- ynic-users

Seminar 4pm tomorrow
by Antony Morland 07 Mar '18

07 Mar '18

Hello All, The seminar this week will be delivered by the team at York Instriuments. They will be doing a 'show and tell' about their new software for MEG and will also offer a tour of YI for those who are interested. Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Project presentation today YNiC 4pm
by Andre Gouws 15 Feb '18

15 Feb '18

Today Leah Kelly will present a proposal for her new project "The neural correlate of cognition and visual loss". The talk will be at 4pm and will be followed by refreshments. Hope to see you all there. ... p.s. Not to detract from what I'm sure will be an excellent and interesting presentation by Leah, but just s quick reminder: ** REMINDER - Kalanit Grill-Spector will be giving a seminar at 4pm on Thursday 22 February in B020. Kalanit has made a number of seminal contributions in visual neuroscience over the past 20 years, particularly in the way faces and objects are represented in the brain. I hope you will be able to attend her seminar. ** -- André ************************************************************************ André Gouws PhD York Neuroimaging Centre University of York The Biocentre York Science Park Heslington YO10 5NY Tel: +44 (0) 1904 435327 Fax: +44 (0) 1904 435356

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Seminar today
by Antony Morland 08 Feb '18

08 Feb '18

Hello All, The seminar today will be given by Andre *Scripting FSL – a quick guide to labour saving* All the best Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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GE scanner maintenance complete
by Andre Gouws 02 Feb '18

02 Feb '18

Hi all, GE have now completed maintenance on the GE and the system is available for booking. The system should operate normally - if you do encounter any problems please contact one of the YNiC team. Thanks, -- André ************************************************************************ André Gouws PhD York Neuroimaging Centre University of York The Biocentre York Science Park Heslington YO10 5NY Tel: +44 (0) 1904 435327 Fax: +44 (0) 1904 435356

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This week at YNiC
by Antony Morland 29 Jan '18

29 Jan '18

Hi All, We have a project presentation this week at 4pm, Thursday 1st February. Holly Brown will be talking about 'Exploring connectivity in individuals with visual loss'. Unfortunately, our GE scanner is down at present. A large component in the system has failed and based on previous experience the problem can take a week to fix. We are liaising with the GE engineers and will be in touch with further updates. Tip of the week: When booking the scanners, please enter the participant ID. If you do the appropriate forms will be printed out for your booking, which saves you and the staff at YNiC time. Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Updates
by Antony Morland 24 Jan '18

24 Jan '18

Hello All, The seminar this week (Thursday at 4pm) will be given by Andre Gouws: Why PsychoPy? This will be of particular value to those of you wanting to design and present stimuli for scanning. Demos and examples to try will be given. Refreshments will follow. For further details on seminars, please see https://www.ynic.york.ac.uk/events/thursday-sessions (note loggin into the website may be required to access the information). Tip of the week: use the cluster to speed up your analysis. See the following URL for details. https://www.ynic.york.ac.uk/docs/ITPages/IT/ClusterScripts Also, if you are having issues with things, please email: support(a)ynic.york.ac.uk Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Issues for the YNIC Science Board
by Jonny Smallwood 16 Jan '18

16 Jan '18

Hello all, Please let me know if there are any issues that you would like raised at this months meeting of the YNIC Science Committee meeting. Just in case you forgot this is a chance for users, or potential users, to raise issues that they would like to be considered by YNIC moving forward. Please contact me by Friday if you have anything you would like to be discussed. Best wishes Jonny -- Jonathan Smallwood, Reader in Psychology / Cognitive Neuroscience Room C023, Department of Psychology, University of York, England. YO10 4PH. Telephone: 01904 324651

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Updates
by Antony Morland 15 Jan '18

