- ynic-users

by Rebecca E Millman

Dear Users This afternoon there will be a project proposal presentation given by David Watson. The title of the talk is "How are Scenes Represented in the Brain?". Please note that the talks will start at the usual time of 4.15 pm but these talks will take place in Psychology in the Venables room (A202). Please below for the talk abstract. Best wishes Rebecca Abstract: Human ventral visual cortex has been noted to contain regions showing selectivity for higher level visual objects categories – including faces, body parts, inanimate objects, and place scenes. A key question in this area is whether such regions may best be regarded as discrete modules with no finer internal structure and not belonging to any wider overarching structure, or whether such regions may exist as points along a wider topographical map of object category. The current project aims to investigate this question within the context of cortical regions responsive to place scenes. It has been shown that scene images can be categorised along their semantic categories (e.g. cityscape, forest, coastline, etc.) based on their underlying low-level visual properties (Oliva & Torralba, 2001). As such, scene category forms a possible dimension along which scene selective cortical regions could be organised. Using fMRI, we propose to compare patterns of cortical activity elicited by fixed blocks of natural scene sub-categories (coasts, forests, and mountains) against those elicited by mixed blocks containing all sub-categories. If scene selective regions are found to respond uniformly to all scene categories, this would support a modular-based hypothesis. If, on the hand, these regions are shown to respond heterogeneously to different scene categories, this would suggest the presence of a larger scale topographical map of scene / object category. -- Dr. Rebecca E. Millman York Neuroimaging Centre The Biocentre York Science Park York YO10 5DG Email: rem(a)ynic.york.ac.uk Tel: 01904 435 5373

13 years, 4 months

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Downtime for Psycmail : THIS WILL AFFECT YOU

by Gary Green

As previously notified, we need to take psycmail out of service for a short period. This will be at 10am on Wednesday the 6th of March. It will last for an hour at most. Then psycmail should restart and then will be running on what we hope will be more reliable and resilient equipment in the refurbished IT server room. Any problems, do contact A.Morland(a)psych.york.ac.uk, Mark.Hymers(a)ynic.york.ac.uk AND me Gary.Green(a)ynic.york.ac.uk. Of course, you will not be able to contact us when the email service is down, but if necessary, just ring me Gary -- Gary Green York Neuroimaging Centre The Biocentre York Science Park York YO10 5DG tel (+44) (0) 1904 435349 fax (+44) (0) 1904 435356 mobile 07986778954

13 years, 4 months

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Important : break in Psych mail services

by Gary Green

Dear users of the psychology email services We are currently moving data and services off of vulnerable equipment on to new machines. To complete this process we need to disable Psycmail for a period of about an hour. Restarting the psycmail will not require much down time, but physical relocation of associated servers will take longer. We would like to do this sometime tomorrow afternoon, Tuesday, or sometime on Wednesday. IF the loss of psycmail will inconvenience anyone at any time on Tuesday afternoon or Wednesday, please let Mark.Hymers(a)ynic.york.ac.uk, A.Morland(a)psych.york.ac.uk AND Gary.Green(a)ynic.york.ac.uk know. So if you have a grant deadline, an urgent publication submission time or any other reason why psycmail migration should be delayed, please let us know. If no-one objects then we will write again to give as much notice as possible of the time when psycmail will not be available. Gary -- Gary Green York Neuroimaging Centre The Biocentre York Science Park York YO10 5DG tel (+44) (0) 1904 435349 fax (+44) (0) 1904 435356 mobile 07986778954

13 years, 4 months

1
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YNiC seminar 8th March (in Venables room - A202)

by Rebecca E Millman

Dear Users This Thursday there will be a project proposal presentation given by David Watson. The title of the talk is "How are Scenes Represented in the Brain?". Please note that the talks will start at the usual time of 4.15 pm but these talks will take place in Psychology in the Venables room (A202). Please below for the talk abstract. Best wishes Rebecca Abstract: Human ventral visual cortex has been noted to contain regions showing selectivity for higher level visual objects categories – including faces, body parts, inanimate objects, and place scenes. A key question in this area is whether such regions may best be regarded as discrete modules with no finer internal structure and not belonging to any wider overarching structure, or whether such regions may exist as points along a wider topographical map of object category. The current project aims to investigate this question within the context of cortical regions responsive to place scenes. It has been shown that scene images can be categorised along their semantic categories (e.g. cityscape, forest, coastline, etc.) based on their underlying low-level visual properties (Oliva & Torralba, 2001). As such, scene category forms a possible dimension along which scene selective cortical regions could be organised. Using fMRI, we propose to compare patterns of cortical activity elicited by fixed blocks of natural scene sub-categories (coasts, forests, and mountains) against those elicited by mixed blocks containing all sub-categories. If scene selective regions are found to respond uniformly to all scene categories, this would support a modular-based hypothesis. If, on the hand, these regions are shown to respond heterogeneously to different scene categories, this would suggest the presence of a larger scale topographical map of scene / object category. -- Dr. Rebecca E. Millman York Neuroimaging Centre The Biocentre York Science Park York YO10 5DG Email: rem(a)ynic.york.ac.uk Tel: 01904 435 5373

