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YNiC seminar 18th February
by rem 15 Feb '10

15 Feb '10

Dear Users This week (and next week) the Cognitive Neuroscience MSc students will be giving project proposal presentations in YNiC open plan. Please note that the presentations will start 30 minutes later than usual at *4.30 pm*. The late start is necessary to give the MSc students enough time to get to YNiC after completing an exam in the Department of Psychology. 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

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RE: ynic-users Digest, Vol 43, Issue 3
by Datta, Avijit 11 Feb '10

11 Feb '10

Apologies - can't make it this week Avijit -----Original Message----- From: ynic-users-request(a)ynic.york.ac.uk [mailto:ynic-users-request@ynic.york.ac.uk] Sent: 08 February 2010 12:00 To: ynic-users(a)ynic.york.ac.uk Subject: ynic-users Digest, Vol 43, Issue 3 Send ynic-users mailing list submissions to ynic-users(a)ynic.york.ac.uk To subscribe or unsubscribe via the World Wide Web, visit https://www.ynic.york.ac.uk/mailman/listinfo/ynic-users or, via email, send a message with subject or body 'help' to ynic-users-request(a)ynic.york.ac.uk You can reach the person managing the list at ynic-users-owner(a)ynic.york.ac.uk When replying, please edit your Subject line so it is more specific than "Re: Contents of ynic-users digest..." Today's Topics: 1. YNiC seminar 11th February (Rebecca E Millman) ---------------------------------------------------------------------- Message: 1 Date: Mon, 8 Feb 2010 11:26:12 -0000 (GMT) From: "Rebecca E Millman" <rem(a)ynic.york.ac.uk> Subject: YNiC seminar 11th February To: ynic-users(a)ynic.york.ac.uk Message-ID: <23025.84.13.221.49.1265628372.squirrel(a)www.ynic.york.ac.uk> Content-Type: text/plain;charset=iso-8859-15 Dear Users This week (4-5 pm in YNiC open plan) there will be a YNiC project proposal presentation by Katya Krieger-Redwood, from the Department of Psychology. "Speech Perception in the Brain: A Transcranial Magnetic Stimulation Study" The motor theory of speech perception states that brain areas involved in producing speech, such as the PMC, also participate in processing spoken language. This study aims to establish the necessity of the PMC in the perception of spoken language, using rTMS. It is predicted that the PMC area is necessary for the resolution of difficult phonological judgement tasks but not for understanding speech in more naturalistic tasks. Everyone is welcome to attend. Best wishes Rebecca -- Dr. Rebecca E. Millman York Neuroimaging Centre The Biocentre York Science Park York YO10 5DG Email: rem(a)ynic.york.ac.uk Tel: 01904 435 5373 ------------------------------ _______________________________________________ ynic-users mailing list ynic-users(a)ynic.york.ac.uk https://www.ynic.york.ac.uk/mailman/listinfo/ynic-users End of ynic-users Digest, Vol 43, Issue 3 *****************************************

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YNiC seminar TODAY
by rem 11 Feb '10

11 Feb '10

Dear Users Today (4-5 pm in YNiC open plan) there will be two talks: 1) A YNiC project proposal presentation by Katya Krieger-Redwood, Department of Psychology. "Speech Perception in the Brain: A Transcranial Magnetic Stimulation Study" The motor theory of speech perception states that brain areas involved in producing speech, such as the PMC, also participate in processing spoken language. This study aims to establish the necessity of the PMC in the perception of spoken language, using rTMS. It is predicted that the PMC area is necessary for the resolution of difficult phonological judgement tasks but not for understanding speech in more naturalistic tasks. 2) An MEG clinical case report by Garreth Prendergast, YNiC. (addendum to original programme) "MEG observations in an individual with visual hallucinations" 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

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YNiC seminar 11th February
by Rebecca E Millman 08 Feb '10

08 Feb '10

Dear Users This week (4-5 pm in YNiC open plan) there will be a YNiC project proposal presentation by Katya Krieger-Redwood, from the Department of Psychology. "Speech Perception in the Brain: A Transcranial Magnetic Stimulation Study" The motor theory of speech perception states that brain areas involved in producing speech, such as the PMC, also participate in processing spoken language. This study aims to establish the necessity of the PMC in the perception of spoken language, using rTMS. It is predicted that the PMC area is necessary for the resolution of difficult phonological judgement tasks but not for understanding speech in more naturalistic tasks. Everyone is welcome to attend. Best wishes Rebecca -- Dr. Rebecca E. Millman York Neuroimaging Centre The Biocentre York Science Park York YO10 5DG Email: rem(a)ynic.york.ac.uk Tel: 01904 435 5373

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Fwd: [NLC2009] NLC 2010 Updates
by Gareth Gaskell 04 Feb '10

04 Feb '10

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YNiC seminar cancelled
by rem 03 Feb '10