15 Jan '18

Hello All, This week's seminar will be allocated to a project presentation: *'The relationship between emotion regulation and mind-wandering'* - Haakon Engen & Jonny Smallwood It will start at 4pm on Thursday, 18th January. Could I remind investigators to have their participants registered 24 hours before any scan appointment. Otherwise, we can't guarantee that we will be able to register the participant in time for their scan appointment. Finally, we are hosting a school visit on the afternoon of 17th between 1230 and 330pm. As part of the visit there will be talks in open plan. We will therefore be closing open plan for a few hours to allow things to run smoothly. Apologies and thanks for your co-operation. Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Updates from YNiC
by Antony Morland 09 Jan '18

09 Jan '18

Hello All, Happy New Year from all of us at YNiC! The YNiC Seminar Series will resume next week, 4pm, 18th January, with a talk by Haakon Engen, from the MRC CBU, Cambridge. The title will follow, but Haakon has collaborated with Jonny Smallwood, who is hosting him, so I expect the talk may include some work on resting state fMRI. Over the Christmas break, we successfully upgraded the servers and cluster. The cluster's performance has been improved by some optimization. It is hoped that the work we've done will therefore improve functionality. If you do have any bugs that arise, please get in touch support(a)ynic.york.ac.uk. Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Talk today at 4pm
by Antony Morland 07 Dec '17

07 Dec '17

Hi All, Some more details about the talk today. Koen Haak *Title*: Connectopic mapping with resting state fMRI *Abstract*: How does the organisation of the human brain in terms of its connectivity subserve cognitive and perceptual processes? In this talk, I will give an overview of my work on mapping individualised connection topographies based on the spontaneous brain activity fluctuations that occur when a subject is at rest (resting-state fMRI). I will demonstrate that these connection topographies predict subject-by-subject differences in behaviour and I will discuss how this approach opens up the possibility of studying the neural underpinnings of human perception and cognition across thousands of individuals, from neonates to the elderly, in health and disease. Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Talk this week and updates
by Antony Morland 06 Dec '17

06 Dec '17

Hello All, We have a visitor, Koen Haak, who will be giving a talk about his modelling work. He has developed 'Connective Field' modelling for fMRI and applied it to the visual system and more generally. He'll start at 4pm Thursday and we will be heading out for a meal afterwards, if anyone would like to join us. Upcoming closures and changes to access to the centre: 1. December 13 -15th. We will be closed. There will be no access to the centre other than for staff. We will be performing IT server upgrades. This will also mean that all remote services will be unavailable. 2. Week Commencing 18th December. There will be no operator slots during this week. We will be managing the year end issues associated with the period of closure for the Christmas break. 3. Week Commencing 25th December. The centre will be closed. No access will be possible. Remote services will be available. 4. YNiC will open 2nd January and operator cover will commence 4th January. 5. Week Commencing 8th January normal service resumes Something to note: The university spam filters have been diverting many messages to YNIC-Users to spam folders. We have updated things at our end, so hope this will no longer occur. Tip to the week: Check your SPAM folder Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Seminar this week
by Antony Morland 27 Nov '17

27 Nov '17

Hello All, This Thursday at 4pm we will have a talk given by Janine Mendola (McGill) entitled 'Neuroimaging studies of binocular vision: States, traits, debates' Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Fwd: Computational neuroscience data in the Wolfram Knowledgebase
by Philip Quinlan 16 Nov '17

