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ynic-users@ynic.york.ac.uk

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2778 discussions

by Mark Hymers

Hi, As some of you will know, due to an interesting issue [0] caused by GE installing an MRI scanner update, we have been having some problems with transferring and processing MRI data recently. Because GE (despite having admitted that this is their fault) are unable to fix this in a timely manner, we've now managed to work around it in house and have processed the backlog of data. Everything up until last week has now been processed and uploaded and last weeks' scans will be processed by the end of today. Apologies for the delay but this came out of nowhere and even diagnosing the problem took quite a bit of time. If anybody thinks that scans they have performed since the start of the year have not been processed, can you please send an email to mri-support(a)ynic.york.ac.uk with details and we'll look into it. Cheers, Mark [0] For Those Who Care About Technical Details The executive summary is that they've changed the two values which represent the Minimum (0028,0108) and Maximum (0028,0109) pixel values in the image from 16 bit signed to 16 bit unsigned. The data which is exported is still 16 bit signed and so this change makes absolutely no sense whatsoever. Quite a bit of DICOM code I've looked at will cope with either US or SS for these values but expects them to be consistent with the actual data (which makes sense, if you're expressing a minimum or maximum, it should be done using the same data type as the data). A full dissection of the problem follows: Old DICOM Image (selected tags only): (0028,0103) US 1 # 2, 1 PixelRepresentation (0028,0106) SS 0 # 2, 1 SmallestImagePixelValue (0028,0107) SS 275 # 2, 1 LargestImagePixelValue New DICOM Image (selected tags only): (0028,0103) US 1 # 2, 1 PixelRepresentation (0028,0106) US 0 # 2, 1 SmallestImagePixelValue (0028,0107) US 2211 # 2, 1 LargestImagePixelValue As you can se from the second column, the two bottom tags have changed their Value Representation from SS (Signed Short) to US (Unsigned Short). I've included the tag (0028,0103) because it explains how the actual pixel data is to be interpreted. MR is fixed at 16 bits which leaves two options: signed (2's complement) and unsigned. To quote from the DICOM Standard: Pixel Representation (0028, 0103): Data representation of the pixel samples. Each sample shall have the same pixel representation. Enumerated values: 0000H = unsigned integer 0001H = 2's complement So, the data is still written as signed, whilst the min and max values are written as unsigned. This is, at least in spirit if not letter, a violation of the DICOM standard. Note that although I state that according to the DICOM spec, MR is fixed at 16 bits, the interpretation of those 16 bits isn't fixed. See the tags BitsStored, BitsAllocated and HighBit if you're interested. (In practice, this is usually fixed for MR at 16, 16 and 15 respectively). The fix is to read the value out of the file and hack the relevant VRs back to being a signed integer instead of an unsigned one. The interesting thing is that images processed with Clariview (e.g. the YNiC Structurals which have FL_E in them) still use the signed value. So not only are GE wrong, they're inconsistently wrong too. -- Mark Hymers York Neuroimaging Centre

