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2786 discussions

FSL 4.1 upgrade
by Mark Hymers 06 May '10

06 May '10

Hi, I intend to upgrade FSL 4.1 on the YNiC Systems over the weekend from the current version (4.1.4) to the latest release 4.1.5.2. Details of the changes (which are only minor) are available at: http://www.fmrib.ox.ac.uk/fsl/fsl/whatsnew.html#revisions The only thing which is really relevant is that FLAMEO has a fix in it (which is strangely listed in the 4.1.4 errata, but seems to have only been released in 4.1.5) In addition, I've merged two extra bug fixes, one in fslmaths (related to TFCE calculation) and a syntax error fix in one of the scripts. Details are below as a patch series. Thanks, Mark diff --git a/debian/changelog b/debian/changelog index f2b3942..0c7f3ce 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,8 +1,10 @@ fsl-4.1 (4.1.5.2-1~yniclenny1) unstable; urgency=low * Merge 4.1.5.2 release. + * Merge syntax fix in rotate_bvecs. + * Merge fix for TFCE calculation in fslmaths. - -- Mark Hymers <mark.hymers(a)ynic.york.ac.uk> Wed, 05 May 2010 17:52:06 +0100 + -- Mark Hymers <mark.hymers(a)ynic.york.ac.uk> Thu, 06 May 2010 10:16:07 +0100 fsl-4.1 (4.1.4-3~yniclenny3) unstable; urgency=low diff --git a/src/avwutils/fslmaths.cc b/src/avwutils/fslmaths.cc index 0df7ef3..c47c854 100644 --- a/src/avwutils/fslmaths.cc +++ b/src/avwutils/fslmaths.cc @@ -823,7 +823,7 @@ if (!separatenoise) int connectivity = atoi(argv[++i]); for(int t=0;t<input_volume.tsize();t++) - tfce(input_volume[t], height_power, size_power, connectivity, 0, 0); + tfce(input_volume[t], height_power, size_power, connectivity, 0, input_volume[t].max()/100.0); } // }}} diff --git a/src/fdt/rotate_bvecs b/src/fdt/rotate_bvecs index e6aade9..2c10968 100755 --- a/src/fdt/rotate_bvecs +++ b/src/fdt/rotate_bvecs @@ -18,7 +18,7 @@ if [ -f ${bvecs}_old ];then echo "If you want to force this program to run, please remove the file ${bvecs}_old" echo "" exit 1 -done +fi /bin/cp ${bvecs} ${bvecs}_old #/bin/rm -f ${bvecs} -- Mark Hymers York Neuroimaging Centre

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YNiC seminar TODAY
by rem 06 May '10

06 May '10

Dear Users Today Katie Wheat will give a talk at 4 pm in YNiC open plan on "Further MEG explorations of early activation in Broca's area during visual word recognition". Purpose of talk: "We will summarise the previous MEG and behavioural work we have done, before outlining our proposal for a new MEG experiment. We are particularly interested in getting feedback on the MEG task design and ways of incorporating DTI data." 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 6th May
by rem 05 May '10

05 May '10

Dear Users This week Katie Wheat will give a talk at 4 pm in YNiC open plan on "Further MEG explorations of early activation in Broca's area during visual word recognition". Purpose of talk: "We will summarise the previous MEG and behavioural work we have done, before outlining our proposal for a new MEG experiment. We are particularly interested in getting feedback on the MEG task design and ways of incorporating DTI data." 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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FW: [NLC2009] NLC2010: Abstract Submission is Now Open!
by Ekaterini Klepousniotou 04 May '10

04 May '10

FYI ****************************************************************** 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: nlc_distribution-bounces(a)nlc2009.angularis.org [nlc_distribution-bounces(a)nlc2009.angularis.org] On Behalf Of Pascale Tremblay [tremblay(a)neurolang.org] Sent: 03 May 2010 23:31 To: nlc_distribution(a)nlc2009.angularis.org Subject: [NLC2009] NLC2010: Abstract Submission is Now Open! Dear colleague, It is our great pleasure to announce that abstract submission for the second Neurobiology of Language Conference (NLC 2010) is now open! For more information, please visit our new website at http://www.neurolang.org or send us an email. Don’t miss this opportunity to share your research with the neurobiology of language scientific community! The abstract submission deadline is Tuesday, June 1st at midnight (CST). Also note that early registration is now open: to take advantage of early registration rates, visit our website now.<http://www.neurolang.org/abstracts/ConferenceRegistration.php> NLC 2010 will be held on November 11-12 2010 in San Diego as a satellite of the Society for Neuroscience annual meeting. A reminder that you do not need to attend the Society for Neuroscience (SfN) annual meeting, or be a member of SfN, to attend NLC. If you are planning to attend SfN, however, please note that SfN regulations allow individuals to present their SfN abstracts during satellite events. We look forward to seeing you in San Diego! Kind regards, Pascale Tremblay, Ph.D., Postdoctoral Scholar, The University of Chicago Steven L. Small, Ph.D., M.D., Professor, The University of Chicago The Neurobiology of Language Planning Group: Jeffrey Binder, M.D., Medical College of Wisconsin, USA Vincent Gracco, Ph.D., McGill University, Canada Yosef Grodzinsky, Ph.D., McGill University, Canada Murray Grossman, M.D., Ed.D., University of Pennsylvania, USA Peter Hagoort, Ph.D., Max Planck Institute, Netherlands Gregory Hickok, Ph.D., University of California, Irvine, USA Marta Kutas, Ph.D., The University of California, San Diego, USA Alec Marantz, Ph.D., New York University, USA Howard Nusbaum, Ph.D., The University of Chicago, USA Cathy Price, Ph.D., University College London, UK David Poeppel, Ph.D., New York University, USA Rita Salmelin, Ph.D., Helsinki University of Technology, Finland Kunioshi Sakai, Ph.D., Tokyo University, Japan Steven L. Small, Ph.D, M.D., The University of Chicago, USA Sharon Thompson-Schill, University of Pennsylvania, USA Pascale Tremblay, Ph.D., The University of Chicago, USA Richard Wise, M.D., Ph.D, Imperial College, London, UK Kate Watkins, Ph.D., University of Oxford, UK

