ynic-users September 2010

ynic-users@ynic.york.ac.uk

10 participants
18 discussions

Re: BET settings
by Chris Racey 15 Sep '10

15 Sep '10

I ran 3 identical first level FSL analyses of a localiser scan in order to compare the different bet settings (applied to all structural and functional images). I can confirm that BET with the recursive flag (-R) produces the best outcomes with higher Z values when transformed to standard space. The -B option looks good when examining the resulting BET images, and deals nicely with residual neck artefacts, but actually produces worse results at the level of the statistics. Below are images showing zstats from each first level analysis (face-place localiser), converted to standard space and displayed on the MNI brain. PPA (blue), FFA (orange), standard space - BET with no options http://i.imgur.com/q3FdX.png PPA (blue), FFA (orange), standard space - BET with -B option http://i.imgur.com/QC9al.png PPA (blue), FFA (orange), standard space - BET with recursive option (-R) http://i.imgur.com/Nqob1.png Activation is more extensive and more significant with the -R option. Images of the structural scans after each bet extraction can be seen in the album below http://laserdragon.imgur.com/brainimaging It seems that the standard pipeline involves using the -R option anyway, but I thought people might be interested to see the difference it makes, and that the -B option turns out to be pretty bad. Chris

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Re: BET settings
by Mark Hymers 13 Sep '10

13 Sep '10

On Mon, 13, Sep, 2010 at 05:53:51PM +0100, Chris Racey spoke thus.. > Actually, after my last message, Padraig came to see me and mentioned > another option -R which iteratively repeats the BET procedure from different > starting points. He suggested that this may achieve the same improved > result. I tried this option instead and indeed it does still seem to be an > improvement. However it runs considerably quicker and doesn't seem to result > in intensity changes in the image. That was going to be my suggestion too. I don't now normally run bet without using the -R flag. As Andre says, changing the starting co-ords can also help - for the record, the standard automatic cleanup for the structural scans currently uses -c 90 116 166 but doesn't use -R. I'm not entirely sure why it doesn't as I thought it did (and was about to say it did until I double checked). I'll probably change this to use -R by default (for the automatic ones) unless someone can remind me why it doesn't... Mark -- Mark Hymers York Neuroimaging Centre

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Re: BET settings
by Andre Gouws 13 Sep '10

13 Sep '10

the -c option flag too can be useful and has virtually no cost .. this simple sets the centre of gravity to which the initial sphere is fitted. find the coordinates of the AC in your participant (slice numbers) set the -c flag to this and usually the initial extraction is vastly improved. Andre' Chris Racey wrote: > Thanks Tony, > > That's a good point, I will be in a position to do this comparison in the > next day or so, after the analysis I'm running finishes. > > Actually, after my last message, Padraig came to see me and mentioned > another option -R which iteratively repeats the BET procedure from different > starting points. He suggested that this may achieve the same improved > result. I tried this option instead and indeed it does still seem to be an > improvement. However it runs considerably quicker and doesn't seem to result > in intensity changes in the image. > > I will investigate the results of these procedures on statistical outcomes > and post a comparison in the next couple of days. > > Chris > > -----Original Message----- > From: ynic-users-bounces(a)ynic.york.ac.uk > [mailto:ynic-users-bounces@ynic.york.ac.uk] On Behalf Of > am501(a)psych.york.ac.uk > Sent: 13 September 2010 17:43 > To: Chris Racey > Cc: ynic-users(a)ynic.york.ac.uk > Subject: Re: BET settings > > Thanks for this Chris. Have you any side by side fMRI analysis with and > without the -B option? Ti would be interesting to see whether or the > results of statistical treatments change and in what way. > > Tony > >> 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 >> >> -- >> ynic-users mailing list >> ynic-users(a)ynic.york.ac.uk >> https://www.ynic.york.ac.uk/mailman/listinfo/ynic-users >> > > > > -- > ynic-users mailing list > ynic-users(a)ynic.york.ac.uk > https://www.ynic.york.ac.uk/mailman/listinfo/ynic-users > > > -- > ynic-users mailing list > ynic-users(a)ynic.york.ac.uk > https://www.ynic.york.ac.uk/mailman/listinfo/ynic-users -- Andre' ************************************************************************ Andre Gouws York Neuroimaging Centre The Biocentre York Science Park Heslington YO10 5DG Tel: +44 (0) 1904 435327 Fax: +44 (0) 1904 435356

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Re: BET settings
by am501＠psych.york.ac.uk 13 Sep '10

13 Sep '10

Thanks for this Chris. Have you any side by side fMRI analysis with and without the -B option? Ti would be interesting to see whether or the results of statistical treatments change and in what way. Tony > 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 > > -- > ynic-users mailing list > ynic-users(a)ynic.york.ac.uk > https://www.ynic.york.ac.uk/mailman/listinfo/ynic-users >

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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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ynic-users September 2010