- ynic-users

Level 0 & level 1 MRI operators
by Eleanor Cole 25 Jan '17

25 Jan '17

Hello Everyone, I am having trouble finding someone to act as a level 0 operator at 9am on Friday (I know it is the morning after Richard's viva celebrations so the Morland lab group won't be feeling too fresh). If anyone is available to help out then please let me know. Otherwise I will have to cancel this scan with one of my ASD participants. Thanks, Ellie

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MEG
by Antony Morland 25 Jan '17

25 Jan '17

Dear All, Sorry to report that MEG is proving to be unreliable at present. We hope to be able to re-establish service as soon as possible. In the meantime, please don't book the MEG scanner. Thanks Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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User issues for discussion at the YNIC Science Commitee
by Jonny Smallwood 19 Jan '17

19 Jan '17

Hello everyone, The next meeting for the YNIC Science committee is on the 23rd of January. Please send me an email describing any issues you would like me to raise, ideally by the end of tomorrow. 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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Seminar today
by Antony Morland 19 Jan '17

19 Jan '17

Hello all, Kirstie Wailes-Newson will be giving a project presentation at 4pm at YNiC today. Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Teaching times for Spring Term
by Mark Hymers 11 Jan '17

11 Jan '17

Hi all, As usual, YNiC open plan will be used for teaching over the Spring term. During this times, the open plan area will be unavailable to anybody not involved in teaching. The times at which teaching will occur are: Week 2: * Monday 16th January 1200-1600 * Tuesday 17th January 1100-1500 Week 3: * Friday 27th January 1200-1600 Week 4: * Monday 30th January 1200-1600 * Friday 3rd February 1200-1600 Week 5: * Tuesday 7th February 1200-1600 Week 7: * Monday 20th February 1200-1600 * Tuesday 21st February 1200-1600 Week 8: * Friday 3rd March 1200-1600 Week 9: * Monday 6th March 1200-1600 * Friday 10th March 1200-1600 Week 10: * Friday 17th March 1200-1600 If you have a University of York account, the teaching timetable can also be accessed by going to https://www.york.ac.uk/viewtimetables , choosing YNiC as a room and choosing View Room. Thanks, Mark -- Mark Hymers, Lecturer in Neuroimaging Methods York NeuroImaging Centre and Department of Psychology University of York, UK Please note that my email address is: mark.hymers(a)ynic.york.ac.uk Responses to messages sent to other addresses may be delayed

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Lab Led Seminars
by Jonny Smallwood 11 Jan '17

11 Jan '17

Hello YNIC Users As part of the new schedule for YNIC we thought it might be helpful to provide sessions in which users of the centre provide information on (i) the methods that they use and (ii) the research questions that these are helpful in addressing. The next available slot will be in mid March. Please get in contact if you are interested in giving one of these talks. Thanks -- 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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Thursday seminar
by Antony Morland 11 Jan '17

11 Jan '17

Hello Everyone, This Thursday (12th Jan) I'll be giving a talk about 'People and Procedures at YNiC'. It's targeted at introducing the YNiC staff, new and old, and how investigators can use the centre. Refreshments will be provided. The talk will be held at YNiC. I'll also be sending out a programme for this term's seminars soon. We are hoping to follow a scheme whereby we alternate between talks that cover what is provided at YNiC and talks that share research being undertaken on labs that use YNiC. The aim is to have short talks (30mins of so) to allow for project presentations to be made at the same sessions as the need arises. Cheers Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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YNiC Seminar Thursday 5th January
by Antony Morland 04 Jan '17

04 Jan '17

Hello All, Happy New Year! 2017 is kicking off with a seminar from Matthew Brett, who will be talking about neuroimaging methods at YNiC tomorrow at 4pm. Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Matthew Brett Talk 5th January
by Antony Morland 21 Dec '16

21 Dec '16

Hello Everyone, We are fortunate to have Matthew Brett coming through York in January and he will be giving a talk 4pm, 5th January at YNiC. Details to follow. Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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YNiC downtime this Friday
by Paul Elliott 15 Dec '16

