ynic-users

ynic-users@ynic.york.ac.uk

1 participants
2786 discussions

Software updates at YNiC
by Mark Hymers 26 Jan '10

26 Jan '10

Dear all, Some changes and updates to supported software are being made this evening at YNiC. Information about these changes can be found at https://www.ynic.york.ac.uk/doc/ITPages/FAQ/Misc/ChangeLog A brief summary follows: These changes should be mainly user invisible (except for those who build their own software from source which uses VTK, please contact me for help): * VTK and the python bindings are being updated from 5.0 to 5.4 * Various libraries and FSLView have been updated to be built against VTK 5.4 New software: * pygame 1.8.1, pyglet and psychopy 1.51 have been added to the image * Freesurfer dependencies: libvxl1.13, ebtks 1.6.2, kwwidgets 1.0.0 and teem 1.10 have been added to the image * n3 1.11.0 (from MNI) and libmni-perl have been added to the image (mainly as freesurfer dependencies but some people may have other uses for them) * Slicer 3.4.0 has been added to the image (http://www.slicer.org/) * Freesurfer 4.5 has been added to the image but is not fully tested. Please contact me before using this for instructions. There will be some testing work performed in the next week or so and Liat, Padraig, Tom and myself have discussed running a training session once we're sure it's working. * ANTS (http://www.picsl.upenn.edu/ANTS/) has been installed. Please see https://www.ynic.york.ac.uk/doc/ITPages/FAQ/Misc/ANTS for notes on YNiC specific things for this software. * Nutmeg 3.1 has been added to the system (using the ynicInit system in Matlab; please see https://www.ynic.york.ac.uk/doc/ITPages/FAQ/Matlab/ExtraToolboxes ) As ever, please let me know if you see anything problematic. Thanks, Mark -- Mark Hymers York Neuroimaging Centre

1 0

update on status of MEG
by rem 26 Jan '10

26 Jan '10

Dear Users As many of you will know, the MEG scanner underwent preventative maintenance earlier this month. We are happy to report that this work was carried out successfully. Due to the re-cooling of the sensors and some calibration work the scanner is working well. The noise floor has improved considerably. However, one of the inherent dangers of this thermal cycling is the potential loss of sensors. Until now we had been very fortunate in that we had not lost any channels but this is no longer the case. Users should take note of the following: 1) "Dead" channels There are 3 channels in the MEG scanner that do not work. These channels are A55, A84 and A237. There had recently been suspicion about the quality of the data from channel 237 and during the maintenance it was confirmed that this channel is not working correctly. On a more positive note this is an electronics problem and will be solved once our new MEG electronics are in place. For now, anyone collecting new MEG data should exclude channels A55, A84 and A237 from their analyses. There will be some minor changes to some YNiC software to allow for channel exclusions. 2) REI board error (ONLY for MEG operators) Although currently stable, we are aware of a problem with one of the electronics boards (the REI board). MEG operators will know when the REI board is not working because of an error message that appears in the ACP window on the Sun work station. For this reason the ACP, DCP, AVP and VIP windows must be open when you are acquiring MEG data so that any problems with the MEG scanner can be tracked. If any of these windows are not open, they can be opened from the "acquisition setup" window in the database on the Sun workstation. Click on the "utilities" menu and from here open the relevant window/s. Please record any faults in the "MEG error log book" (left-hand side of the Sun machine). In the event of an REI board error, please contact a member of YNiC staff. Please do not hesitate to contact me if you have any further questions about these matters. 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

1 0

YNiC seminar 28th January
by rem 26 Jan '10

26 Jan '10

Dear Users This Thursday (4-5 pm in YNiC open plan) there will be feedback from the recent "MEG UK" meeting provided by YNiC staff. 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

1 0

Human Brain Mapping and More
by Chris Racey 25 Jan '10

25 Jan '10

I've been asked to forward this on to all the YNiC users by Ramon, who did his Cognitive Neuroscience masters here a couple of years ago and is now working in a research hospital in Barcelona. As part of this year's HBM, which will be held in Barcelona this year in June (http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=1), Ramon is involved in the organisation of a congress on 'The Default Mode Network and other intrinsic networks in the brain'. He would like to invite anyone from York who's interested along to the Congress, which takes place just before HBM on the 4th and 5th of June. The website is below. http://www.defaultmodenetwork.com/index.html If anyone is interested and would like to be put in touch with Ramon, let me know. -- Chris Racey PhD Candidate Department of Psychology, University of York, York, YO10 5DD, UK +44(0)7791 851542

1 0

to those who attended MEG UK
by rem 25 Jan '10

25 Jan '10

For the Thursday seminar this week, it was suggested that YNiC staff give some feedback from the MEG UK meeting. Any volunteers? (Please keep in mind that the following week, there is supposed to be the MEG/fMRI debate after Gary and Andre have been to the meeting in Glasgow.) ************************************************************************ 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

1 0

no YNiC seminar this week
by rem 18 Jan '10

18 Jan '10

Dear Users There will not be a YNiC seminar this Thursday (21st) because the MEG UK meeting is being held on Wednesday and Thursday. YNiC seminars will resume next week (28th January). 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