16 Nov '17

Sorry for cross posting but this looks quite a useful resource? Philip. > Begin forwarded message: > > From: Keiko Hirayama <keiko.hirayama(a)wolfram.com> > Subject: Computational neuroscience data in the Wolfram Knowledgebase > Date: 15 November 2017 at 17:14:06 GMT > To: philip.quinlan(a)york.ac.uk > > Hello, > Computational neuroscience is a rapidly growing area of study, from neuronal network analysis to the construction of the comprehensive cognitive map of the human brain. As the next phase of Wolfram Research's endeavor to make biology computable, we have recently released a collection of computable neuroscience-related data. > Our curated collection has information about the human brain's anatomy as well as its network connectivity, neuronal characteristics and mapped cognitive function. Along with programmatic access to these resources, the Wolfram Language provides the tools necessary to analyze and visualize such information. Please see my interactive notebook for details on our neuroscience data <http://url.wolfram.com/2EmhiWI8/>. > It is our ongoing effort to expand our Wolfram Knowledgebase in the computational neuroscience areas to offer a better and broader perspective on the structure and function of the nervous system. We would be interested to hear what you think and what additional topics or functionality could be useful for your research. > I would greatly appreciate your feedback. > Sincerely, > > Keiko Hirayama > Wolfram Research, Inc. • 100 Trade Center Dr. • Champaign, IL 61820 • USA > Privacy Policy <http://www.wolfram.com/legal/privacy/wolfram-research.html> • Update your email <http://www.wolfram.com/emailchange/?email=philip.quinlan@york.ac.uk> • Remove yourself from these mailings <http://www.wolfram.com/unsubscribe/?email=philip.quinlan%40york.ac.uk&maili…>

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Important: Ethics forms have changed
by Andre Gouws 14 Nov '17

14 Nov '17

Please not that the YNiC Research Governance Committee has released a new version of the YNiC RGC application form, along with updated guidance for completion of the form. The new versions can be found at on the "How to apply to use the centre for a study" page (https://www.ynic.york.ac.uk/information/application) or directly at the forms download page (https://www.ynic.york.ac.uk/forms). These versions should be used for all future submissions. Thanks, -- André ************************************************************************ André Gouws PhD York Neuroimaging Centre University of York The Biocentre York Science Park Heslington YO10 5NY Tel: +44 (0) 1904 435327 Fax: +44 (0) 1904 435356

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Updates this week
by Antony Morland 13 Nov '17

13 Nov '17

Dear All, A few things this week: 1. The GE scanner will be down for maintenance of the gradient cooling system on Wednesday and Thursday. 2. There will be a seminar this week explaining the projects we have planned for this academic cycle. This will include details of software and equipment upgrades and updates to services and training. 3. We will be closing for three days - 13/12-15/12 - for server upgrades. 4. There will be no operator cover for the week commencing 18/12. The scanners may be booked if you have an operator, however. Tip of the week: Sometimes you may need to change file permissions to gain access to them. Here is some useful information on how to do it. You will need to log on to the wiki to get to the link. https://www.ynic.york.ac.uk/docs/ITPages/FilePermissions?highlight=%28permi… -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Update
by Antony Morland 06 Nov '17

06 Nov '17

Dear All, This week we have a GE planned maintenance on Thursday. We are also cooling down the MEG scanner to allow new electronics to be installed later this year. This will mean that (a) there may be some disruption because of the movement of equipment and liquid gases and (b) staff time for support may be limited this week because of the nature and extent of the work involved in cooling MEG. Tip of the week: Send all support requests to support(a)ynic.york.ac.uk -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Updates
by Antony Morland 01 Nov '17

01 Nov '17

Dear All, This week, Andre will be giving a seminar 'Managing your project at YNiC'. As usual the seminar will start at 4pm and will be followed by refreshments. We have been having some issues with the GE scanner recently, but are monitoring the situation. Next week we will be servicing the MEG scanner by bringing it down to operating temperature. The centre will be busy with extra staff present and equipment being used throughout the week. Best wishes Tony Tip: type *man* followed by a function you would like to know how to use e.g. man ls man is the abbreviated form of manual -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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News this week
by Antony Morland 18 Oct '17

18 Oct '17

Hello All, This weeks seminar is 'How to apply to use the centre'. This will be relevant to all newbies, but will also give an overview of updates that are in the pipeline that will affect all applicants. In other news we are continuing with our programme of training for operators of the Siemens and GE scanners. Best wishes Tony Tip of the week: At the command line you can type ls > list.txt it will generate a text file of the files and directories in the current directory (as long as you have write permissions in the current directory) ls *is the 'list' command* > *allows the output of the ls command to be redirected to a file* mylist.txt * is the file name you supply to capture the output of the ls command* Why is this useful? The generation of a file that lists directories or files can be useful when you are writing scripts to perform analysis on multiple directories or files. Note that this help with ls can be obtained by typing man ls -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Updates and news
by Antony Morland 12 Oct '17

