Hello All,
This weeks seminar is 'How to apply to use the centre'. This will be
relevant to all newbies, but will also give an overview of updates that are
in the pipeline that will affect all applicants.
In other news we are continuing with our programme of training for
operators of the Siemens and GE scanners.
Best wishes
Tony
Tip of the week:
At the command line you can type
ls > list.txt
it will generate a text file of the files and directories in the current
directory (as long as you have write permissions in the current directory)
ls *is the 'list' command*
> *allows the output of the ls command to be redirected to a file*
mylist.txt * is the file name you supply to capture the output of the ls
command*
Why is this useful? The generation of a file that lists directories or
files can be useful when you are writing scripts to perform analysis on
multiple directories or files.
Note that this help with ls can be obtained by typing
man ls
--
Antony Morland, PhD.
Director, York Neuroimaging Centre
Department of Psychology, University of York, York YO10 5DD, UK.
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.