13 years, 4 months

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no YNiC seminar today

by Rebecca E Millman

Dear Users There will not be a YNiC seminar today. Thanks Rebecca -- Dr. Rebecca E. Millman York Neuroimaging Centre The Biocentre York Science Park York YO10 5DG Email: rem(a)ynic.york.ac.uk Tel: 01904 435 5373

13 years, 4 months

1
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[Fwd: senior researcher position at the Donders Institute]

by Gary Green

FYI -- Gary Green York Neuroimaging Centre The Biocentre York Science Park York YO10 5DG tel (+44) (0) 1904 435349 fax (+44) (0) 1904 435356 mobile 07986778954 -------------------------------------------------------------------------- Dear colleagues, I would like to bring your attention to the position below. Alt the best, Ole Jensen http://www.neuosc.com ------------------------ *Senior Researcher for 'Neuronal Oscillations and Networks' (1,0 fte) * *Donders Institute, Centre for Cognitive Neuroimaging* *Vacancy number: 30.01.12* *Closing date: 15 April 2012* *Responsibilities* The Neuronal Oscillation group at the Donders Institute for Brain, Cognition and Behaviour has funding available for a senior researcher position. The position has a strong research component, but also includes additional management and teaching responsibilities. The management tasks involve active participation in structuring the research group, including supervision of MSc and PhD students (who will receive senior authorship where applicable). Further, you will contribute to grant writing. The research responsibilities focus on investigating the role of oscillatory neuronal activity involved in shaping the functional architecture of the working brain. This will be done in the context of advanced cognitive paradigms on attention, perception and memory. There will be a strong focus on the role of phase, network interactions and subcortical structures. You will have the following state-of-the-art equipment to your disposal: MEG, (f)MRI, EEG combined with TMS, and EEG combined with fMRI. A further aim is to link structural (e.g. DTI) and functional measurements. You will also participate in conceptually developing the framework for understanding the functional role of brain oscillations. *Work environment* The Donders Institute for Brain, Cognition and Behaviour consists of the Centre for Cognition, the Centre for Cognitive Neuroimaging and the Centre for Neuroscience. The mission of the Centre for Cognitive Neuroimaging is to conduct cutting-edge fundamental research in cognitive neuroscience. Much of the rapid progress in this field is being driven by the development of complex neuro-imaging techniques for measuring activity in the human working brain - an area in which the Centre plays a leading role. The research themes cover central cognitive functions such as perception, action, control, decision making, attention, memory, language, learning and plasticity. The internationally renowned centre currently hosts more than 100 PhD students and postdoctoral researchers from more than 20 countries, offering a stimulating and multidisciplinary research environment. The centre is equipped with three MRI scanners (7T, 3T, 1.5T), a 275-channel MEG system, an EEG-TMS laboratory, several (MR-compatible) EEG systems, and high-performance computational facilities. English is the lingua franca at the centre. You will work within the Neuronal Oscillations group. *What we expect from you* As a candidate for the position, you should have a PhD degree and several years of experience as postdoctoral researcher in a field related to cognitive neuroscience. Selection criteria will consider the record of published research, familiarity with neuroimaging techniques (fMRI, EEG, MEG, and/or TMS) and supervision experience. Proficiency in oral and written English is a prerequisite. You are expected to work in a team, sharing technical know-how and ideas. *What we have to offer* We offer you: - employment: 1,0 fte; - in addition to the salary: an 8% holiday allowance and an 8.3% end-of-year bonus; - the gross salary will be between EUR3,195 and EUR4,970 (scale 12), depending on experience; - salary scale 11 will apply during the first year; - duration of the contract: 6 years maximum. Are you interested in our excellentemployment conditions <http://www.ru.nl/english/arbeidsvoorwaarden>? *Would you like to know more?* Further information on:DCCN <http://www.ru.nl/donders> Further information on:Neuronal Oscillations group <http://www.neuosc.com/> Dr. Ole Jensen Telephone: +31 24 3610884 E-mail:ole.jensen@donders.ru.nl <mailto:ole.jensen@donders.ru.nl> *Applications* Are you interested? It is Radboud University Nijmegen's policy to only accept applications by e-mail. Please send your application,/stating vacancy number 30.01.12/, tovacatures(a)dpo.ru.nl <mailto:vacatures@dpo.ru.nl>, for the attention of Dr. Ole Jensen, before 15 April 2012. For more information on the application procedure: +31 24 3611173

