Dear YNiC users,
This is a reminder that the YNiC Science Committee will meet next Monday,
27th April, at 2pm in B002. YNiC users are welcome to come along to this
meeting to ask questions and make suggestions about the running of YNiC. If
you wish to raise something, please drop me a line (
beth.jefferies(a)york.ac.uk) before the meeting so that I can add it to the
agenda. If you are unable to come along but you want to raise a point for
discussion, that is fine too - just get in touch.
The YNiC Science Committee meets on Monday week 3 of each term at 2pm.
With best wishes
Beth
--
Beth Jefferies
Department of Psychology, University of York, UK
+44 01904 324368
Dear all,
As of 1st October this year, YNiC is re-introducing an induction
procedure for new centre users. This induction will cover various
health & safety, organisational and practical issues regarding using the
centre. Induction sessions will take around one hour.
This induction is mandatory for all new centre users. To ensure this,
fobs and IT accounts will not be issued to any new user who has not
completed an induction. We have to be able to show the insurers that we
have taken action to ensure that all users are aware of the issues
involved in using the centre.
If you have been using the centre and have not attended an induction
event in the past, please do take the opportunity to attend one of the
sessions.
Dates and registration details can be found at:
https://www.ynic.york.ac.uk/information/induction
For taught courses (MSc / MPsych), we run a special set of induction
sessions in the Autumn term. We would encourage new PhD students to
also register to attend these sessions. This year, these sessions take
place on Monday 5th October. Please contact
<reception(a)ynic.york.ac.uk> if you wish to attend these sessions.
Gary Green
Dear Users
This afternoon (from 4 pm in B020) Ellie Cole will give an internal
project proposal presentation on "*Concurrent Activity in the Mirror
Neuron System and the Mentalizing System*".
Everyone is welcome to attend and refreshments will be available after
the seminar.
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
Dear all,
The YNiC software upgrade has now been completed.
As a reminder, the main changes are:
* The default FSL version is now 5.0. Details on switching this for
those wishing to continue using 4.1 are at
https://www.ynic.york.ac.uk/docs/ITPages/FAQ/FSL/Versions
* The default Matlab version is now 8.5 (2015a). 7.4 (2012a) is still
available.
* The available Psychopy version is now 1.82.02.
* The default Python version is now 2.7. Nearly all python modules
have been upgraded.
One other smaller change:
* clusterFeat now submits jobs in a way which will make them run in
parallel when possible. This should speed up FSL analyses (especially
higher level analyses)
The remote desktop server is available immediately and YNiC Open plan
will be open as usual from Wednesday morning.
Any issues should be sent to it-support(a)ynic.york.ac.uk
Thanks,
Mark
--
Mark Hymers, York Neuroimaging Centre
Please note that my email address is: mark.hymers(a)ynic.york.ac.uk
Responses to messages sent to other addresses may be delayed
Hi all,
We are in the process of updating the door access rights to the centre
and in order to facilitate this process are compiling a list of current
key holders.
*Please can you email me by *_*30th September*_*__if you hold a set of
keys for the centre? *
Please note: Once we have the list of key holders we will be amending
the access rights accordingly. Therefore, if you have keys but don't
tell us, you may find yourself unable to access the centre.
Many thanks
Sarah
--
Sarah Finch | PA to Gary Green, Director
York Neuroimaging Centre | The Biocentre | York Science Park | Heslington | York | YO10 5NY
01904 435329
Working hours are Tues 8.15 -14.45, Weds 8.15-17.15, Thurs 9.30-17.30 and Fri 8.15-14.45
Dear Users
This Thursday (4-5 pm in B020), Xiaoqian Yan, will give a project presentation on a new fMRI experiment to investigate the cross-cultural differences
in the neural presentation of faces.
Everyone is welcome to attend. Refreshments will be available after the seminar.
Best wishes
--
Sarah Finch | PA to Gary Green, Director
York Neuroimaging Centre | The Biocentre | York Science Park | Heslinton | York | YO10 5NY
01904 435329
Working hours are Tues 8.15 -14.45, Weds 8.15-17.15, Thurs 9.30-17.30 and Fri 8.15-14.45
Dear all,
As announced previously, YNiC staff will be performing a large software
upgrade on Monday and Tuesday next week. All systems (including remote
desktop) will be unavailable for the duration of the upgrade and the
centre itself will be closed to users.
An email will be sent to ynic-users once systems are back online and the
centre is open.
Details of the upgrade can be found at:
https://www.ynic.york.ac.uk/docs/ITPages/Summer2015Upgrade
**Please note that we are changing default versions of a range of
software, including some analysis software - please ensure that you have
read this email or the page concerned**
A summary of the current version of the page follows:
===================================================================================
Operating System
----------------
The primary YNiC operating system will change from Debian 7.0 (wheezy)
to Debian 8.0 (jessie). The window system in use will remain as XFCE and
we do not expect many major changes in the appearance of the system.
General Applications
--------------------
The following applications will be replaced:
* evince (PDF viewer) will be replaced by atril
* eog (Image viewer) will be replaced by eom
* File Roller (File compression utility) will be replaced by engrampa
* Gedit (Text editor) will be replaced by pluma
FSL
---
The default version of FSL will change to 5.0.8. This is a major change
from 4.1.
FSL 4.1.9 is still available on the system. Details of how to use a
non-default FSL version can be found at docs/ITPages/FAQ/FSL/Versions.
Our advice is not to mix and match versions of FSL within analyses, but
to start new projects using 5.0.
FSL 5.0 includes new atlases and segmentations - these are all installed
in the usual location /usr/share/fsl/data.
Python
------
python2.7 and python3.4 are available on the YNiC systems.
