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2841 discussions

BET settings
by Chris Racey 13 Sep '10

13 Sep '10

Hi all, I was having some problems bet extracting some of my structural scans, I was getting a lot of left over neck that was screwing up the alignment. I noticed the current version of bet has a new option flag (to me at least), which focuses on cleaning up the neck. The option is -B . When using this flag the processing takes considerably longer, something along the lines of 10-15 mins per scan. However, not only did it resolve the issue, but the resulting image looks cleaner and more precise than I would expect from a normal bet. I've attached a comparison image so you can see the effect. I did similar comparisons running this flag with functional data and it also shows improvements. At the moment I'm re-processing my data files in this way before running my analysis. I thought I'd mention this in case it might be a useful option for other people to use, but also in case anyone knows any reason why it might be problematic. I'd be keen to know if anyone knows of any reason why I shouldn't use it? I notice the overall intensity seems slightly lower when this flag has been used, is this likely to be a problem? Cheers, Chris Racey

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YNiC seminar 16th September
by rem 13 Sep '10

13 Sep '10

Dear Users This week (4-5 pm YNiC open plan) Miriam Johnson from the Hull York Medical School will give a talk on "Magnetoencephalography appearances in breathless patients with and without air flow directed to the face." Everyone is welcome to attend. Best wishes Rebecca Background: Intractable breathlessness is a common and devastating consequence of many diseases. Breathlessness affects all aspects of life, causing major distress for both patient and caregiver. Many patients face psychological, social and physical repercussions of persistent breathlessness, which require, long-term NHS support especially out of hours. Research into possible mechanisms for the perception of breathlessness has largely concentrated on peripheral pathways. However there is a growing interest in functional brain imaging using positron electron tomography scanning and functional MRI (fMRI), mainly in induced breathlessness in healthy volunteers. Similarities with pain perception are striking. However, little is known of these processes in patients with chronic breathlessness due to lung disease, indeed, one study suggests that patients with asthma demonstrate habituation and down-regulation of perceived unpleasantness due to breathlessness. Moreover we know nothing of the effect of interventions to improve breathlessness; patients with chronic breathlessness tolerate fMRI poorly. Magnetoencephalography (MEG) scanning is a possibly tolerated method but has not been tried. There is some clinical evidence that the use of a handheld fan reduces the sensation of breathlessness and may reduce the need for nebulisers and oxygen. The fan directs airflow to the area innervated by the 2nd and 3rd branches of the trigeminal nerve. It is universally available, cheap, non-invasive and easy to use in any setting alongside any other breathlessness intervention with no contra-indications. As the cost to the NHS of oxygen, nebulisers and inhalers and hospital admission are considerable, this area warrants research both with regard to clinical effect but also to mechanism of action. -- ************************************************************************ 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] Postdoctoral and graduate RA positions University of Oxford
by Ekaterini Klepousniotou 07 Sep '10

07 Sep '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 [mailto:nlc_distribution-bounces@nlc2009.angularis.org] On Behalf Of Kate Watkins Sent: 07 September 2010 10:01 To: nlc_distribution(a)nlc2009.angularis.org Subject: [NLC2009] Postdoctoral and graduate RA positions University of Oxford We are advertising two jobs (one graduate research assistant and one postdoctoral researcher) in the Speech and Brain Research Group ((http://www.fmrib.ox.ac.uk/speech-and-brain) at the University of Oxford - Department of Experimental Psychology and FMRIB Centre. The research will investigate interactions between auditory and motor areas in the brain during speech perception and production. The project will employ a variety of techniques either separately or in combination; these include behavioural measures, TMS, MEG and functional MRI. Both positions are funded from 1 January 2011 for two years in the first instance with the possibility of renewal. Initial scientific enquiries about the post or the project may be directed to Dr Kate Watkins (email: kate.watkins(a)psy.ox.ac.uk<mailto:kate.watkins@psy.ox.ac.uk>) or Dr Riikka Mottonen (email: riikka.mottonen(a)psy.ox.ac.uk<mailto:riikka.mottonen@psy.ox.ac.uk>). Further particulars, including instructions on applying for these posts and a copy of the application form, are available from the Administration Offices (email: applications(a)psy.ox.ac.uk) or can be accessed on the departmental website at http://www.psy.ox.ac.uk/. The closing date for applications is 12 noon on 8 October 2010. Please quote reference number CQ/10/013 (postdoc) CQ/10/014 (graduate) on all correspondence. Interviews are scheduled for the end of October 2010. Kate Watkins, PhD University Lecturer in Department of Experimental Psychology South Parks Road, Oxford, OX1 3UD Tel: +44 (0)1865 271314 / 222581 http://www.fmrib.ox.ac.uk/speech-and-brain

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RE : Seminar today at 2pm
by Gary Green 02 Sep '10