13 years, 4 months

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YNIC Connection

by Susana Maia

Hi everyone, I am involved in the project P1125 at YNIC. I've been trying to connect through the remote server and, although I can do the connection, when I try to initiate the NX Client for Windows I always get this error: NX> 203 NXSSH running with pid: 8348 NX> 285 Enabling check on switch command NX> 285 Enabling skip of SSH config files NX> 285 Setting the preferred NX options ssh: connect to host nirem001.ynic.york.ac.uk port 22: Connection timed out I'm aware that you guys had a flood, and are encountering some problems. Do you have any idea of when am I going to be able to have access again? I'm a little bit worried because I'm going to a conference next 4th of March and there are still some data that I'd like to analyse. Best, Susana Maia Bolseira de Investigação Departamento de Psicologia Básica, Universidade do Minho tel: +351 933290673

13 years, 4 months

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Analysis Plans

by science.manager＠ynic.york.ac.uk

Hello all, Further to the scanning loss details, it would also be very useful to know to what extent analysis has been interrupted. Obviously this is much harder to quantify, but an estimate would be very helpful. If you were planning on using any of the YNiC facilities over the next month or so, could you let us know: * What you were working towards (e.g. conference presentation, publication, thesis etc) * Roughly how much time you were setting aside for your analysis * Any upcoming deadlines for ongoing work Thanks again, Sam

13 years, 4 months

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Scanning plans

by science.manager＠ynic.york.ac.uk

Hello all, As part of the insurance and recovery process it would be very helpful to get an estimate of how much scanning we have lost/will lose due to the flooding. If you were planing to scan over the next few weeks (including last week if you hadn't already booked it), could you let me know: * the project number you want to scan under * roughly how many hours you want to scan * what timescale you want to scan over (over the next month) * which machine you want to scan on. This will also help us plan for the load we can expect as and when we get the intermediate service up and running. Thanks, Sam

13 years, 4 months

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YNiC seminar 23rd February (in B020)

by Rebecca E Millman

Dear Users This Thursday the Cognitive Neurosciences MSc students will again be giving project proposal presentations for their empirical research projects. Please note that the talks will start at the usual time of 4.15 pm but these talks will take place in Psychology (B020). Please below for details of project titles and speakers. Best wishes Rebecca (1) People or Faces - The neural correlates of recognition - Tim Andrews (fMRI) GUDER, ZEYNEP RICE, GRACE SLEZAK, MARTINA (2) The hippocampus and anxiety: a structural MRI study using Voxel based morphometry - Tom Hartley, Liat Levita BOIS, CATHERINE PAPAKONSTANTINOU, EVANGELIA SMYLLIE, EMMA HEALEY, ANDREW (3) Approach and Avoidance - neural circuitry of pain and pleasure - Liat Levita (fMRI) WALSH, SEAN DANIEL GREAVES, ASHA MARIE PEASE, CHRISTOPHER RYAN ROUND, JASON TONY (4) The neural basis of Deutsch's speech-to-song illusion - Mark Hymers, Rebecca Millman SCHULZE, ANJA YOUNG, MICHELLIE LIU, CAN -- Dr. Rebecca E. Millman York Neuroimaging Centre The Biocentre York Science Park York YO10 5DG Email: rem(a)ynic.york.ac.uk Tel: 01904 435 5373