12 Oct '17

Hello All, Quite a few things this week: 1) IMPORTANT: Our MRI screening safety screening forms have been updated. The updates are explained in our revised local rules. 2) A reminder: Our training documentation (including the local rules referred to above) is held at the following URL https://www.ynic.york.ac.uk/ docs/forms. A login in required to access the URL. 3) Last weeks seminar, which was postponed, will go ahead this week and will follow the project presentation by Shogo Kajimura entitled '*Decoding contents of mind wandering'*. The seminar series details can be found here: https://www.ynic.york.ac.uk/events/thursday-sessions#preview 4) We are currently training 14 operators at YNiC. Best wishes Tony *Tip of the week* You can control the transparency of your overlays in *fslview *by using the blue transparency slider located a the bottom right of the window - see attached -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Update - GE MRI system repair
by Andre Gouws 09 Oct '17

09 Oct '17

HI all, The GE engineer has attended and diagnosed the fault with the system. A replacement part is required for the Oxygen monitor to work correctly. This part is on express order and we hope to have it installed tomorrow, although it is unclear at what point in the day this will be. We are hoping that normal scanning service will resume by Wednesday (11th), but please keep alert for further updates which we will send once we have more information. Thanks, -- André ************************************************************************ André Gouws PhD York Neuroimaging Centre University of York The Biocentre York Science Park Heslington YO10 5NY Tel: +44 (0) 1904 435327 Fax: +44 (0) 1904 435356

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GE MRI system fault
by Andre Gouws 08 Oct '17

08 Oct '17

Hi all, I am afraid to report that a sensor fault has developed on the GE system over the weekend. This sensor monitors the safe oxygen level in the MRI environment, and thus the scanner cannot be used until the fault is fixed. GE have said the will attend on Monday AM - we hope to have the scanner up and running as soon as possible. Sorry for those affected by the scanner downtime. André ************************************************************************ André Gouws PhD York Neuroimaging Centre University of York The Biocentre York Science Park Heslington YO10 5NY Tel: +44 (0) 1904 435327 Fax: +44 (0) 1904 435356

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Posters
by David Coggan 06 Oct '17

06 Oct '17

Hello all, We are still looking for posters to put up around YNiC open plan. If you would like to contribute one, please get in touch or drop it off at YNiC. Best wishes, Dave

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Postponed: Today's YNiC seminar.
by Andre Gouws 05 Oct '17

05 Oct '17

Hi all, Due to some unforeseen circumstances we have to postpone today's seminar - We will reschedule and update you in next week's update bulletin. Best wishes, -- André ************************************************************************ André Gouws PhD York Neuroimaging Centre University of York The Biocentre York Science Park Heslington YO10 5NY Tel: +44 (0) 1904 435327 Fax: +44 (0) 1904 435356

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Next YNIC Science Meeting
by Jonny Smallwood 03 Oct '17

03 Oct '17

Hello all, We are holding the next meeting of the YNIC Science Committee next Monday. Please send any items you would like me to raise by Thursday so I can add them to the agenda. Thanks Jonny -- Jonathan Smallwood, Reader in Psychology / Cognitive Neuroscience Room C023, Department of Psychology, University of York, England. YO10 4PH. Telephone: 01904 324651

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Disruption
by Antony Morland 03 Oct '17

03 Oct '17

Hello All, We have a Heating and Cooling contractor in attendance today. Alarms may sound. Apologies if they disrupt your work. If an alarm does and stops within 30s there is no need to act. Please be aware that staff may need to ask you to leave at short notice. Thanks Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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