ynic-users May 2016

ynic-users@ynic.york.ac.uk

3 participants
11 discussions

YNiC talks today
by Junior Whiteley 09 Jun '16

09 Jun '16

Dear users, Two talks will be given today at 4pm in B020. Mladen Sormaz will help us understand the contents of this thoughts on resting state brains in a talk entitled: ‘Understanding the content of thought’ Charlotte Murphy will then dazzle us with her eloquence and sagacity via a talk entitled: ‘Distinguishing stimulus independence from representation’ As always there will be refreshments in C Block reception after the talks. We look forward to seeing you there. All the best, Junior -- Junior Whiteley York Neuroimaging Centre junior.whiteley(a)ynic.york.ac.uk

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celebration of 150th paper
by Gary Green 26 May '16

26 May '16

I thought you would be pleased to hear that the 150th paper associated with the Imaging Centre has just been accepted. A good excuse for a party I suggest Gary -- --------------- Gary Green York Neuroimaging Centre & Centre for Hyperpolarisation in Magnetic Resonance The Biocentre York Science Park Innovation Way Heslington York YO10 5NY tel +44 (0) 1904 435349 fax +44 (0) 1904 435356 mobile +44 (0) 788 191 3004 http://www.ynic.york.ac.uk http://www.york.ac.uk/chym/ https://www.ynic.york.ac.uk/about-us/people/ggrg

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MRI delivery
by Gary Green 24 May '16

24 May '16

Dear Colleagues I am pleased to announce that the new MRI scanner is now in the magnet room and the RF cage has been sealed. Commissioning is now under way. For those of you who watched the first installation 11 years ago, this one was considerably faster. From lifting out of the lorry, the magnet was in the building less than 40 minutes later. No bumps or scratches. Two pictures are now available on the ynic website showing the magnet coming out of the lorry and being prepared to be pushed (all 13 Tons of it) into the building. Gary -- --------------- Gary Green York Neuroimaging Centre & Centre for Hyperpolarisation in Magnetic Resonance The Biocentre York Science Park Innovation Way Heslington York YO10 5NY tel +44 (0) 1904 435349 fax +44 (0) 1904 435356 mobile +44 (0) 788 191 3004 http://www.ynic.york.ac.uk http://www.york.ac.uk/chym/ https://www.ynic.york.ac.uk/about-us/people/ggrg

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Fwd: Re: RE Biocentre - Fire Alarm Test - Tuesday 24th May 2016
by Gary Green 24 May '16

24 May '16

Please note =================== Hi All, Would you please be advised that we are now reaching the completion of the Biocentre's MRI Extension project; with this in mind, would you please be advised that I will be testing the operation of the fire alarm system on Tuesday 24th May 2016 between the hours of 14.00pm and 17.00pm. Due to the nature of the test being that the alarms will need to be activated; so to avoid anyone leaving the building, on each activation and it may need to be carried out on a number of occasions; the alarm will only sound for a short period of time (30 seconds approx). Although it is anticipated that a smooth operation of the above will be carried out successfully; should the alarm sound continuously for more than 1 minute, then all precautions need to be taken and all personnel should leave the building and go to their designated muster point. It is also assumed that these tests will at some point effect the Fire Alarm System in CHyM; although these will be alerts rather than full sounder activation; however, once again, should the alarms sound for more than 1 minute; the same will apply to the occupants of CHyM and all personnel should make their way out of the building as appropriate. In order to assist in making the end user / operatives aware, I will be affixing notices at the entrance doors of both the Biocentre and CHyM Buildings advising of this test on Tuesday afternoon (24/5/16). Hi Nick / / Gary G / Vicky, Could you please assist by sending out an email to all personnel within the two buildings. Should you have any queries regarding the above, please do not hesitate in giving me a call. Regards Kevin **Kevin Roberts** ****Contract Supervisor - University of York Mobile: 07494 425807 / kevin.roberts(a)york.ac.uk <mailto:kevin.roberts@york.ac.uk> Tel: 01904 325104 Ext: 5104 Estates Services University of York Providence House Innovation Close York YO10 5ZF *P****Please consider your environmental responsibility - think before you print!*

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YNiC Cluster maintenance
by Paul Elliott 23 May '16

23 May '16

Dear all, Tomorrow afternoon (24th May) the YNiC compute cluster will be taken off-line to investigate a problem that is currently limiting available capacity on the cluster. The work will begin at 1pm and will last up to 5 hours. During this time any jobs submitted to the queue will be held and will automatically run when service is resumed. Jobs submitted after 8am tomorrow morning will be held so that they are not running at 1pm when the work commences and any jobs running at 1pm will be stopped. Thanks, Paul. -- Paul Elliott, UNIX Systems Administrator York Neuroimaging Centre (YNiC), University of York

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Magnet delivery
by Gary Green 23 May '16

23 May '16

Dear Colleagues The new MRI machine arrived early this morning. The crane is also here and the lift into the new building should start some time after 9.15 and should be complete an hour later. Gary -- --------------- Gary Green York Neuroimaging Centre & Centre for Hyperpolarisation in Magnetic Resonance The Biocentre York Science Park Innovation Way Heslington York YO10 5NY tel +44 (0) 1904 435349 fax +44 (0) 1904 435356 mobile +44 (0) 788 191 3004 http://www.ynic.york.ac.uk http://www.york.ac.uk/chym/ https://www.ynic.york.ac.uk/about-us/people/ggrg

