Hi all,
There will be some disruptive building work in the MRI corridor next week
(w/c 2nd Oct). The Siemens scanner will be up and running, data quality
will not be affected, and the Siemens control room will not be affected.
However, the work may be noisy in the MRI corridor at times and
participants will have to walk past construction barriers to access the
SIemens scanner. Please bear this in mind when booking any scans next week.
If you already have slots booked for next week, you can keep them as is, or
let us know if you would prefer and we will remove them free of charge in
this instance.
Thanks
Becky
--
Rebecca Lowndes
Research Technician
York Neuroimaging Centre
Hello,
Don't forget our new semester of seminars kicks off today at 4pm with two
exciting talks!
We will be hearing from Dr Lauren Welbourne with a short talk titled
"*Measuring
binocular combination of luminance and chromatic stimuli using fMRI"* and
Dr David Watson with a talk titled *"Mapping the connectivity of the scene
network in the human brain"* (see abstract below).
We really hope to see everyone at YNiC! The talks will take place *today
(Thursday the 28th) at 4pm*. If you are unable to attend the talk in
person, you can catch it on zoom using the following link:
https://york-ac-uk.zoom.us/j/96762553290?pwd=UEluT1lMd3V5azY5YzNmWkJCV1VTdz…
<https://www.google.com/url?q=https://york-ac-uk.zoom.us/j/96762553290?pwd%3…>
.
We look forward to seeing you then!!
Many thanks,
Becky
*Dr David Watson*
*Mapping the connectivity of the scene network in the human brain*
The perception of places has been linked to a network of scene-selective
regions in the human brain (OPA: occipital place area; PPA: parahippocampal
place area; RSC: retrosplenial complex). However, the connectivity of these
regions to each other and the rest of the brain remains poorly understood.
Here, we measured the functional and structural connectivity of the scene
network. Functional connectivity, measured at rest and during movie
watching, revealed a bias between posterior and anterior scene regions that
have been implicated in perceptual versus mnemonic aspects of scene
perception. For example, OPA and posterior PPA showed greater connectivity
with visual and dorsal attention networks, which may play a role in the
visual representation of scenes. In contrast, anterior PPA and RSC showed
preferential connectivity with default-mode and frontoparietal control
networks and the hippocampus, which may reflect our memory for places. We
also measured the structural connectivity of the scene network using
diffusion tractography. This indicated both similarities and differences
with the functional connectivity, highlighting distinctions between
posterior and anterior but also ventral and dorsal scene regions. These
findings provide a map of the connectivity of the scene network, informing
possible roles for scene-selective regions in brain function and human
behaviour.
--
Rebecca Lowndes
Research Technician
York Neuroimaging Centre
Hello,
We have a new semester of YNiC Seminars kicking off this week!!
We will be hearing from Dr Lauren Welbourne with a short talk titled
"*Measuring
binocular combination of luminance and chromatic stimuli using fMRI"* and
Dr David Watson with a talk titled *"Mapping the connectivity of the scene
network in the human brain"* (see abstract below).
We really hope to see everyone at YNiC! The talks will take place *tomorrow
(Thursday the 28th) at 4pm*. If you are unable to attend the talk in
person, you can catch it on zoom using the following link:
https://york-ac-uk.zoom.us/j/96762553290?pwd=UEluT1lMd3V5azY5YzNmWkJCV1VTdz…
<https://www.google.com/url?q=https://york-ac-uk.zoom.us/j/96762553290?pwd%3…>
.
We look forward to seeing you then!!
Many thanks,
Jennifer
*Dr David Watson*
*Mapping the connectivity of the scene network in the human brain*
The perception of places has been linked to a network of scene-selective
regions in the human brain (OPA: occipital place area; PPA: parahippocampal
place area; RSC: retrosplenial complex). However, the connectivity of these
regions to each other and the rest of the brain remains poorly understood.
Here, we measured the functional and structural connectivity of the scene
network. Functional connectivity, measured at rest and during movie
watching, revealed a bias between posterior and anterior scene regions that
have been implicated in perceptual versus mnemonic aspects of scene
perception. For example, OPA and posterior PPA showed greater connectivity
with visual and dorsal attention networks, which may play a role in the
visual representation of scenes. In contrast, anterior PPA and RSC showed
preferential connectivity with default-mode and frontoparietal control
networks and the hippocampus, which may reflect our memory for places. We
also measured the structural connectivity of the scene network using
diffusion tractography. This indicated both similarities and differences
with the functional connectivity, highlighting distinctions between
posterior and anterior but also ventral and dorsal scene regions. These
findings provide a map of the connectivity of the scene network, informing
possible roles for scene-selective regions in brain function and human
behaviour.
--
Jennifer Ashton, PhD
Senior Research Technician
York Neuroimaging Centre
Working days: Monday, Tuesday and Wednesday
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