13 years, 4 months

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YNiC update : Friday 17th

by Gary Green

Dear Colleagues A brief update. The most important thing that happened today is that the 'Complex and Major Loss' Adjuster visited the site. Tony Morland and I described the situation and gave him a tour of the Centre. It is clear that we are going to get considerable support from the insurers, the disaster recovery team and others. Some good news: 5 of the 6 'partitions' of the main disc storage area have now been rebuilt and verified. As this has been done on hardware that could fail, the data has been written to tape and this has been put in the fireproof/waterproof safe. We already had a backup - now we have two. They will be placed in different locations. Backups of psychmail are now back to the regular four hourly schedule. The vulnerable partition is with ta data recovery team in Surrey. At this point we cannot be optimistic or pessimistic. We just do not know whether this data is recoverable from the discs. We will not know until next Friday at the earliest. Work has started on creating a temporary IT server room. Today, we managed to get our hands on the last 30 3Terabyte discs in the UK that are compatible with our HP hard disc enclosure. Apparently discs are in very short supply. No 2 terabyte discs were available at all. This is due to a flood in Thailand. All the manufacturers have factories within a few miles of each other! Extra drying machines have been installed. We have been told that drying will continue for at least one more week. I hope you can have a reasonably worry free weekend. It is good to see some green lights here again on the front of machines. Gary -- Gary Green York Neuroimaging Centre The Biocentre York Science Park York YO10 5DG tel (+44) (0) 1904 435349 fax (+44) (0) 1904 435356 mobile 07986778954

13 years, 4 months

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Psych mail outage

by Gary Green

Dear Colleagues You may have just noticed a temporary loss of psych mail. Apologies for that. It was caused by a temporary routing problem, not a failure of a server or discs. At about 18:30 tonight (Thursday), we will have to stop and restart the mail server. This is so that we can reroute cables to and from a network switch that has to be physically moved. This should take approximately 45 minutes. It will increase the resilience of the temporary IT service as we continue to rebuild YNiC. Please accept our apologies for the inconvenience that will be caused. Gary -- Gary Green York Neuroimaging Centre The Biocentre York Science Park York YO10 5DG tel (+44) (0) 1904 435349 fax (+44) (0) 1904 435356 mobile 07986778954

13 years, 4 months

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Data at YNiC

by Gary Green

Dear Users Many users have contacted the ynic team as they are understandably very concerned about their data, programs, documents and other critical material that was stored on the disc arrays at YNiC. The first thing to say is that all of the raw data (MRI, MEG) is safe. Everyday we store this material on tape backups. The same is also true of Users' home and Group/Project home data. The last major complete tape backup was carried out three days before the calamity. But we are hoping not to have to resort to recovery from tape. We are working on forcing the RAID to rebuild itself and this is why we are closing the psych mail service later today. In the meantime we have asked for quotations to replace any damaged equipment. Some good news (well a tiny bit). Some services are now working eg the database, RT and other internal services. These will help us in terms of the recovery plan. The loss adjustor attended the site this morning and is helping formulate this plan. TMS should be available in room 54 on the ground floor of the Biocentre within 24 hours. Next update will be tomorrow, Thursday. Gary Gary Green York Neuroimaging Centre The Biocentre York Science Park York YO10 5DG tel (+44) (0) 1904 435349 fax (+44) (0) 1904 435356 mobile 07986778954

13 years, 4 months

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Urgent : YNiC update : this will affect you

by Gary Green

Dear Colleagues I am sorry to announce that psych email will have to be suspended for one hour today at 5pm. I am apologise for any inconvenience caused. This is necessary so that we can attempt to salvage another area of disc storage on the RAID arrays. Gary -- Gary Green York Neuroimaging Centre The Biocentre York Science Park York YO10 5DG tel (+44) (0) 1904 435349 fax (+44) (0) 1904 435356 mobile 07986778954

13 years, 4 months

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update on the situation in YNiC

