EEG (https://link.springer.com/article/10.1007/s10548-021-00882-w).
All are welcome to come along
Thanks,
Becky
--
Rebecca Lowndes
Research Technician
York Neuroimaging Centre
Hi all,
As many of you will have noticed, the Siemens scanner was blocked out for
use next week for the removal of GE. This work has now been postponed, so
we have released the scanner for booking next week. We are not able to
provide operator cover, as we have already committed to covering MEG, but
if you are able to operate yourselves, please go ahead and book.
Apologies for the late notice and any inconvenience caused
Thanks
Becky
--
Rebecca Lowndes
Research Technician
York Neuroimaging Centre
Hello,
Please find details about submitting poster abstracts to this year's
MEG-UKI meeting below. You can find more information about the meeting
here https://meguk.ac.uk/meg-uki-2023-conference/
Many thanks,
Jennifer
--
Jennifer Ashton, PhD
Senior Research Technician
York Neuroimaging Centre
Working days: Monday, Tuesday and Wednesday
---------- Forwarded message ---------
From: Redmond O'Connell <REOCONNE(a)tcd.ie>
Date: Fri, Jun 23, 2023 at 2:54 PM
Subject: poster abstracts for MEG-UKI
Hi all,
Just a very quick word. Places are filling up nicely for the MEG-UKI
meeting but we haven't had a lot of poster abstract submissions as yet.
Please do encourage your labs and colleagues to submit something (not
obligatory that there be MEG data involved specifically). We understand
that some are not ready to commit to an abstract just yet so please note
that *we're happy for people to register now and submit a poster abstract
later on* through the conference e-mail address (meguki2023(a)gmail.com) with
the deadline for the abstracts being 1st August.
All the best
Redmond
Hi all,
I am sorry to report that due to coolant leak the MRI scanner is offline
for the rest of today, all day tomorrow (Tues 20th) and possibly Wed 21st.
We have diagnosed the problem but it will take a while to ship the parts
for repair from Germany - this could happen today but may only happen
tomorrow.
If you have the scanner booked on tomorrow Tues 20th you will need to
reschedule. If you have the scanner booked on Wed / Thu you may want to
let your participants know that there may be a cancellation, but we are
hopeful to be back online.
We will update you as soon as we have any further information.
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,
We have a system fault with the Siemens MRI scanner at YNiC, as such the
scanner will be down for the rest of the day. We are working to get this
fixed and we will keep you updated on our progress.
Many thanks,
Jennifer
--
Jennifer Ashton, PhD
Senior Research Technician
York Neuroimaging Centre
Working days: Monday, Tuesday and Wednesday