1 0

YNiC seminar TODAY
by rem 14 Jan '10

14 Jan '10

Dear Users Today (4-5 pm in YNiC open plan) there will be a project proposal presentation by Richard Harris on "How information about expression and identity is represented in face-selective regions". Richard will be talking about a planned fMRI experiment in which he will use an fMR adaptation paradigm to determine whether expression and identity are represented independently in face-selective brain areas. 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

1 0

YNiC seminar 14th January
by rem 11 Jan '10

11 Jan '10

Dear Users This Thursday (4-5 pm in YNiC open plan) there will be a project proposal presentation by Richard Harris on "How information about expression and identity is represented in face-selective regions". Richard will be talking about a planned fMRI experiment in which he will use an fMR adaptation paradigm to determine whether expression and identity are represented independently in face-selective brain areas. 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

1 0

[Fwd: International Congress in Konstanz]
by Gary Green 16 Dec '09

16 Dec '09

from a colleague that many of you will remember --------------------------------------- Dear colleagues, there will be an international congress "Changing People, Changing Brains" in Konstanz next year (see: http://www.psychologie.uni-konstanz.de/abteilungen/clinicalpsychology/chang… and the flyer attached). There are sixteen travel awards (travel, accomodation, attendance) for outstanding junior scientists. Interested people can apply for the travel awards via the homepage. Would you be so kind to forward this email to people who might be interested? Thank you very much! Isabella -- *Dr. Isabella Paul-Jordanov* http://www.clinical-psychology.uni-konstanz.de/member-55.html University of Konstanz, Germany Departments of Clinical Psychology and Neuropsychology PO-Box D23 D-78457 Konstanz Email: Isabella.Paul-Jordanov(a)uni-konstanz.de <mailto:Isabella.Paul-Jordanov@uni-konstanz.de> Tel.: +49 7531 882696 Fax: +49 7531 884601 -- Gary Green York Neuroimaging Centre The Biocentre York Science Park Innovation Way Heslington York YO10 5DG http://www.ynic.york.ac.uk https://www.ynic.york.ac.uk/about-us/people/ggrg tel. +44 (0) 1904 435349 PA (Sara Narayan) +44 (0) 1904 435329 fax +44 (0) 1904 435356 mobile +44 (0) 788 191 3004

1 0

FW: post-doctoral job offer
by Ekaterini Klepousniotou 15 Dec '09

15 Dec '09

This may be of interest to some. Best wishes for the holiday season, Katerina ****************************************************************** Dr. Ekaterini Klepousniotou Lecturer in Cognitive Neuroscience & Neuropsychology Institute of Psychological Sciences University of Leeds Leeds LS2 9JT UK Tel: +44 (0)113 3435716 Fax: +44 (0)113 3435749 ________________________________ From: bic-announce-bounces(a)bic.mni.mcgill.ca [bic-announce-bounces(a)bic.mni.mcgill.ca] On Behalf Of Jennifer Chew, Ms. [jennifer.chew(a)mcgill.ca] Sent: 14 December 2009 18:26 To: bic-announce(a)bic.mni.mcgill.ca Subject: [BIC-announce] FW: post-doctoral job offer Posted on behalf of Pierre Bellec . Jennifer ---------- Forwarded message ---------- From: Saad Jbabdi <saad(a)fmrib.ox.ac.uk<mailto:saad@fmrib.ox.ac.uk>> Date: 2009/12/14 Subject: Re: TF diagrams To: Pierre Bellec <pbellec(a)bic.mni.mcgill.ca<mailto:pbellec@bic.mni.mcgill.ca>> -- Postdoctoral Research Assistant: Modelling Brain Connectivity Oxford University Centre for Functional MRI of the Brain (FMRIB) Academic-related salary scale, Grade 7: Salary £28,839 – 35,469 p.a. The Centre for Functional Magnetic Resonance Imaging of the Brain (FMRIB) seeks a postdoctoral research assistant to work with Drs. Tim Behrens and Saad Jbabdi in diffusion MRI methods development. Employment could begin from March 2010 and is funded by the European Commission for a period of 2 years as part of a pan-European consortium of diffusion-imaging researchers “CONNECT”. Oxford’s contribution to this project aims to integrate biophysical models of white matter architecture into Bayesian tractography routines. Candidates should have a doctorate in a relevant discipline, together with knowledge of statistics and preferably Bayesian learning, with the necessary mathematical and computational skills to put these into practice. Knowledge in methods for analysing neuroimaging data, in particular diffusion MRI, is desirable but not essential. Skills in computer programming (especially Matlab and C++) are essential. For links to further information seewww.fmrib.ox.ac.uk/analysis<http://www.fmrib.ox.ac.uk/analysis>. Applications, including a curriculum vitae and details of two referees, should be sent to Mrs Marilyn Goulding, FMRIB Centre, John Radcliffe Hospital, Oxford OX3 9DU, fax: (01865) 222717; e‑mail: marilyn(a)fmrib.ox.ac.uk<mailto:marilyn@fmrib.ox.ac.uk>. Please quote reference HM09-024. The closing date for applications is January 8th 2010. -- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK +44 (0) 1865 222466 (fax 717) www.fmrib.ox.ac.uk/~saad<http://www.fmrib.ox.ac.uk/%7Esaad> --

1 0

Jump to page:

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

ynic-users