by Gary Green

Dear Colleagues As promised here is a short update on the current situation in YNiC. We now know that 12 separate leaks occurred from a pressurised water system within the plant area in the top floor of the Biocentre sometime on Sunday. The water had descended throughout the building mainly down the cavity wall of the offices and through the risers. The first we knew of the incident was that one of the disc RAID controllers emailed the IT manager that it was failing. He went straight to YNiC and started evacuating the server area. This prompt action may, I emphasise may, have allowed us to save some equipment. Today we have had building surveyors inspecting the building. We have been informed that we should continue to dehumidify and heat the affected areas for at least a week. A further inspection will take place next Monday, the 20th. New areas of water ingress are appearing so the full extent of the damage has yet to be revealed. The University's insurance manager has attended the site. She is our link to the insurers and we have been informed that a loss adjustor has been appointed and will attend YNiC tomorrow, Wednesday the 15th. Disaster Recovery experts have also been appointed and they will advise on the best methods for dealing with the damage and also with the consequential loss of all the YNiC services, not just IT. We have set in motion a recovery plan. Tony Morland is co-ordinating this and we would be grateful if people could inform him if they are working to particular deadlines, contracts or clinically critical timelines. The recovery plan will, eventually, include contingency planning if recovery is going to be lengthy. Within YNiC we are systematically going through all the equipment to try and establish what is irrevocably lost. We should point out though that we know that all our warranties are void. Therefore we will be discussing our options with the advisors tomorrow about how to recreate a working system that will last the original estimated life. We are attempting to rebuild the RAID arrays. As these contain a very large amount of data this will take time, maybe days. At this stage we are unable to say which, if any, data is lost from the discs. We do know that some discs within the RAID were lost. We do have backups on tape in a fireproof safe. But at the moment we do not have an infrastructure that will allow us to use these backups. The ideal scenario will be that RAIDs will be largely rebuilt but we cannot guarantee that. Moreover, we do not have the network switches, servers and analysis machines that would allow useful access to the discs. We do appreciate that many, many, projects, PhDs, staff, external collaborators will be seriously affected by this. We will do all we can to get a system working as soon as we can. Please note, the current emails services are vulnerable. We even lost service yesterday when another drive failed. Please keep local drafts as often as you can. You will be pleased to note that the MATLAB licence service is now active. Gary -- Gary Green York Neuroimaging Centre The Biocentre York Science Park York YO10 5DG tel (+44) (0) 1904 435349 fax (+44) (0) 1904 435356 mobile 07986778954

13 years, 4 months

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YNiC seminar 16th February (room change)

by Rebecca E Millman

Dear Users This Thursday the Cognitive Neurosciences MSc students will be giving project proposal presentations for their empirical research projects. Please note that the talks will start at the usual time of 4.15 pm but these talks will take place in Psychology (B020). Please below for details of project titles and speakers. Best wishes Rebecca (1) MEG to faces: is M170 on the blink? - Pat Johnston JOHNSON, EILEANOIR BRIDGET, KOKKINAKIS, ATHANASIOS (2) Cortical mechanisms involved in attention to colour - Alex Wade (fMRI) OLIVER, ZOE, SMITH, AARON, WONG, PEONY (3) Imaging using hyperpolarised molecules - Gary Green ALI, SHELIZA CAMILLERI, JULIA ANN, TROY, DAVID MAURICE, CHEN, JING, ROBERTS, INDIA MELANIE SUZANNE (4) A combined fMRI-TMS study of semantic representation and control - Beth Jefferies (fMRI/TMS) COSTIGAN, ALISON GRACE LIU, YANNAN MURPHY, NICHOLAS GOGOLEV, PAVEL (5) Understanding Misunderstanding - S.A. Rueschemeyer (EEG) STONER, CATHERINE GARDNER, TOM -- Dr. Rebecca E. Millman York Neuroimaging Centre The Biocentre York Science Park York YO10 5DG Email: rem(a)ynic.york.ac.uk Tel: 01904 435 5373

13 years, 4 months

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News about the flood in YNiC

by Gary Green

Dear Colleagues and Users As you may have heard, there has was a major flood within the Biocentre building on Sunday afternoon. Unfortunately we only found out about this when computers went off line. By that time water had been leaking into our area for about two hours. It took a further three hours before the problems were brought under control. Water came through the ceilings into YNiC and has caused damage within a number of rooms. The most seriously affected area was the server room. Mark Hymers and his colleagues managed to get a large amount of the equipment out of the room but not before some serious damage had been done. We now have to assess the extent of that damage. I am sorry to say that this will take time. We have already emptied water out of many disc drives, servers, network switches and power supplies. In other words we are very badly affected by this flood. The University insurers have been informed and we are waiting for a loss adjustor to come to the site. A very basic set of services have been re-established. These allow psych-mail and ynic-mail to work as we realise that people would have been greatly affected by the loss of those services. But we have to say that these services are not guaranteed. The machines that are running may have been affected by the water damage and may fail. We may also have to change the servers managing these services at short notice. I apologise for any inconvenience that may be caused. We do not have any other services within YNiC. The desktop computers, data-stores (MEG/MRI), remote access, tape-backups and other core services are not available. As the MRI and MEG devices depend on these services they are also not available. The Scratch spaces within the disc space have been affected and some data/analyses will be lost. Water leaked into the TMS area and is also not useable. I am unable at this stage to tell you when these facilities and resources will be available again. As information becomes available I will let you know of any changes. The YNiC open plan area is not accessible. We have used some desks for the temporary server configuration. Cables have had to be run across the floor and as there are no user accessible services we would be grateful if everyone can stay away from YNiC until further notice. This will affect a large number of people. We will try hard to get serive back to normal. at this stage I cannot tell you when this will be. It will certainly take at least two weeks as we will have to order some replacement machines and discs to be able to get anyway close to normal operation. Gary -- Gary Green York Neuroimaging Centre The Biocentre York Science Park York YO10 5DG tel (+44) (0) 1904 435349 fax (+44) (0) 1904 435356 mobile 07986778954