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YNiC seminar TODAY
by rem 29 Apr '10

29 Apr '10

Jodie Davies-Thompson will give a talk at 4 pm in YNiC open plan on "The localization and functional connectivity of face-selective regions in the human brain". Abstract: "This talk will outline a new method for localizing face-selective regions of interest. Face-selective regions are typically defined by contrasting the response to a face with the response to a control stimulus. However, many different control stimuli are possible. So, the choice of control stimulus could influence the location and extent of the face-selective regions. Our aim was to define face-selective regions in visual and non-visual regions of the brain using a localiser paradigm that minimises potential confounds . Finally, we have developed a method for showing the functional connectivity between face-selective regions." 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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School visit in Open Plan, Wednesday 28th April.
by Michael Simpson 27 Apr '10

27 Apr '10

Dear all, just to let you know that we will have a school visit in YNiC tomorrow, Wednesday 28th April. Therefore, YNiC Open Plan will be busy between 2.00 pm and 3.30 pm. Although the pupils will not be using the I.T. workstations, it may be preferable for you not to use the six workstations nearest the projector, nor to try and have a lab meeting in Open Plan until after 3.30 pm on Wednesday 28th April. However, in general, access to Open Plan Workstations will not be affected by this, only the level of background noise. Thanks, Michael -- Dr Michael Simpson Science Liaison Officer York Neuroimaging Centre Innovation Way York YO10 5DG Tel: 01904 567614 Web: http://www.ynic.york.ac.uk

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[Fwd: Neuroimaging post-doc, University of Cambridge]
by Gary Green 26 Apr '10

26 Apr '10

FYI Neuroimaging post-doctoral Research Associate University of Cambridge, Department of Experimental Psychology Salary: £27,319 - £35,646 pa Applications are invited for an experienced and enthusiastic neuroimager to work on a research programme investigating the effect of normal ageing on language and cognition. The applicant will join the Centre for Speech, Language and the Brain, an inter‑disciplinary team led by Professor L.K. Tyler. The research focuses on neurocognitive models of healthy ageing, with an emphasis on issues relating to reorganisation and plasticity. The Centre has access to a research-dedicated 3T Siemens MR scanner, EEG and MEG facilities. We currently use a variety of imaging analysis methods such as fMRI analysis, voxel based structure-function correlational analyses, DTI analyses, multivariate analyses, and functional and anatomical connectivity analyses. Applicants should have a PhD (or equivalent) and postdoctoral experience with excellent computer programming (especially MATLAB) and statistical skills, experience with fMRI and DTI analyses, an understanding of the basis of MR imaging, and an interest in language function. Given the nature of the research, candidates should be native English speakers or fully fluent in English. The successful candidate will be required to apply for an Enhanced CRB Disclosure. Closing date: 21 May 2010 Start date: 1 October 2010 Limit of tenure: The fund for this post are available until 30 September 2012 in the first instance, but may be extended with future funding initiatives. For further details, please see our website at http://csl.psychol.cam.ac.uk/vacancies.html. Applications including a covering letter, CV, names and addresses (incl. e-mail addresses) of three referees, and a completed PD18 coversheet (Part I, Section B of Part II, and Part III) should be sent to Mrs M Dixon at csladmin(a)csl.psychol.cam.ac.uk or by post to Mrs M Dixon, Centre for Speech, Language and the Brain, Department of Experimental Psychology, University of Cambridge, Downing Street, Cambridge, CB2 3EB. The PD18 can be obtained from Mrs Dixon or downloaded from http://www.admin.cam.ac.uk/offices/hr/forms/pd18/. The Vacancy Number for this position is PJ06538. The University values diversity and is committed to equality of opportunity. The University has a responsibility to ensure that all employees are eligible to live and work in the UK.

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YNiC seminar 29th April
by rem 26 Apr '10

26 Apr '10

Dear Users This Thursday Jodie Davies-Thompson will give a talk at 4 pm in YNiC open plan on "The localization and functional connectivity of face-selective regions in the human brain". Abstract: "This talk will outline a new method for localizing face-selective regions of interest. Face-selective regions are typically defined by contrasting the response to a face with the response to a control stimulus. However, many different control stimuli are possible. So, the choice of control stimulus could influence the location and extent of the face-selective regions. Our aim was to define face-selective regions in visual and non-visual regions of the brain using a localiser paradigm that minimises potential confounds . Finally, we have developed a method for showing the functional connectivity between face-selective regions." 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 TODAY
by rem 22 Apr '10

22 Apr '10

Dear Users Today Will Woods will give a presentation at 4 pm in YNiC. There will be 2 short talks: 1) Coregistration of MEG and MRI using a stereo camera 2) Issues with beamforming statistics and regions of interest These talks will be followed by a drinks reception for Will. 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 22nd April
by rem 20 Apr '10

20 Apr '10

Dear Users As you may know, Will Woods is leaving YNiC at the end of this month. As part of an event on Thursday evening to thank Will for all his contributions to YNiC, he will give a talk at 4 pm in YNiC. There will be 2 short talks: 1) Coregistration of MEG and MRI using a stereo camera 2) Issues with beamforming statistics and regions of interest These talks will be followed by a drinks reception for Will. 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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