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YNiC Seminar this Thursday
by Gary Green 24 May '10

24 May '10

This Thursday (May 27th), David Crewther will give a project proposal talk at 4 pm in YNiC open plan entitled "Nonlinearities in Multi-focal Magnetoencephalography" Abstract Multi-focal visual evoked potentials have become a standard tool in the diagnosis of glaucoma and retinal vascular disease. However, the randomization techniques employed to de-correlate sequences for stimulation of patches of visual field also offer the opportunity for analysis of non-linearities in evoked responses. These have been used to derive separate magnocellular and parvocellular contributions to the cortical VEP. Here we propose to develop similar m-sequence based pseudo-random stimulation techniques to MEG with the purpose of localizing the time-course of activation of the M and P pathways as they extend into dorsal and ventral cortical streams. A beam-former approach to this question will be followed, answering questions regarding the role of the “magnocellular advantage” in object recognition. An initial 13 patch cortically scaled m-sequence multi-focal stimulus has been developed. Extensions to higher resolution cortical imaging are proposed. However multi-focal fMRI imaging indicates eye-movement control is vital. Hence a gaze-contingent system using retinally-stabilized presentation is being developed that will allow an estimate of the optimal high resolution MEG mapping of visual cortex. All welcome YNIC 5th Birthday drinks will be held immediately after the seminar -- 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 (Claire Fox) +44 (0) 1904 435329 fax +44 (0) 1904 435356 mobile +44 (0) 788 191 3004

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Seminar today
by Gary Green 24 May '10

24 May '10

Vitaly Napadow "Neuroimaging in basic and translational acupuncture research" This talk will take place today from 12-1 pm. Link to Vitaly Nadapow's website: Vitaly Napadow's webpage: http://www.nmr.mgh.harvard.edu/~vitaly/ *Brief Bio* Dr. Vitaly Napadow is an assistant professor at Harvard Medical School and the Department of Radiology at Massachusetts General Hospital. He received his Ph.D. in biomedical engineering from the Massachusetts Institute of Technology. Vitaly also graduated from the New England School of Acupuncture (NESA), and practices acupuncture at Brigham & Women's Hospital Pain Management Center. His research interests focus on the processing of acupuncture by the brain, and the mechanisms underlying acupuncture efficacy for various disease states including chronic pain. **Abstract** Acupuncture is an ancient East Asian healing modality that has been in use for more than 2000 years. Unfortunately, its mechanisms of action are not well understood, and controversy regarding its clinical efficacy remains. Importantly, acupuncture needling often evokes complex somatosensory sensations and may modulate the cognitive/affective perception of pain, suggesting that many effects are supported by the brain’s control of central nervous system networks. Modern neuroimaging techniques such as functional magnetic resonance imaging provide a means to safely monitor brain activity in humans and may be used to both characterize brain response to acupuncture stimulation, as well as to map the neurophysiological correlates of acupuncture’s effects on various pathologies. In this talk, I will outline some of our lab’s recent studies including (1) mapping the specific brain correlates of acupuncture sensation, known as deqi, which is thought to be associated with good clinical outcomes, (2) investigating acupuncture’s delayed effects on resting functional connectivity in default mode and sensorimotor brain networks, and (3) evaluating the effects of a course of clinical acupuncture therapy on somatosensory processing and somatotopy in patients with carpal tunnel syndrome. All welcome -- 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 (Claire Fox) +44 (0) 1904 435329 fax +44 (0) 1904 435356 mobile +44 (0) 788 191 3004

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Today in YNiC
by Gary Green 20 May '10

20 May '10

This afternoon, the CEO of the MRC will be visiting YNiC. He will be in MRI and then MEG from 2.20pm until 3pm. If you would like to present an aspect of your work, even for 10minutes, you would be welcome to come along. There is also a seminar today at 4pm This week Gina Humphries will give a project proposal talk at 4 pm in YNiC open plan on "Semantic indeterminacy in the brain: linking production and comprehension processes". Abstract: "This study aims to examine which regions of the brain are recruited during sentence comprehension and sentence production. Gennari and MacDonald (2008, 2009) have recently argued that semantic ambiguity as to who-is-doing-what-to-whom in phrases is an important source of reading difficulty. For example, in reading “the movie that the director…,” a similar interpretation is entertained 90% of the time (that the director wrote the movie), whereas in reading “the director that the movie….,” many interpretations are possible. The authors showed that the proportion of alternative relationships entertained between the nouns, as indexed by a sentence completion study, predicts reading difficulty. Here, we aim to investigate the brain mechanisms underlying the comprehension and production of these structures. Specifically, we ask whether left inferior frontal gyrus (LIFG) and other regions of the language processing network such as posterior middle temporal gyrus (PMTG) are sensitive to the degree of who-is-doing-what-to-whom ambiguity in comprehension and production." Everyone is welcome to attend. -- 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 (Claire Fox) +44 (0) 1904 435329 fax +44 (0) 1904 435356 mobile +44 (0) 788 191 3004

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YNiC seminar 20th May
by rem 17 May '10

17 May '10

Dear Users This week Gina Humphries will give a project proposal talk at 4 pm in YNiC open plan on "Semantic indeterminacy in the brain: linking production and comprehension processes". Abstract: "This study aims to examine which regions of the brain are recruited during sentence comprehension and sentence production. Gennari and MacDonald (2008, 2009) have recently argued that semantic ambiguity as to who-is-doing-what-to-whom in phrases is an important source of reading difficulty. For example, in reading “the movie that the director…,” a similar interpretation is entertained 90% of the time (that the director wrote the movie), whereas in reading “the director that the movie….,” many interpretations are possible. The authors showed that the proportion of alternative relationships entertained between the nouns, as indexed by a sentence completion study, predicts reading difficulty. Here, we aim to investigate the brain mechanisms underlying the comprehension and production of these structures. Specifically, we ask whether left inferior frontal gyrus (LIFG) and other regions of the language processing network such as posterior middle temporal gyrus (PMTG) are sensitive to the degree of who-is-doing-what-to-whom ambiguity in comprehension and production." 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 13 May '10