02 Sep '10

Dear Colleagues Today, Professor Shoogo Ueno from Japan will be giving the IEEE Magnetics Society Distinguished Lecturers seminar in York. The title is "Biomagnetics: An Interdisciplinary Field Where Magnetics, Biology, and Medicine Overlap" Professor Ueno writes.. This lecture focuses on the advances in biomagnetics and bioimaging obtained mostly in our laboratory in recent years. The lecture describes: (1) a method of localized magnetic stimulation of the human brain by TMS with a figure-eight coil; (2) magneto- encephalography (MEG) to measure extremely weak magnetic fields produced from brain electrical activity using superconducting quantum interference device (SQUID) systems; (3) impedance MRI and current MRI; (4) cancer therapy and control of iron-ion release from, and uptake into, ferritin, an iron-storage protein, by using both high frequency and pulsed magnetic fields and magnetic nanoparticles; and (5) magnetic control of biological cell orientation and cell growth by strong static magnetic fields. These new biomagnetic approaches will open new horizons in brain research, brain treatment, and regenerative medicine. The seminar will be in PX001 in the Exhibition Centre of the University, at 14:00 on the 2nd of September. 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 (Richard Lee) +44 (0) 1904 435329 fax +44 (0) 1904 435356 mobile +44 (0) 788 191 3004

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Lecture next week
by Gary Green 27 Aug '10

27 Aug '10

Dear Colleagues Next week, Professor Shoogo Ueno from Japan will be giving the IEEE Magnetics Society Distinguished Lecturers seminar in York. The title is "Biomagnetics: An Interdisciplinary Field Where Magnetics, Biology, and Medicine Overlap" Professor Ueno writes.. This lecture focuses on the advances in biomagnetics and bioimaging obtained mostly in our laboratory in recent years. The lecture describes: (1) a method of localized magnetic stimulation of the human brain by TMS with a figure-eight coil; (2) magneto- encephalography (MEG) to measure extremely weak magnetic fields produced from brain electrical activity using superconducting quantum interference device (SQUID) systems; (3) impedance MRI and current MRI; (4) cancer therapy and control of iron-ion release from, and uptake into, ferritin, an iron-storage protein, by using both high frequency and pulsed magnetic fields and magnetic nanoparticles; and (5) magnetic control of biological cell orientation and cell growth by strong static magnetic fields. These new biomagnetic approaches will open new horizons in brain research, brain treatment, and regenerative medicine. details of the talk and a short biography of Professor Ueno are in the attachment to this email The seminar will be in PX001 in the Exhibition Centre of the University, at 14:00 on the 2nd of September. 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 (Richard Lee) +44 (0) 1904 435329 fax +44 (0) 1904 435356 mobile +44 (0) 788 191 3004

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Early onset?
by Philip Quinlan 27 Aug '10

27 Aug '10

We recently carried out an MRI study and (to keep it simple) we compared two conditions A and B. We found two regions that preferred A to B, region 1 and 2, respectively. I was keen to explore the time series a little further. So what I did was take the A-B difference for each subject in each of the regions and compute the 95%CI for each 2 sec interval from the start of the stimulus presentation. We get a difference time series for each region and for each point we have a 95%CI. I have plotted the CIs for each point on each function (one for region 1 and one for region 2). Now I note at which time point the CIs reflect a sig diff (i.e., dont cross the x axis) and what I find is that the critical difference occurs earlier for region 1 than 2. At last a window on the time course of psychological functioning? I, of course, now want to claim my Nobel Prize but suspect this is completely flawed. Please advise. Philip. ******************************************************************** Philip Quinlan E-Mail: ptq1(a)york.ac.uk Department of Psychology FAX: (01904) 433181 The University of York Tel: (01904) 430000 Ext. 3135 Heslington Direct : (01904) 433135 York YO10 5DD U.K. ********************************************************************

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book on loan
by Gary Green 13 Aug '10

13 Aug '10

I would be very grateful if the person who borrowed the book on Magnetic Resonance Spectroscopy edited by Matthews could return it, thanks Gary -- 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 (Richard Lee) +44 (0) 1904 435329 fax +44 (0) 1904 435356 mobile +44 (0) 788 191 3004

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oh dear
by Philip Quinlan 12 Aug '10

12 Aug '10

http://www.hindawi.com/journals/ijmms/2010/769780.html ******************************************************************** Philip Quinlan E-Mail: ptq1(a)york.ac.uk Department of Psychology FAX: (01904) 433181 The University of York Tel: (01904) 430000 Ext. 3135 Heslington Direct : (01904) 433135 York YO10 5DD U.K. ********************************************************************

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birthday cakes
by Richard Lee 11 Aug '10

11 Aug '10

Birthday cakes in open plan, help yourself Richard

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Today in YNiC
by Gary Green 29 Jul '10

29 Jul '10

There is an additional seminar today At 2pm There will be a talk entitled "NMR and MRI sensitivity enhancement by Parahydrogen Induced Polarization" by Kerstin Münnemann Max Planck Institute for Polymer Research, Mainz, Germany Despite its wide applicability in chemistry, biology and medicine, Nuclear Magnetic Resonance (NMR) spectroscopy still suffers from its inherently low sensitivity. Exploiting the large signal enhancements associated with hyperpolarization techniques, such as Parahydrogen Induced Polarization (PHIP), however, NMR or MRI qualify for monitoring dynamic processes in real time. In this lecture, the synthesis and hyperpolarization of several biocompatible molecules like barbiturates, Vinylpyrrolinidon (blood plasma expander) or Dimethylcarboxylat (precursor to fumarate) will be presented. Polarization transfer to 13C in these molecules by using adequate pulse sequences is demonstrated. Moreover, constant NMR signal enhancement of 1H and 13C is shown using a continuous delivery of parahydrogen by hollow fiber membranes. This allows the acquisition of two-dimensional NMR experiments requiring multiple excitations with constant initial polarization. The membrane technique can be easily extended to produce a continuous flow of a hyperpolarized liquid as will be shown for MRI applications. All welcome

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