13 years, 4 months

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no YNiC seminar this week

by rem

Dear Users There will not be a YNiC seminar this week (9th February). Normal service will resume next week when the MSc CN students will be giving project proposal presentations for their empirical research projects. 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

13 years, 5 months

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YNiC seminar today

by rem

Dear Users Today (4.15-5.15 pm) Mark Hymers and Padraig Kitterick will be giving a talk on "Safe levels of noise exposure in MR scanning at YNiC". Please see below for the talk abstract. Everyone is welcome to attend. Best wishes Rebecca Abstract: In 2011 Mark Hymers, Padraig Kitterick, Rebecca Millman and Quentin Summerfield were awarded a small grant by the Department of Psychology to investigate the feasibility of carrying out auditory fMRI research safely at YNiC. This talk will present the main findings of the work funded by this grant and should be 1) of interest to anyone who uses MRI and 2) of particular interest to those who wish to carry out auditory fMRI experiments. MR scanners generate very loud levels (>105 dB SPL) of noise. Exposure to intense noise can potentially damage hearing and the effects of exposure to very loud sounds are cumulative over the total exposure time. Researchers who use MR scanners must protect their participants against hearing damage by ensuring that exposure to noise levels in MR remain within the UK legal limits. Important considerations that will impact the design of all MRI experiments are 1) the duration of the structural scans/fMRI experiments and 2) the amount of attenuation of unwanted noise provided by hearing protection available at YNiC. For auditory fMRI experiments, researchers must also take into account the effects of adding the presentation level of auditory stimuli to the scanner noise. The talk will provide an overview of the guidelines written by Hymers et al. in the full report and present easy-to-use tools for calculating levels of noise exposure in MRI experiments. -- ************************************************************************ 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

13 years, 5 months

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Re : Downtime

by Gary Green

Apologies for cross-postings ------------------------------- Dear Colleagues, On Friday 10th February, YNiC Open Plan and Offices will be closing at midday. This is to allow for some essential maintenance and debugging to occur on one of the core IT systems. We will be taking the opportunity to also move certain data to new storage and perform some other system upgrades at the same time which would have otherwise required separate downtime. The MRI scanner will still be usable during this period and the Psychology mail server will not be affected. Systems which will be affected include the YNiC website, booking system, remote desktop, VPN service and all YNiC desktops. We expect these systems to be back online around 5pm. We apologise for any inconvenience caused Gary Gary Green York Neuroimaging Centre The Biocentre York Science Park Innovation Way Heslington York YO10 5NY http://www.ynic.york.ac.uk https://www.ynic.york.ac.uk/about-us/people/ggrg tel. +44 (0) 1904 435349 PA - Denize Chessa : +44 (0) 1904 435329 or email dcds500(a)ynic.york.ac.uk fax +44 (0) 1904 435356 mobile +44 (0) 788 191 3004

13 years, 5 months

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Update on participant policy

by Sam Johnson

Hello all, As part of the continuous review of our participant safety guidelines there has been an amendment to the YNiC policy on scanning volunteers. With immediate effect any participant with fixed dental braces will not be scanned as part of an experiment. Although we have had no incidents locally, there is the possibility of significant heating of dental braces during an MRI scan. This is a small but unnecessary risk, and so we have excluded this group from any future experimental scanning. Our participant information and scan consent/safety questionnaire forms have been updated accordingly and you should make sure you have the most up to date versions of these forms when recruiting participants. The current versions of all YNiC forms should always be available at: https://www.ynic.york.ac.uk/forms and as ever, please let us know of any errors/omissions. Thanks, Sam -- Sam Johnson Science Manager, York NeuroImaging Centre University of York http://www.ynic.york.ac.uk