13 May '10

Dear Users Today Azizah Almaghyuli will give a project proposal talk at 4 pm in YNiC open plan on "Naming and comprehension after transcranial direct current stimulation in health volunteers and patients with stroke aphasia". The study will evaluate the effect of transcranial direct current stimulation( tDCS) on picture naming and synonym judgement in healthy participants, with the ultimate aim of evaluating whether this technique could be used to improve naming and comprehension difficulties following a stroke. 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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[Fwd: [SPM] Engineer position at USC, Los Angeles, January 2011]
by Gary Green 13 May '10

13 May '10

FYI ------------------------------------------------------------------------ Research Programmer, University of Southern California, Los Angeles, USA The Department of Electrical Engineering at the University of Southern California is seeking a research programmer to participate in the development, distribution and support of software for functional brain mapping. The programmer will be responsible for implementing software for all phases of the analysis of magnetoencephalograpy (MEG) and electroencephalography (EEG) data and its integration of other functional and structural imaging modalities. The resulting software, which will be developed under grant support from the National Institutes of Health, will be distributed to researchers throughout the US and the rest of the world, for analysis of data collected in cognitive neuroscience and clinical research studies. This project will be conducted under the supervision of Professor Richard Leahy in the Department of Electrical Engineering and will involve close collaboration with researchers at USC and other institutions. Responsibilities * Play a leading role in developing common workflow, data structures, and file formats for use in analysis of MEG and EEG data. * Develop and document code to implement algorithms for analysis and display of M/EEG data. * Development of procedures for automated testing of software and software updates. * Develop and support procedures for distribution and documentation of new software. * Participate in training of users * Participate in research meetings and interact with PhD students, postdocs and research faculty in Dr. Leahy's lab in the development of new approaches to the analysis of MEG and EEG data. * Work with collaborators who are also developing software to facilitate interoperability between software packages with the ultimate goal of producing a single software package for EEG and MEG data analysis. * More information about Brainstorm, the existing software package: http://neuroimage.usc.edu/brainstorm Minimum qualifications * Masters Degree in Computer Science or Electrical Engineering * 2 years post graduate experience * Knowledge of the basic principles underlying EEG and MEG signal processing * Programming experience with Matlab and Java Conditions of employment * Starting from January 2011 * Duration: position available for a minimum of two years * Salary: depends on experience and qualifications * USC has excellent benefits, including health benefits and retirement plans with employer contributions after six months. * The University of Southern California values diversity and is committed to equal opportunity in employment. Application * To apply, please send an email to Francois Tadel, main developer of the Brainstorm software: tadel(a)usc.edu. * Your application should include: your CV, a description of your programming skills, a detailed description of your previous software development projects. * Application deadline: Open until filled.

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YNiC seminar 13th May
by rem 10 May '10

10 May '10

Dear Users This week Azizah Almaghyuli will give a project proposal talk at 4 pm in YNiC open plan on "Naming and comprehension after transcranial direct current stimulation in health volunteers and patients with stroke aphasia". The study will evaluate the effect of transcranial direct current stimulation( tDCS) on picture naming and synonym judgement in healthy participants, with the ultimate aim of evaluating whether this technique could be used to improve naming and comprehension difficulties following a stroke. 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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external speaker at YNiC on 24th May
by rem 07 May '10

07 May '10

Dear Users Vitaly Napadow from the Department of Radiology, Harvard Medical School, will be giving a talk on "Neuroimaging in basic and translational acupuncture research" on Monday 24th May. This talk will take place from 12-1 pm in YNiC open plan. Everyone is welcome to attend. Best wishes Rebecca Link to Vitaly Nadapow's website: http://www.nmr.mgh.harvard.edu/~vitaly/ <http://www.nmr.mgh.harvard.edu/%7Evitaly/> *Brief Bio* Dr. Vitaly Napadow is an assistant professor at Harvard Medical School and the Department of Radiology at Massachusetts General Hospital. He received his Ph.D. in biomedical engineering from the Massachusetts Institute of Technology. Vitaly also graduated from the New England School of Acupuncture (NESA), and practices acupuncture at Brigham & Women's Hospital Pain Management Center. His research interests focus on the processing of acupuncture by the brain, and the mechanisms underlying acupuncture efficacy for various disease states including chronic pain. **Abstract** Acupuncture is an ancient East Asian healing modality that has been in use for more than 2000 years. Unfortunately, its mechanisms of action are not well understood, and controversy regarding its clinical efficacy remains. Importantly, acupuncture needling often evokes complex somatosensory sensations and may modulate the cognitive/affective perception of pain, suggesting that many effects are supported by the brain’s control of central nervous system networks. Modern neuroimaging techniques such as functional magnetic resonance imaging provide a means to safely monitor brain activity in humans and may be used to both characterize brain response to acupuncture stimulation, as well as to map the neurophysiological correlates of acupuncture’s effects on various pathologies. In this talk, I will outline some of our lab’s recent studies including (1) mapping the specific brain correlates of acupuncture sensation, known as deqi, which is thought to be associated with good clinical outcomes, (2) investigating acupuncture’s delayed effects on resting functional connectivity in default mode and sensorimotor brain networks, and (3) evaluating the effects of a course of clinical acupuncture therapy on somatosensory processing and somatotopy in patients with carpal tunnel syndrome. -- ************************************************************************ 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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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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