Hello All,
Quite a few things this week:
1) IMPORTANT: Our MRI screening safety screening forms have been updated.
The updates are explained in our revised local rules.
2) A reminder: Our training documentation (including the local rules
referred to above) is held at the following URL https://www.ynic.york.ac.uk/
docs/forms. A login in required to access the URL.
3) Last weeks seminar, which was postponed, will go ahead this week and
will follow the project presentation by Shogo Kajimura entitled '*Decoding
contents of mind wandering'*. The seminar series details can be found
here: https://www.ynic.york.ac.uk/events/thursday-sessions#preview
4) We are currently training 14 operators at YNiC.
Best wishes
Tony
*Tip of the week*
You can control the transparency of your overlays in *fslview *by using the
blue transparency slider located a the bottom right of the window - see
attached
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
HI all,
The GE engineer has attended and diagnosed the fault with the system. A
replacement part is required for the Oxygen monitor to work correctly.
This part is on express order and we hope to have it installed tomorrow,
although it is unclear at what point in the day this will be.
We are hoping that normal scanning service will resume by Wednesday
(11th), but please keep alert for further updates which we will send
once we have more information.
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
Hi all,
I am afraid to report that a sensor fault has developed on the GE
system over the weekend. This sensor monitors the safe oxygen level in
the MRI environment, and thus the scanner cannot be used until the fault
is fixed.
GE have said the will attend on Monday AM - we hope to have the scanner
up and running as soon as possible. Sorry for those affected by the
scanner downtime.
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
Hello all,
We are still looking for posters to put up around YNiC open plan. If you would like to contribute one, please get in touch or drop it off at YNiC.
Best wishes,
Dave
Hi all,
Due to some unforeseen circumstances we have to postpone today's seminar
- We will reschedule and update you in next week's update bulletin.
Best wishes,
--
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
Hello all,
We are holding the next meeting of the YNIC Science Committee next Monday.
Please send any items you would like me to raise by Thursday so I can add
them to the agenda.
Thanks
Jonny
--
Jonathan Smallwood, Reader in Psychology / Cognitive Neuroscience
Room C023, Department of Psychology, University of York, England. YO10 4PH.
Telephone: 01904 324651
Hello All,
We have a Heating and Cooling contractor in attendance today. Alarms may
sound. Apologies if they disrupt your work. If an alarm does and stops
within 30s there is no need to act. Please be aware that staff may need to
ask you to leave at short notice.
Thanks
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Hello All,
Two things this week
1) The will be a seminar held in the Chemistry Department this week that
may interest users:
Dr Luisa Ciobanu: Functional MRI at ultra-high magnetic fields
Wednesday 4th October 13.00-14.00
In room Chemistry/B101
Abstract
Despite the fact that BOLD-fMRI is routinely used to map brain activity and
connectivity in preclinical and clinical settings its exact relation with
the underlying microscopic changes, either vascular or neuronal, is still
not fully elucidated. The development of high magnetic fields promise
substantial improvements in the contrast to noise ratio and the spatial
resolution with which functional MRI maps are acquired possibly allowing
the comparison with other, microscopic, techniques.
In the first part of my talk I will review the advantages, but also the
challenges, imposed by imaging at ultra-high magnetic fields. Following
this, I will present recent results demonstrating that BOLD fMRI faithfully
reports microvascular hyperemia, and that the detection of the smallest
neuronal activation is limited only by its sensitivity.
Beside improved BOLD acquisitions, high magnetic fields allow the
development of other alternative ways for studying neuronal activation. In
the last part of my presentation, I will describe a novel metabolic imaging
approach, based on Chemical Exchange Saturation Transfer (CEST), for
assessing the changes induced by neuronal stimulation in rat brains at
17.2T. Specifically, I will present images acquired under
glucose-sensitizing conditions showing a significant negative contrast that
highlights the same brain regions as those activated in conventional BOLD
maps.
2) We are to give 'Tips of the week', hopefully, as the name suggests on a
weekly basis. This will largely give advice on IT tricks and work-arounds
for commonly occurring analysis tasks. Here's this week's:
Scenario: You've submitted a load of jobs to the cluster which you find out
will be of no use to you and you want to bring them to a halt.
Solution
typing: qdel -u <username> into a terminal will stop all cluster jobs
submitted by that user, e.g.
qdel -u ddc506
Best wishes
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
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
Hi all,
No presentations this week, but the centre will be busy with the MSc CN
project hand in deadline looming.
Please note:
* CENTRE CLOSURE Tuesday 21st - Friday 24th August. - A reminder that we
are closed for part of next week for system upgrades.
* RETURN OF SCREENING/CONSENT FORMS: With the reception works complete,
please return all signed screening / general consent forms to the gray
postbox next to the reception office door if the office is closed.
* CENTRE ACCESS AND ALARMS: Keyholders should be aware that the main
reception alarm will now be set when the centre is closed. If you are
the first to enter, you will need to deactivate the alarm before opening
the main shutter to the reception area. This alarm is in the cupboard
immediately next to the key that opens the shutter. The alarm code is
the same for all areas. -- If you have any queries please see a member
of the team.
--
André
************************************************************************
André Gouws
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,
No project presentations this week, so just a couple of reminders:
* Reception services are back to normal at YNiC - please use the normal
YNiC entrance again.
* The servicing of the GE scanner was successful so we should be back up
to "full speed" now.
* ** DATES FOR YOUR DIARY ** - a reminder that the YNiC IT systems
upgrade is scheduled for the week commencing Monday the 21st of August.
There will be no scanning or access to computing facilities during that
week. We will let you know if anything changes.
--
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,
Thank you for your patience and cooperation during the remodeling of the
YNiC reception area. A few minor cosmetic issues aside, the work is now
completed and we can start to use the reception area as just that!
Please enter and leave YNiC via this area from now on rather than the
Biocentre entrance, and instruct anyone taking part in your studies to
do so too.
Best wishes,
--
André
************************************************************************
André Gouws
York Neuroimaging Centre
University of York
The Biocentre
York Science Park
Heslington
YO10 5NY
Tel: +44 (0) 1904 435327
Fax: +44 (0) 1904 435356
A reminder that Richard Vernon will be giving a project presentation at
4pm today: "Curvature and angular-position shape manipulations".
--
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,
* Please join us at YNiC this Thursday at 4pm where there will be a
project presentation by Richard Vernon entitled "Curvature and
angular-position shape manipulations".
* Thank you for you patience as the improvement works on the new
reception area continue - we are awaiting the installation of some glass
panels and then normal service will resume. Until further notice, please
do continue to use the Biocentre entrance.
* GE Scanner service: Some components of the image reconstruction
hardware on the GE scanner are showing a fault and will need to be
replaced on Thursday afternoon - the scanner is still in use and should
perform normally for most users - just be aware that there may be a
slightly longer delay between scans as the images are processed.
Best wishes,
--
André
************************************************************************
André Gouws
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,
Pleas note the centre will be closed for all research scanning and analysis
from 5pm, Monday 21st August until the end of the week. This is to upgrade
our IT provision and perform annual maintenance.
Best wishes
Tony
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
Hi all,
* Please join us at YNiC this Thursday at 4pm where there will at least
2 project presentations from the Smallwood / Jefferies Labs:
"Understanding the gridlike encoding of associative information" -
Deniz Vatansever
"Understanding the neural basis of spontaneous thought" - Charlotte
Murphy
"TBC" - Jonny Smallwood *
* Work on the YNiC reception continues this week, and we hope to resume
service as usual ASAP. We will keep you updated but, for now, please
continue to use the Biocentre entrance.
--
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