13 years, 5 months

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Fwd: Position at OHBA - pass along if you know anyone interested

by Gary Green

FYI ----------------------------- Dear Colleague, Sorry to intrude in the inbox. We have a couple of positions on a new project along the lines of one of the priority areas in the collaborative grant (imaging, cognition in aging). If you know of any good candidates for this, please pass this along to them. The deadline is imminent (3rd Feb)! thanks, and nice to see everyone in London, Kia * * *Postdoctoral and Postgraduate Research Assistants* available at the Oxford Centre for Human Brain Activity (OHBA) and Department of Psychiatry, Warneford Hospital, Oxford We are recruiting a postdoctoral fellow and a postgraduate research assistant to work on an exciting new programme of research concerned with assessing cognitive functions during aging and developing psychological interventions for improving cognitive health and preventing cognitive decline. The programme of research involves a combination of neuropsychological assessments; cognitive testing; and brain imaging using structural and functional magnetic resonance imaging (MRI), magnetoencephalogram (MEG) and electroencephalography (EEG). The post will provide experience of clinically relevant research. The positions are funded for two years, and are supported the Programme in Cognitive Health, NIHR Biomedical Research Centre Oxford The deadline for applications is *midday on* *Friday 3rd February* For *details* of the position, please link to the advert: Postdoctoral: http://www.psych.ox.ac.uk/jobvacancies/101899 Postgraduate research assistant: http://www.psych.ox.ac.uk/jobvacancies/101897 *Application forms* and further details can be found at the following links: Postdoctoral: https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobs… <https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobs…> Postgraduate research assistant: https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobs… <https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobs…> For *informal enquiries* contact Professor Kia Nobre (kia.nobre(a)ohba.ox.ac.uk <mailto:Kia.nobre@ohba.ox.ac.uk>) or Professor Emily Holmes (emily.holmes(a)psych.ox.ac.uk <mailto:emily.holmes@psych.ox.ac.uk>) directly:

13 years, 5 months

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YNiC seminar 2nd February

by rem

Dear Users This Thursday (4.15-5.15 pm) Mark Hymers and Padraig Kitterick will be giving a talk on "Safe levels of noise exposure in MR scanning at YNiC". Please see below for the talk abstract. Everyone is welcome to attend. Best wishes Rebecca Abstract: In 2011 Mark Hymers, Padraig Kitterick, Rebecca Millman and Quentin Summerfield were awarded a small grant by the Department of Psychology to investigate the feasibility of carrying out auditory fMRI research safely at YNiC. This talk will present the main findings of the work funded by this grant and should be 1) of interest to anyone who uses MRI and 2) of particular interest to those who wish to carry out auditory fMRI experiments. MR scanners generate very loud levels (>105 dB SPL) of noise. Exposure to intense noise can potentially damage hearing and the effects of exposure to very loud sounds are cumulative over the total exposure time. Researchers who use MR scanners must protect their participants against hearing damage by ensuring that exposure to noise levels in MR remain within the UK legal limits. Important considerations that will impact the design of all MRI experiments are 1) the duration of the structural scans/fMRI experiments and 2) the amount of attenuation of unwanted noise provided by hearing protection available at YNiC. For auditory fMRI experiments, researchers must also take into account the effects of adding the presentation level of auditory stimuli to the scanner noise. The talk will provide an overview of the guidelines written by Hymers et al. in the full report and present easy-to-use tools for calculating levels of noise exposure in MRI experiments. -- ************************************************************************ 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: [Sackler] PHD studentship available at Sussex on causality analysis of FMRI data