03 Feb '10

Dear Users The YNiC seminar that was scheduled for 4th February (tomorrow) has been cancelled. The purpose of this week's seminar was to provide feedback on a meeting about the source of the fMRI BOLD response. This fMRI meeting should have taken place in Glasgow this week but it was cancelled at very short notice. YNiC seminars will be back to normal next week. 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

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FW: [BIC-announce] FW: RBIQ - Poste de bio-informaticien / QBIN Bioinformatician position
by Ekaterini Klepousniotou 28 Jan '10

28 Jan '10

This may be of interest to some. All the best, 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 [mailto:bic-announce-bounces@bic.mni.mcgill.ca] On Behalf Of Jennifer Chew, Ms. Sent: 28 January 2010 16:18 To: bic-announce(a)bic.mni.mcgill.ca Subject: [BIC-announce] FW: RBIQ - Poste de bio-informaticien / QBIN Bioinformatician position FOR YOUR INFORMATION. Jennifer Jennifer Chew McConnell Brain Imaging Centre MNI - WB317 3801 University Street Montreal, Qc H3A 2B4 Telephone: 514-398-8554 Fax: 514-398-2975 ________________________________ From: Francine Bélanger [mailto:francine.belanger@criugm.qc.ca] Sent: Thursday, January 28, 2010 11:09 AM To: Jennifer Chew, Ms. Subject: RBIQ - Poste de bio-informaticien / QBIN Bioinformatician position Profil recherché / Required profile * Bilingue (français et anglais) / Bilingual (French English). * Bonnes capacités de communication et de coordination / Good communication and coordination skills * Bonne connaissance de Linux, Windows et/ou Macintosh (préférablement les 3) / Good knowledge of Linux, Windows and/or Macintosh (preferably all three) * Excellentes capacités de programmation dans un ou plusieurs languages (Matlab, C, Perl, Python, etc.) / Excellent programming skills with one or more languages (Matlab,C, Perl, Python etc.) * Familier avec les concepts des bio-imagerie (IRMf, IRMa, TEP, EEG, MEG, etc.) / Familiar with theoretical concepts in bio-imagery (fMRI, aMRI, PET, EEG, MEG etc.) * Connaissance d'un ou plusieurs outils d'analyse (SPM, fmristat, BrainVisa, AFNI, FSL, MINC, etc.) / Knowledge of one or more functional analysis tools (SPM, fmristat, BrainVisa, AFNI, FSL, MINC etc.) * Motivé, sens de l'initiative, capacité à organiser des événements avec un minimum de supervision / Motivated and self-starter capable of organizing and executing events, unsupervised. Description des fonctions / Description of tasks * Contribuer à la bonne marche des activités scientifiques du RBIQ tout en collaborant avec différentes équipes techniques / Contribute to the smooth functioning of QBIN scientific activities while collaborating with various technical teams. * Gérer et metre en place des activités de formation sur une base mensuelle (ateliers, séminaires, école d'été, etc.) / Manage and implement training activities on a monthly basis (Workshops, seminars, summer school etc.). * Coordonner les échanges de personnel hautement qualifié entre les differentes plateformes technoloques du RBIQ / Coordinate the exchanges with highly qualified personnel at the various imaging centers within the reach of QBIN. * Apporter un support technique et logistique aux différentes plateformes technologiques du RBIQ / Bring technical and logistic support to the various imaging centers within the reach of QBIN. * Maintenir à jour une liste des besoins en termes de formation des différentes plateformes technologiques du RBIQ / Maintain a list of training needs to support the various imaging centers within the reach of QBIN. * Maintenir le site Web et le forum du RBIQ et, lorsque requis, apporter un support général aux membres / Manage QBIN website and forums, providing aggregate support when required (front line support, redirecting questions to relevant parties). * Maintenir à jour un calendrier des événements et insérer tous les événements reliés à la bio-imagerie dans le calendrier du RBIQ / Maintain events calendar, placing all bio-imaging events on the QBIN calendar. Faire parvenir votre c.v./Mail your cv : julien.doyon(a)umontreal.ca<mailto:julien.doyon@umontreal.ca> _______________________________________ Francine Bélanger Coordonnatrice administrative UNF / RNQ / RBIQ-QBIN Centre de recherche, Institut universitaire de gériatrie de Montréal 4565, chemin Queen-Mary, Montréal (Québec) H3W 1W5 Tél.: (514) 340-3540 # 4785 Téléc.: (514) 340-3530 Courriel: francine.belanger(a)criugm.qc.ca Web UNF: www.unf-montreal.ca Web RBIQ: www.rbiq-qbin.qc.ca

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YNiC seminar TODAY
by rem 28 Jan '10

28 Jan '10

Dear Users Today from 4-5 pm at YNiC there will be an update on research and other MEG-related issues presented at the recent "MEG UK" meeting. 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

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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

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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

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