18 years, 3 months

Pulvermüller's talk abstract

by Silvia Gennari

Dear all, Dr Pulvermuller will be giving a talk on Thursday the 1st of March at 4PM at YNic (tomorrow). Here goes his abstract Early time course of psycholinguistic information access in the brain as revealed by neurophysiological imaging (EEG and MEG) Friedemann Pulvermüller, MRC Cognition and Brain Sciences Unit, Cambridge, UK, friedemann.pulvermuller(a)mrc-cbu.cam.ac.uk The main stream view in neurophysiological psycholinguistics has been that relatively late components of the brain response with latencies of 300-500 ms reflect higher stages of language processing, such as lexical access, semantic processing and context integration. This view is in contrast with data from psycholinguistics indicating very early psycholinguistic information access. Why, then, would ERP studies reveal late neurophysiological effects, but not the early ones psycholinguistic behavioral work would suggest? As language stimuli are very variable physically and psycholinguistically, the early components of the linguistic brain response, which are both focal and short-lived, may fall victim to the neurophysiological reflection of such stimulus variance [1]. Studies keeping stimulus variance to a minimum [2-3] or using new paradigms and analysis techniques [4-5] reported early (<250 ms) near-simultaneous effects of lexical and semantic processing in word recognition. The talk will discuss these effects, using neurophysiological data to judge linguistic models of the time course of psycholinguistic information access. A neurobiological model will be used to account for both the near-simultaneity of psycholinguistic information access as well as the minimal time delays observed. Distributed cell assemblies with specific cortical topographies binding information about word form and meaning may be the basis of near-synchrony and precise spatio- temporal patterning [5-7]. [1] Pulvermüller, F. (1999). Words in the brain's language. Behavioral and Brain Sciences, 22, 253-336. [2] Pulvermüller, F., Lutzenberger, W., et al. (1995). Electrocortical distinction of vocabulary types. Electroencephalography and Clinical Neurophysiology, 94, 357-370. [3] Pulvermüller, F., Assadollahi, R., & Elbert, T. (2001). Neuromagnetic evidence for early semantic access in word recognition. European Journal of Neuroscience, 13(1), 201-205. [4] Hauk, O., Davis, M. H., Ford, M., Pulvermüller, F., & Marslen- Wilson, W. (2006). The time course of visual word-recognition as revealed by linear regression analysis of ERP data. Neuroimage, in press. [5] Pulvermüller, F. (2005). Brain mechanisms linking language and action. Nature Reviews Neuroscience, 6(7), 576-582. [6] Pulvermüller, F. (2006). Word processing in the brain as revealed by neurophysiological imaging using EEG and MEG. In G. Gaskell (Ed.), Handbook of Psycholinguistics (pp. in press). Oxford: Oxford University Press. [7] Pulvermüller, F., & Shtyrov, Y. (2006). Language outside the focus of attention: the mismatch negativity as a tool for studying higher cognitive processes. Progress in Neurobiology, 79, 49-71. Silvia Gennari Department of Psychology University of York Heslington, York YO10 5DD United Kingdom

18 years, 3 months

MRI participants

by Claire Fox

I am looking for 6 people to volunteer for MRI, on the 6th (3 people) and (3 people) 9th of March, between 12 and 2pm. Please let me know if our available and if you are already registered on the data base. Thank you * Participants are paid £5.

18 years, 3 months

YNiC Closing at 5pm today

by Mark Hymers

The YNiC open plan area will be closing at 5pm today as we need to perform some IT maintenance which cannot be done with users present. We will open again as normal tomorrow (Friday) morning. Apologies for the short notice. Mark -- Mark Hymers York Neuroimaging Centre

18 years, 4 months

Friedemann Pulvermuller

by Silvia Gennari

Dear all, There will be a talk by Friedemann Pulvermüller (MRC-CBU) on Thursday the 1st of March at 4PM at the YNic. Dr. Pulvermüller will be teaching Advanced Neuroimaging to the master students (CNS) earlier in the day and has kindly agreed to give a second talk for a more general audience. Dr. Pulvermüller works in cognitive neuroscience of language and has written extensively on the topic. He has used fMRI, TMS and MEG techniques to ask question about both time course and localization of brain activity during language processing. He has also investigated neuropsychological issues such as aphasia. Here is a link to his website http://www.mrc-cbu.cam.ac.uk/people/people-pages.php?id=105 Everybody is welcome. Silvia Silvia Gennari Department of Psychology University of York Heslington, York YO10 5DD United Kingdom

18 years, 4 months

Re Use of the Biocentre facilities at YNiC

by Gary Green

Apologies to anyone who this may not concern. We have had another complaint from the receptionist of the Biocentre who is passing on the other tenants views. We are being asked not to use the kitchen facilities to socialise and there should be no more than two people in there at any one time. The other tenants are especially upset as the kettle has been broken and that we are using their coffee amongst other things. As you can imagine this has caused problems as the biocentre rely on the receptionist for catering for meetings. We rely on the goodwill of the receptionists in the Biocentre and problems of this kind could damage the long term benefits we get from working with them. Please can I ask users not to use the kitchen next to reception. There is a kitchen along the corridor in the glassed roof area. DO NOT use other people's milk/coffee/food/cutlery/bowls etc YNiC will put a kettle in the meeting room in the MRI corridor. While we are on the subject I would also like to add that YNIC has visits regularly and the standards of the open plan have started to drop dramatically again, I and other members of the team do not have time to clean up after users on a morning. The cleaners are not here to tidy up coffee cups etc, or rearrange furniture. Please leave the open plan area and desks as you find them ready for the next person. If you have cups with liquid still in you can empty this in the sink in MRI corridor. Please flush the fluids away after you. Thank you -- Gary Green York Neuroimaging Centre The Biocentre York Science Park Innovation Way Heslington York YO10 5DG http://www.ynic.york.ac.uk tel. 01904 435349 fax 01904 435356 mobile 07986 778954

