Hi,
We've added Matlab 7.12 (R2011a) to the YNiC systems. The default has
not yet changed and remains 7.10 (R2010a). Details of the supported
versions are at:
https://www.ynic.york.ac.uk/doc/ITPages/FAQ/Misc/SupportedVersions#Matlab
At the same time, we've updated SPM8 to the latest revision which is
8+svn4290.
Can people please test the new Matlab version as we'll change the
default in September unless any major issues are found. We'll also be
looking to withdraw Matlab 7.8 in September (as previously announced) as
part of a major set of software upgrades. More on this later.
Thanks,
Mark
--
Mark Hymers
York Neuroimaging Centre
Dear Users
Today (4-5 pm in YNiC) there will be a project proposal presentation by
Carin Whitney. The title of the project is "Investigating semantic
cognition with MEG, fMRI and TMS". Please see below for the talk abstract.
Everyone is welcome to attend and refreshments will be provided after
the talk.
Best wishes
Rebecca
Abstract:
Beth Jefferies, Carin Whitney, Piers Cornelissen and Andy Ellis
This project investigates how semantic cognition – referring to our
ability to understand the meaning of words, pictures, faces, sounds, and
smells – is represented in the brain. We will focus on semantic control,
which is one of two principal components of semantic cognition and
relates to executive mechanisms that enable us to retrieve and select
conceptual knowledge according to the current task or context.
Research has been plentiful in describing the spatial extent of the
brain regions that underpin semantic control, and has identified a
distributed fronto-temporo-parietal network. However, it remains largely
unknown how this system is organised (i.e., what the specific functions
of each component are) and how well they interact. In the proposed
project, we will apply a novel approach to investigate these questions
by combining MEG with TMS and fMRI. In particular, we will use MEG to
track neural activity, allowing us to generate predictions about likely
patterns of communication within the semantic control network and its
relation to other components of semantic cognition (i.e., brain areas
that encode conceptual knowledge). Follow-up TMS will then be used to
impair brain functioning at specific time points to prove causality.
Equivalent fMRI data – taken from the same participants and tasks – will
guide coil positioning for TMS and act as a spatial localiser for MEG.
The project hence aims to establish a neural model of semantic cognition
that is based on convergent evidence across different methods,
generating potentially strong conclusions about how meaning retrieval is
achieved.
--
************************************************************************
Dr. Rebecca E. Millman
Science Liaison Officer
York Neuroimaging Centre
The Biocentre
York Science Park
Heslington
YO10 5DG
Tel: +44 (0) 1904 567614
Fax: +44 (0) 1904 435356
Dear Users
This Thursday (4-5 pm in YNiC) there will be a project proposal
presentation by Carin Whitney. The title of the project is
"Investigating semantic cognition with MEG, fMRI and TMS". Please see
below for the talk abstract.
Everyone is welcome to attend and refreshments will be provided after
the talk.
Best wishes
Rebecca
Abstract:
Beth Jefferies, Carin Whitney, Piers Cornelissen and Andy Ellis
This project investigates how semantic cognition – referring to our
ability to understand the meaning of words, pictures, faces, sounds, and
smells – is represented in the brain. We will focus on semantic control,
which is one of two principal components of semantic cognition and
relates to executive mechanisms that enable us to retrieve and select
conceptual knowledge according to the current task or context.
Research has been plentiful in describing the spatial extent of the
brain regions that underpin semantic control, and has identified a
distributed fronto-temporo-parietal network. However, it remains largely
unknown how this system is organised (i.e., what the specific functions
of each component are) and how well they interact. In the proposed
project, we will apply a novel approach to investigate these questions
by combining MEG with TMS and fMRI. In particular, we will use MEG to
track neural activity, allowing us to generate predictions about likely
patterns of communication within the semantic control network and its
relation to other components of semantic cognition (i.e., brain areas
that encode conceptual knowledge). Follow-up TMS will then be used to
impair brain functioning at specific time points to prove causality.
Equivalent fMRI data – taken from the same participants and tasks – will
guide coil positioning for TMS and act as a spatial localiser for MEG.
The project hence aims to establish a neural model of semantic cognition
that is based on convergent evidence across different methods,
generating potentially strong conclusions about how meaning retrieval is
achieved.