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Fwd: RE Biocentre - Fire Alarm Test - Tuesday 24th May 2016
by Gary Green 23 May '16

23 May '16

Apologies for this but we need to test the fire alarm system to the new MRI suite. This will happen tomorrow afternoon. The tests will be short bursts of the alarm. There is no need to leave the building. If the alarm is continuous then that is not a test and it is a real alarm. I apologise for any inconvenience caused Gary --------------- Gary Green York Neuroimaging Centre & Centre for Hyperpolarisation in Magnetic Resonance The Biocentre York Science Park Innovation Way Heslington York YO10 5NY tel +44 (0) 1904 435349 fax +44 (0) 1904 435356 mobile +44 (0) 788 191 3004 http://www.ynic.york.ac.uk http://www.york.ac.uk/chym/ https://www.ynic.york.ac.uk/about-us/people/ggrg Hi All, Would you please be advised that we are now reaching the completion of the Biocentre's MRI Extension project; with this in mind, would you please be advised that I will be testing the operation of the fire alarm system on Tuesday 24th May 2016 between the hours of 14.00pm and 17.00pm. Due to the nature of the test being that the alarms will need to be activated; so to avoid anyone leaving the building, on each activation and it may need to be carried out on a number of occasions; the alarm will only sound for a short period of time (30 seconds approx). Although it is anticipated that a smooth operation of the above will be carried out successfully; should the alarm sound continuously for more than 1 minute, then all precautions need to be taken and all personnel should leave the building and go to their designated muster point. It is also assumed that these tests will at some point effect the Fire Alarm System in CHyM; although these will be alerts rather than full sounder activation; however, once again, should the alarms sound for more than 1 minute; the same will apply to the occupants of CHyM and all personnel should make their way out of the building as appropriate. In order to assist in making the end user / operatives aware, I will be affixing notices at the entrance doors of both the Biocentre and CHyM Buildings advising of this test on Tuesday afternoon (24/5/16). Hi Nick / / Gary G / Vicky, Could you please assist by sending out an email to all personnel within the two buildings. Should you have any queries regarding the above, please do not hesitate in giving me a call. Regards Kevin **Kevin Roberts** ****Contract Supervisor - University of York Mobile: 07494 425807 / kevin.roberts(a)york.ac.uk <mailto:kevin.roberts@york.ac.uk> Tel: 01904 325104 Ext: 5104 Estates Services University of York Providence House Innovation Close York YO10 5ZF *P****Please consider your environmental responsibility - think before you print!*

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new MRI machine
by Gary Green 18 May '16

18 May '16

Dear Colleagues I hope you will be pleased to hear that we are close to accepting the new MRI scanner and building. Over the next few weeks there are some important events that you may be interested in or want to note This week the decoration of the inside of the building is completed and the final stages of installation of electrics, air con, fire alarm and security should be reached. Monday the 23rd : MRI delivery. Crane on site at 7.30am, delivery starts at 8am. They expect to complete by 2pm. Heavy rain is predicted, of course. Tuesday the 24th : the MRI access route will be bricked up and a door installed. The RF cage will be completed. Wednesday the 25th : commissioning of the MRI magnet begins. This includes attaching to the power supply, installing all the MRI equipment, attaching all the cooling systems. Importantly (for those on site) Tuesday the 31st : The MRI is topped up with Helium. Large Helium dewars will be wheeled along the MRI corridor. Tuesday the 31st : The first ramp of the magnet to 3Tesla starts. This allows the shimming of the magnet. The magnet is then taken back to earth's field, adjustments are made and it is taken back up to 3 Tesla. although the risk is small, this is the time when a quench can occur. If that happens, large amounts of Helium gas is released and the field, momentarily extends out beyond the 0.5milliTesla line. Later that day: MRI the final phase commissioning starts. 6th June : The handover of the building starts. On that day the operation of the building is demonstrated (air con, power, plumbing, security, alarms,...) 8th June : MRI testing by our team begins. 9th June : final acceptance tests of all the building operations is completed 10th June : Building handover. Issues still to be resolved Integration into the IT system Editing of local rules for MRI use Applications training (likely to be late July) Pulse programming training (date being negotiated - this is in Carolina, US) Installation of parahydrogen generator Installation of polariser Installation of stim PC(s) and stimulus delivery Hope that helps Gary -- --------------- Gary Green York Neuroimaging Centre & Centre for Hyperpolarisation in Magnetic Resonance The Biocentre York Science Park Innovation Way Heslington York YO10 5NY tel +44 (0) 1904 435349 fax +44 (0) 1904 435356 mobile +44 (0) 788 191 3004 http://www.ynic.york.ac.uk http://www.york.ac.uk/chym/ https://www.ynic.york.ac.uk/about-us/people/ggrg

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Fwd: Reminder - Research Seminar TODAY
by David Halliday 09 May '16