18 years, 4 months

Research design in neuroimaging students' project presentations

by Silvia Gennari

Dear all, Sorry if you receive this message twice. Masters students in Cognitive Neuroscience will be giving presentations at YNic tomorrow and next Thursday at 4PM. They will present the research they are planning to conduct during the summer. Everyone is welcome. The schedule is as follows Thursday February 15th 4PM - Is it a face or a house? Using binocular rivalry to investigate visual awareness (supervisor: Tim Andrews). Pippa Baird Jenny Cox 4.15PM - Do specialized visual areas really exist in the human ventral stream? (supervisors: Tim Andrews and Tom Hartley) Alex Clarke Phil Pell 4.30PM - Representing actions through language (supervisor: Gennari) Claire Moody (Veronica) Tzu-Hui Chuang Thursday - February 22nd. 4PM - What is the difference between familiar and unfamiliar face perception? (Tim Andrews) Jodie Davies Spyroula Spyrou 4.15PM - Hemispheres and handwriting: an MEG project (Andy Ellis) Nuria Donamayor Alonso 4.30 PM - Localisation of auditory function with fMRI and MEG (Quentin Summerfield) Emma Knowles Sam Matthias 4.45PM -Brain functional connectivity from MEG data (Gary Green) Dave Cole Chris Neale John Griffiths Lisa Brindley Alana James Silvia Gennari Department of Psychology University of York York, YO10 5DD United Kingdom

18 years, 4 months

Re: project presentations at YNic

by Tim Andrews

Hi Silvia, Could you send an email to ynic-users(a)ynic.york.ac.uk to let them know about the MSc sessions on the following Thursdays. Cheers, Tim Silvia Gennari wrote: > Dear all, > > This is just a remainder that the CNS master students' project > presentations is starting this week at YNic on Thursday at 4PM. Here > is a provisional list of presenters for this and next week, please let > me know if there is any problem with the arrangements. > > > Thursday February 15th > > > 4PM - Is it a face or a house? Using binocular rivalry to > investigate visual awareness (supervisor: Tim Andrews). > Pippa Baird > Jenny Cox > > 4.15PM - Do specialized visual areas really exist in the human > ventral stream? (supervisors: Tim Andrews and Tom Hartley) > Alex Clarke > Phil Pell > > > 4.30PM - Representing actions through language (supervisor: Gennari) > Claire Moody > (Veronica) Tzu-Hui Chuang > > > > Thursday - February 22nd. > > > > 4PM - What is the difference between familiar and unfamiliar face > perception? (Tim Andrews) > Jodie Davies > Spyroula Spyrou > > > 4.15PM - Hemispheres and handwriting: an MEG project (Andy Ellis) > Nuria Donamayor Alonso > > > 4.30 PM - Localisation of auditory function with fMRI and MEG > (Quentin Summerfield) > Emma Knowles > Sam Matthias > > > 4.45PM -Brain functional connectivity from MEG data (Gary Green) > Dave Cole > Chris Neale > John Griffiths > Lisa Brindley > Alana James > > > Hope to see you all there. > > > Silvia > > Silvia Gennari > > Department of Psychology > > University of York > > Heslington, York > > YO10 5DD > > United Kingdom > > > > > -- Dr Tim Andrews Department of Psychology University of York York, YO10 5DD UK Tel: 44-1904-434356 Fax: 44-1904-433181 http://www-users.york.ac.uk/~ta505/ http://www.york.ac.uk/depts/psych/www/admissions/cns/

18 years, 4 months

new web page

by Gary Green

A new web page has been added to ynic's user resource section https://www.ynic.york.ac.uk/user-resources/conferences-and-abstract-deadlin… It tells you dates of conference and submission times. Entries are automatically deleted once the conference has passed. If you know of any neuroimaging conferences that should be added please send an email to rem(a)ynic.york.ac.uk -- Gary Green York Neuroimaging Centre The Biocentre York Science Park Innovation Way Heslington York YO10 5DG http://www.ynic.york.ac.uk tel. 01904 435349 fax 01904 435356 mobile 07986 778954

18 years, 4 months

One day closure of YNiC - 25th January 2007

by Gary Green

Dear Users On Thursday the 25th of January, 2007, YNiC will be closed for the day. This is so that the YNiC team can review and plan their strategy for the year. We apologise for any inconvenience that this might cause. Later in the year there will be an opportunity for all users to contribute to discussions of the future plans of YNiC. -- Gary Green Director York Neuroimaging Centre The Biocentre York Science Park York YO10 5DG tel (+44) (0) 1904 435349 fax (+44) (0) 1904 435356

18 years, 5 months

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