--
************************************************************************
Dr. Rebecca E. Millman
Science Liaison Officer
York Neuroimaging Centre
The Biocentre
York Science Park
Heslington
YO10 5DG
Tel: +44 (0) 1904 567614
Fax: +44 (0) 1904 435356
Dear Users
Today (4-5 pm in YNiC) there will be a talk by Prof. Peter Redgrave from
the University of Sheffield.
http://www.sheffield.ac.uk/psychology/staff/academic/peter-redgrave
The title of Prof. Redgrave's talk is "Goal-directed and habitual
control in the basal ganglia: implications
for Parkinson's disease". Please see below for the talk abstract.
Everyone is welcome to attend and refreshments will be provided after
the talk.
Best wishes
Rebecca
Abstract:
Progressive loss of the ascending dopaminergic projection in the basal
ganglia is a fundamental pathological feature of Parkinson’s disease.
Studies in animals and humans have identified spatially segregated
functional territories in the basal ganglia for the control of
goal-directed and habitual actions. In patients with Parkinson’s disease
the loss of dopamine is predominantly in the posterior putamen, a region
of the basal ganglia associated with the control of habitual behaviour.
These patients may therefore be forced into a progressive reliance on
the goal-directed mode of action control that is mediated by
comparatively preserved processing in rostro-medial striatum. Thus, in
addition of the loss of habits, the behavioural difficulties of
Parkinson patients may also be subject to distorting output signals from
habitual control circuits which impede the expression of goal-directed
action.
--
************************************************************************
Dr. Rebecca E. Millman
Science Liaison Officer
York Neuroimaging Centre
The Biocentre
York Science Park
Heslington
YO10 5DG
Tel: +44 (0) 1904 567614
Fax: +44 (0) 1904 435356
Dear Users
This Thursday (4-5 pm in YNiC) there will be a talk by Prof. Peter
Redgrave from the University of Sheffield.
http://www.sheffield.ac.uk/psychology/staff/academic/peter-redgrave
The title of Prof. Redgrave's talk is "Goal-directed and habitual
control in the basal ganglia: implications
for Parkinson's disease". Please see below for the talk abstract.
Everyone is welcome to attend and refreshments will be provided after
the talk.
Best wishes
Rebecca
Abstract:
Progressive loss of the ascending dopaminergic projection in the basal
ganglia is a fundamental pathological feature of Parkinson’s disease.
Studies in animals and humans have identified spatially segregated
functional territories in the basal ganglia for the control of
goal-directed and habitual actions. In patients with Parkinson’s disease
the loss of dopamine is predominantly in the posterior putamen, a region
of the basal ganglia associated with the control of habitual behaviour.
These patients may therefore be forced into a progressive reliance on
the goal-directed mode of action control that is mediated by
comparatively preserved processing in rostro-medial striatum. Thus, in
addition of the loss of habits, the behavioural difficulties of
Parkinson patients may also be subject to distorting output signals from
habitual control circuits which impede the expression of goal-directed
action
--
************************************************************************
Dr. Rebecca E. Millman
Science Liaison Officer
York Neuroimaging Centre
The Biocentre
York Science Park
Heslington
YO10 5DG
Tel: +44 (0) 1904 567614
Fax: +44 (0) 1904 435356
Hi,
We have just pushed some core changes to the YNiC NAF Beamforming code.
The change is that nafEpochRejection will no longer produce what have
become known as "Epoch Rejection Files" but will instead produce "Slice
Rejection Files".
"Epoch Rejection File" are simply a list of epochs of data which should
be rejected during analysis due to artifacts. This can be problematic,
as if you change your pre-trigger or epoch duration, the timings of the
epochs will move around and you will reject data you didn't mean to,
whilst not rejecting the data around your artifacts.
The replacement for these are "Slice Rejection Files". These are a list
of slice ranges containing bad data - simply a list of comma separated
slice ranges; one per line.
The analysis (beamformer) code itself will continue to accept Epoch
Rejection Files which are listed in YAML files for analysis, but will
produce "Deprecation Warnings" to remind you that you should consider
converting.