09 May '16

Reminder - Today P/L002 1-2PM The Human Connectome: Linking Brain Network Features to Healthy and Pathological Information Processing Monday 9 May 2016, 1.00PM to 14:00 *Speaker: *Professor Marcus Kaiser, Newcastle University Synopsis Our work on connectomics over the last 15 years has shown a small-world, modular, and hub architecture of brain networks [1,2]. Small-world features enable the brain to rapidly integrate and bind information while the modular architecture, present at different hierarchical levels, allows separate processing of various kinds of information (e.g. visual or auditory) while preventing wide-scale spreading of activation [3]. Hub nodes play critical roles in information processing and are involved in many brain diseases [4]. Nonetheless, general observations of human brain connectivity, or of patients at the group-level, have so far had little impact on understanding cognition, or deficiencies in cognition, in individual subjects. As a result, human connectome information is not used as a biomarker for diagnosis or a predictor of the most suitable treatment strategy. After discussing the organisation of brain networks, we will show how connectivity can be used to determine the disease type of individual dementia patients. An important aspect of these brain networks is their spatial organisation in terms of the length of fibre tracts and the location of brain regions [5]. However, simply observing connectivity is insufficient as small changes in network organisation might lead to large changes in network behaviour (dynamics) [6]. We therefore show how simulations can be applied to predict regions that are involved in neural processes. For epilepsy, simulations show us which regions are involved [7], which treatment approach should be used, and whether surgical intervention will be successful or not. We conclude with the role of simulations in understanding the developmental origin of diseases as determining these origins will again inform diagnosis and treatment ( http://www.greenbrainproject.org/ ). These are first steps towards using connectome-based computer simulations as a tool to understand normal and pathological processing in individuals. Developing models that are based on anatomical information will be crucial to define the most suitable intervention [8]. [1] Martin, *Kaiser*, Andras, Young. Is the Brain a Scale-free Network? SfN Abstract, 2001. [2] Sporns, Chialvo, *Kaiser*, Hilgetag. Trends in Cognitive Science, 2004. [3] *Kaiser* et al. New Journal of Physics, 2007. [4] *Kaiser* et al. European Journal of Neuroscience, 2007. [5] *Kaiser* et al. PLOS Computational Biology, 2006. [6] *Kaiser*. Frontiers in Human Neuroscience, 2013. [7] Hutchings, Han, Keller, Weber, Taylor, *Kaiser*. PLOS Computational Biology, 2015. [8] Wang, Hutchings, *Kaiser*. Computational Modelling of Neurostimulation in Brain Diseases. Progress in Brain Research, 2015. *Biography* *Marcus Kaiser* studied biology and computer science at the Ruhr-University Bochum and the Distance University Hagen finishing with a master degree in 2002. He obtained his PhD, funded by a fellowship from the German National Merit Foundation, from Jacobs University Bremen in 2005. He is initiator and co-director of the Wellcome Trust PhD programme in Systems Neuroscience and leader of the UK INCF Special Interest Group in Image-based Neuroinformatics. He authored the first major review (Trends in Cognitive Sciences, 2004; cited 1,300+ times) and more than 50 other publications in the field of brain connectivity. Research interests are understanding the link between structure and function by modelling brain development, neural dynamics, and therapeutic interventions (see http://www.dynamic-connectome.org/ ). *Location: *PL002 -- Miss Helen Fagan Graduate Admissions and Demonstrator Coordinator ******************************************** Department of Electronics University of York Heslington York YO10 5DD Telephone: 01904 324485 Fax: 01904 323224 Email: helen.fagan(a)york.ac.uk *Follow us on:* Facebook (https://www.facebook.com/electronicsyork) Twitter (https://twitter.com/ElectronicsYork) Weibo (http://www.weibo.com/ElectronicsYork <http://www.weibo.com/ElectronicsYork?is_hot=1>) Pinterest (https://uk.pinterest.com/deptelecyork/) EMAIL DISCLAIMER http://www.york.ac.uk/docs/disclaimer/email.htm <http://www.elec.york.ac.uk/EqualityDiversity/award1.png>

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This weekend at YNIC
by Gary Green 06 May '16

06 May '16

Dear Colleagues This weekend, starting tonight, the power and data cables for the new MRI scanner will be installed in the Centre. This means that the floor tiles will be lifted and large cables will be being dragged throughout the whole of the open plan, reception and MRI corridor. We would be grateful if you did not use the Centre this weekend or this evening. For key holders - there are special security arrangements in place this weekend so please do not use the normal alarm setting points or security computer. If for any reason you do come in and the alarm goes off, do not try and reset it but please ring me on 07881913004 Thanks Gary -- --------------- Gary Green York Neuroimaging Centre & Centre for Hyperpolarisation in Magnetic Resonance The Biocentre York Science Park Innovation Way Heslington York YO10 5NY tel +44 (0) 1904 435349 fax +44 (0) 1904 435356 mobile +44 (0) 788 191 3004 http://www.ynic.york.ac.uk http://www.york.ac.uk/chym/ https://www.ynic.york.ac.uk/about-us/people/ggrg

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ynic-users May 2016