YNiC still primarily supports python2, however we are aiming for a
complete python3 system where possible and will attempt to backport any
modules needed to support a full scientific software stack on python3.
We aim to change our default version of python to python3 from Summer
2016 (subject to all modules being available in time). Taught courses
using Python in 2015/16 will use python2, but will aim to use python3
compatible syntax.
Python Modules
--------------
The complete list of python module changes is available at the page
linked above.
Matlab
------
The default version of MATLAB is now 8.5 (R2015a). For backwards
compatibility, MATLAB 7.14 (R2012a) is also available.
MATLAB Toolboxes
----------------
* SPM 2 and 5 remain available at their existing versions.
* SPM 8 has been updated to r6313.
* SPM 12 has been updated to r6470.
R
-
* R has been upgraded from 2.15 to 3.1.1.
* Rstudio has been upgraded from 0.97.551 to 0.99.484.
* Various R libraries have been upgraded.
Freesurfer
----------
Only freesurfer 5.3 will now be supported. Freesurfer 5.1 has been
removed.
The exact revision (CVS date) of freesurfer 5.3 will be confirmed before
upgrade.
The existing pool of automatic freesurfer extractions was generated
using freesurfer 5.1. We intend to archive these and regenerate (over
the next few weeks) all of the extractions using the updated freesurfer
5.3.
===================================================================================
If you have any queries, please contact myself
<mark.hymers(a)ynic.york.ac.uk> or Paul Elliott
<paul.elliott(a)ynic.york.ac.uk>
Thanks,
Mark
--
Mark Hymers, York Neuroimaging Centre
Please note that my email address is: mark.hymers(a)ynic.york.ac.uk
Responses to messages sent to other addresses may be delayed
Please find an advert for positions at the Brain Imaging Centre at the
MNI.:
*From: *"Andrea Bernasconi, Dr." <andrea.bernasconi(a)mcgill.ca>
*Subject: **[BIC-announce] Postdoc, PhD and RA positions available at the
BIC*
*Date: *September 11, 2015 at 4:20:50 PM GMT-4
*To: *BIC-announce <bic-announce(a)bic.mni.mcgill.ca>
We are currently looking for *3* enthusiastic and skilled team players (*1
PhD student, 1 Postdoc, 1 RA*) to join the *Neuroimaging of Epilepsy
Laboratory* at the Brain Imaging Center (BIC) of the Montreal Neurological
Institute (McGill University, Montreal, Canada)
http://www.bic.mni.mcgill.ca/~noel
Our lab is part of the BIC, an internationally recognized and
multidisciplinary centre of neuroimaging, and associated to the Epilepsy
Group of the Montreal Neurological Institute and Hospital, a tertiary
center that evaluates approximately 200 patients per year for the
pre-surgical investigation of drug-resistant seizures. Our group brings
together graduate students and postdoctoral fellows in Neuroscience,
Cognitive Science, Computer Science, Biomedical Engineering, and Neurology.
We use high- and ultra-high field (3 and 7T) structural and functional MRI
analysis to characterize cortical architecture, function, metabolism, and
networks. We seek to identify novel patient phenotypes and biomarkers of
disease. Main topics include automated lesion detection through
neuroimage-based machine-learning, surface-based subcortical and cortical
modelling, analysis of brain networks using graph-theory. We are
interested in tracking disease progression and its consequences on brain
plasticity, connectivity, and cognition.
The *postdoctoral fellow *will carry our research projects that combine
multi-modal neuroimaging with advanced data analysis (graph theoretical
network analysis, machine learning, multivariate modeling) in large and
well-documented cohorts of patients with drug-resistant epilepsy.
Possibility to participate in several multi-centric and longitudinal
studies. Requirements: PhD in Neuroscience, Computer Science, Cognitive
Science, Engineering, or related fields; experience in neuroimaging, data
analysis, programming; strong publication record.
The *PhD student* will perform research centered on the development of
neuroimaging applications to improve our understanding and diagnostic
routines of human epilepsy. The PhD will be carried out within the
Integrated Program in Neuroscience at McGill University (IPN,
https://www.mcgill.ca/ipn/), the largest inter-disciplinary,
inter-departmental graduate program in neuroscience in Canada.
Requirements: MSc in Neuroscience, Cognitive Science, Computer Science,
Biomedical Engineering, or related fields; solid mathematical and
statistical knowledge; previous experience in neuroimaging and data
analysis is an asset.
The *full-time research assistant (RA)* will help with subject recruitment;
administration of questionnaires and neurocognitive tasks; MRI scheduling
and data acquisition (with assistance of technician); data quality-control
and image processing; database management; technical support. Requirements:
BSc/BA in Neuroscience, Cognitive Science, Psychology, or related fields;
organizational talent and computer skills; willingness to accept flexible
working schedule; knowledge of French (spoken and written).
All candidates are expected to show strong communication skills and
willingness to learn and help others within a multidisciplinary team.
Starting dates are flexible.
** Full applications (cover letter, CV, and names of 2 referees; PhD
candidates should also send transcripts) should be sent to:
andrea.bernasconi(a)mcgill.ca
_______________________________________________
BIC-announce mailing list
BIC-announce(a)bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/bic-announce
--
Jonathan Smallwood
Reader in Psychology / Cognitive Neuroscience
University of York, England.
Hello Everyone,
Just a reminder that the second YNiC science day is tomorrow at 13:30, here
in the Psychology department.
I have attached the previously circulated flyer as well as the program for
this year.
YNiC science day 2015 program
<https://docs.google.com/a/york.ac.uk/document/d/12OFO2gwpiwWx41jWTM_g6DotsY…>
Hope to see you all there!
James D