If you wish to convert an existing Epoch Rejection File to a Slice
Rejection File, you can do one of the following:
* Use the nafEpochRejectToSliceReject tool (documented at
/mnt/common/naf/naf-doc/userref/scripts/nafEpochRejectToSliceReject.html )
* Load the Epoch Rejection file into nafEpochRejection using the -e
flag and it will output a slice rejection file.
* Load you study into the Study Definer Tool (nafStudyDefiner) and it
will offer to convert all epoch rejection files into slice rejection
files and update the YAML file for you at the same time.
Although the nafEpochRejection and nafStudyDefiner tool will still read
Epoch Rejection Files (to perform conversions), they will no longer
allow you to edit or output them; they will only work with and output
slice rejection files.
It should be noted that internally, all of the code now converts Epoch
Rejection Files to Slice Rejection Files. This means that strictly
speaking, if you have overlapping epochs, a single epoch number in an
epoch rejection may now result in more than one epoch being rejected.
This should be a rare corner case and if you want to fully understand
and see what is going on, you can use the nafShowEpochs tool to list the
epochs you have and, if a epoch or slice rejection file is present in your
YAML file, whether or not they will be rejected.
This is one of the final big changes before we make the NAF tools
available by default on the system. More on that soon.
Thanks,
Mark
--
Mark Hymers
York Neuroimaging Centre
Dear all,
We need to reboot the main fileservers at YNiC over the weekend, most
likely on Saturday. Can I therefore ask that people log off at the end
of Friday and do not leave jobs running on the cluster which will
continue beyond Saturday morning - any jobs running at that point will
be cancelled.
This does not affect the Psychology email server.
Thanks,
Mark
--
Mark Hymers
York Neuroimaging Centre
FYI
-------------------------------
Dear colleagues,
please find below two separate announcements for open positions
in our research team.
Kind regards,
Alfons Schnitzler & Katja Biermann-Ruben
/**********************************************************************/
PhD Position in Düsseldorf
A *PhD position* is available at the Institute of Clinical Neuroscience
and Medical Psychology, Heinrich-Heine-University Düsseldorf, to study
neural representations of action related concepts.
The successful candidate will be expected to work within the
interdisciplinary collaborative research center (CRC/SFB 991) "The
Structures of Representation in Language, Science and Cognition"
starting July 2011. Within this linguistic CRC and on the theoretical
basis of embodiment and the mirror neuron system our neuroscientific
project investigates the functional relevance of the motor cortex for
conceptual representation of verbs and nouns which derived from action
verbs. Methods will be non-invasive 306-channel MEG, TMS and behavioural
priming.
Successful candidates will have a MSc in psychology, neuroscience or
related fields and are highly motivated to learn MEG and TMS measurement
and data analysis. Preference will be given to candidates with
experimental practice.
We offer a stimulating and inspiring atmosphere in a young,
interdisciplinary team of neurologists, psychologists, physicists, and
biologists.
The position is for an initial period of two years but may be extended.
Earliest start for the position is July 2011. Applications will be
accepted until the position is filled.
To apply, please send a full CV, a brief outline of current research and
interests, certificates, and contact information of two academic
references via email to/: schnitza(a)med.uni-duesseldorf.de and
K.Biermann-Ruben(a)uni-duesseldorf.de/
/ /
Or via regular mail to: Dr. Katja Biermann-Ruben,
Heinrich-Heine-University Düsseldorf, Institute of Clinical Neuroscience
and Medical Psychology, Moorenstr. 5, D-40225 Düsseldorf
//
/**********************************************************************/
//
//
PostDoc Position in Düsseldorf
A *postdoctoral position* is available at the Institute of Clinical
Neuroscience and Medical Psychology, Heinrich-Heine-University
Düsseldorf, to study neural representations of action related concepts.
The successful candidate will be expected to play a key role in our
neuroscientific the interdisciplinary collaborative research center
(CRC/SFB 991) "The Structures of Representation in Language, Science and
Cognition" starting July 2011. Within this linguistic CRC and on the
theoretical basis of embodiment and the mirror neuron system our project
investigates the functional relevance of the motor cortex for conceptual
representation of verbs and nouns which derived from action verbs.