by Silvia Gennari

> > From: Anil Seth [a.k.seth(a)sussex.ac.uk] > Sent: 23 January 2012 16:04 > To: sackler(a)sussex.ac.uk > Subject: [Sackler] PHD studentship available at Sussex on causality analysis of FMRI data > > Apologies for cross-posting: > > Ph.D. studentship available: > Identifying causal interactions in functional MRI data using statistical time series analysis > > Supervised by Dr. Anil Seth, Prof. Hugo Critchley, and Dr. Lionel Barnett. > > University of Sussex, Brighton and Sussex Medical School, Sackler Centre for Consciousness Science > > Deadline: 5.00pm, Tuesday 31st January 2012 > Start date: September 2012 > > Details here: http://www.sebnet.org.uk/apply/seth > Apply here: http://www.sussex.ac.uk/study/funding/2012/opportunities/view/43 > > Our understanding of the brain has been revolutionized by functional neuroimaging, the ability to look at brain activity as a person is doing a task, or even while they do nothing at all. Traditionally, neuroscientists have used neuroimaging to localize different functions to different parts of the brain. However, brain functions depend on dynamical networks spanning many different brain regions. Identifying these networks, and especially networks that show causal interactions among their elements, is a major current challenge. This Ph.D. project will address this challenge for functional MRI (fMRI), the most popular neuroimaging method. fMRI measures time-varying changes in metabolic signatures of neural activity. To identify causal networks, we adopt the framework of Granger causality analysis (GCA) which assumes that causes both precede and help predict their effects. GCA applied to fMRI faces several challenges arising because the fMRI signal is an indirect and incompletely understood reflection of underlying neural activity, is sluggish, delayed, and is sampled only once every 2-3 seconds. The project will address these limitations by novel combinations of theory, modelling and experiment. A first objective will be to adapt recent theoretical findings showing invariance of GCA under filtering to the case of fMRI. A second objective will be to characterize the behavior of GCA on fMRI data via detailed computational models connecting neural activity to simulated fMRI responses. These models will be built by connecting existing large-scale spiking neuron simulations with forward models of hemodynamic responses. Third and finally, the resulting methods will be benchmarked on fMRI data obtained specifically for this purpose. > > The successful candidate will benefit from being part of the Sackler Centre for Consciousness Science (www.sussex.ac.uk/sackler), a world-leading research group in computational neuroscience, functional analysis of neuroimaging data, and consciousness research. The student will enjoy collaborative input from the Department of Informatics, the Brighton and Sussex Medical School, and the School of Psychology; will work within a thriving multidisciplinary group integrating many areas of neuroscience, and will have full access to state-of-the-art computational and neuroimaging facilities. Training in fMRI analysis and statistical methods will be provided. > > Applications should hold, or expect to obtain, a minimum upper-second honours degree (or equivalent) in a quantitative science discipline. Previous experience in neuroimaging and/or time series analysis is desirable but not required. > > Funding Notes: The South-East Biosciences Network (www.sebnet.org.uk) is advertising 33 Doctoral Studentships across the South-East of England. > > Applicants for this 4-year PhD, starting in September 2012, should possess or expect to be awarded an Upper Second or 1st Class Honours degree (or equivalent) in a relevant related subject. Studentships are available to UK nationals and EU students who meet the UK residency requirements. The studentship will support the student’s stipend and tuition fees. > > In the application process (http://www.sussex.ac.uk/study/pg/applying/), select the programme INFORMATICS PHD FULLTIME with SEP 2012 ENTRY. Be sure to mention explicitly that you are applying for the SEBnet studentship under the supervision of Dr Anil Seth. > > Informal enquiries to A.K.Seth-at-sussex.ac.uk > See also www.sussex.ac.uk/sackler > www.sebnet.org.uk/apply/seth > www.anilseth.com/ > -- > Dr. Anil Seth > Sackler Centre for Consciousness Science > Dept of Informatics, University of Sussex > www.anilseth.com > www.sussex.ac.uk/sackler > > ___________________________________________________________ > This email has been scanned by MessageLabs' Email Security > System on behalf of the Brighton and Sussex Medical School. > For more information see http://www.brighton.ac.uk/is/spam/ > ___________________________________________________________ > > ___________________________________________________________ > This email has been scanned by MessageLabs' Email Security > System on behalf of the Brighton and Sussex Medical School. > For more information see http://www.brighton.ac.uk/is/spam/ > ___________________________________________________________ > _______________________________________________ > You've received this email because you are subscribed to the Sackler mailing list at the University of Sussex. > To unsubscribe, or change your subscription options visit > https://lists.sussex.ac.uk/mailman/listinfo/sackler > The University's contact details are at http://www.sussex.ac.uk/about/contactus Silvia Gennari Department of Psychology University of York York, YO10 5DD United Kingdom http://homepage.mac.com/silvia_gennari/

13 years, 5 months

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no YNiC seminar this week

by rem

Dear Users There will not be a YNiC seminar this week as the majority of YNiC staff will be at the MEG UK meeting in London. 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

13 years, 5 months

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