Methods will be non-invasive 306-channel MEG, TMS and behavioural priming.
Successful candidates will have a PhD in neuroscience or related fields.
Preference will be given to candidates with a strong background in
systems level neurophysiological research (MEG/EEG, TMS) and related
signal analysis methods (MEG/EEG analysis in frequency and time domain).
We offer a stimulating and inspiring atmosphere in a young,
interdisciplinary team of neurologists, psychologists, physicists, and
biologists.
The position is for a period of four years. Earliest is July 2011.
Applications will be accepted until the position is filled.
To apply, please send a full CV, a brief outline of current research and
interests, certificates, and contact information of two academic
references via email to/: //schnitza(a)med.uni-duesseldorf.de// and
//K.Biermann-Ruben(a)uni-duesseldorf.de/
/ /
Or via regular mail to: Dr. Katja Biermann-Ruben,
Heinrich-Heine-University Düsseldorf, Institute of Clinical Neuroscience
and Medical Psychology, Moorenstr. 5, D-40225 Düsseldorf
//
//**********************************************************************//
//
*Alfons Schnitzler, MD*
Professor and Chairman
Institute of Clinical Neuroscience and Medical Psychology
Heinrich Heine University Düsseldorf
Universitätstr. 1, D-40225 Düsseldorf
tel. ++49 211-81-13014
fax ++49 211-81-13015
&
Movement Disorders and Neuromodulation
Department of Neurology, University Hospital Düsseldorf
Moorenstr. 5, D-40225 Düsseldorf
tel. ++49 211-81-16756
fax ++49 211-81-19032
*Katja Biermann-Ruben, PhD*
Postdoctoral scientist
Institute of Clinical Neuroscience and Medical Psychology
Heinrich-Heine-University Düsseldorf
Universitätsstr. 1, D-40225 Düsseldorf
tel. ++49 211-81-13015
fax ++49 211-81-13015
FYI
-
MRC Cognition and Brain Sciences Unit – Cambridge
Research Assistant
The MRC Cognition and Brain Sciences Unit (CBSU) is an internationally
renowned research institute with state-of-the-art cognitive neuroscience
facilities, including on-site fMRI, MEG, and EEG laboratories, and
neuropsychological patient panel and large panel of healthy volunteers.
Applications are invited for a Research Assistant to provide scientific
support for Dr Tristan Bekinschtein’s 5 year programme on Transition of
Consciousness in Sleep and Sedation, particularly for acquiring
behavioural, EEG and fMRI data (and the combination of both) during
cognitive experiments on volunteers, patients with sleep disorders and
people under sedation. This is a 2 year post initially, funded by the
Wellcome Trust.
You will be highly motivated and proactive, with a degree in psychology,
biology, computer science or physics. Experience in scientific research,
particularly with human volunteers, is important, as is familiarity with
computer programming and statistics. Experience of research in the area
of sleep and polysomnography is desirable. Experience with EEG or MRI
acquisition and/or analysis would be an advantage. Good communication
skills plus the ability to work as part of a large, multi-disciplinary
team are essential.
The starting salary will be in the range of £20,074 - £27,271 per annum,
depending upon qualifications and experience. We offer a flexible pay
and reward policy, 30 days annual leave entitlement, and an optional MRC
final salary Pension Scheme. On site car and bicycle parking is available.
Applications are handled by the RCUK Shared Services Centre; to apply
please visit our job board at https://ext.ssc.rcuk.ac.uk and complete an
online application form. If you are unable to apply online please
contact us on 01793 867003 quoting reference IRC23030.
Closing date: 2nd July 2011
This position is subject to pre-employment screening
The Medical Research Council is an Equal Opportunities Employer
-------------------------
Gary Green
Dear Users
This afternoon (4-5 pm in YNiC) there will be a talk on "Measuring the
spatial resolution of MEG beamformers" given by Sam Johnson.
Everyone is welcome to attend.
Best wishes
Rebecca
--
************************************************************************
Dr. Rebecca E. Millman
Science Liaison Officer
York Neuroimaging Centre
The Biocentre
York Science Park
Heslington
YO10 5DG
Tel: +44 (0) 1904 567614
Fax: +44 (0) 1904 435356