15 Dec '16

Hi all, This Friday evening from 9pm we will be upgrading several parts of key infrastructure at YNiC. During the work no YNiC services will be available. We expect the maintenance to be completed by the early hours of Saturday morning. Thanks, Paul. -- Paul Elliott, UNIX Systems Administrator York Neuroimaging Centre (YNiC), University of York

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YNiC Seminar
by Antony Morland 13 Dec '16

13 Dec '16

Hello All, We have a project presentation by David O'connor this week. He will present his project 'Exploring the impact of environmental factors on impulsive choice and impulsive action'. The presentation will be at YNiC. Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Software documentation
by Mark Hymers 12 Dec '16

12 Dec '16

Hi all, Those of you who use NAF or the python-megdata module may have noticed that the online documentation has been unavailable for a couple of weeks. For technical reasons, we've had to move the location of the documentation. This can now be found at: https://www.ynic.york.ac.uk/code-docs/ Please update any bookmarks or other references to the old URL (https://vcs.ynic.york.ac.uk/docs) Sorry for the inconvenience, Mark -- Mark Hymers, Lecturer in Neuroimaging Methods York NeuroImaging Centre and Department of Psychology University of York, UK Please note that my email address is: mark.hymers(a)ynic.york.ac.uk Responses to messages sent to other addresses may be delayed

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Presentation
by Antony Morland 09 Dec '16

09 Dec '16

Dear All, We are not aware of anyone needing Presentation software and we are therefore planning to discontinue with providing it from August 2017 onwards. Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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GE MRI is working
by Antony Morland 25 Nov '16

25 Nov '16

Hello All, I'm happy to report that the GE MRI SCANNER is up and running for business tomorrow onwards. Best wishes Tony

2 1

IMPORTANT
by Antony Morland 08 Nov '16

08 Nov '16

Hello Everyone, This one is important. In recent weeks we have found that safety screening forms and consent forms are not being returned appropriately to ynic in all cases. That is, the personal information on these documents is not being kept confidential. Please ensure that after scanning has finished, participant's forms are returned to YNiC reception. You MUST either hand the forms personally to a member of YNiC staff or place the forms in the secure gray post-box behind the reception desk. During the period of time you are responsible for the forms do not leave them in open site anywhere in the building and do note take them away from the building. Thank you -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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IT potential outage
by Antony Morland 08 Nov '16

08 Nov '16

Hello All, We've had reports of intermittent loss of access to some files and folders. We are investigating. We may have to reboot some servers controlling our storage arrays in the near future without notice. More to follow. Bw Tony

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Cluster memory usage
by Mark Hymers 02 Nov '16

02 Nov '16

Dear all, We have made a small change to the YNiC cluster configuration. Until now, each cluster job could use as much memory as they wanted. This has been known to cause problems for users when they submit jobs which require a large amount of RAM. If multiple jobs which require large amounts of RAM are put onto the same machine, the jobs may run out of memory. More problematically, it was sometimes the case that jobs which did not require much RAM were the ones which failed. To prevent this, we have added a default RAM limitation to the cluster. Each "slot" is allocated 8G by default. If the job uses more than this, it will be killed. Jobs which require more RAM can still be run on the cluster. To do this, you will simply need to tell the cluster how much memory to reserve for your job - this will prevent your job from running out of RAM by reserving enough for you. This can be done using the -l h_vmem=xxG argument to the qsub command. We have documented this on the wiki at: https://www.ynic.york.ac.uk/docs/ITPages/IT/ClusterScripts under the "Resource Limitations" section. We estimate that this will not affect many users. For anybody who is affected and are using qsub directly, the instructions above provide information on how to request more RAM to be made available. If you are find that you are getting memory allocation errors when using any of the YNiC provided cluster commands (clusterFeat, clusterR, clusterMatlab, clusterReconAll), or when using NAF, please contact it-support(a)ynic.york.ac.uk and we will make sure that we adapt the scripts to use the correct arguments with the qsub command. If you have any questions, please contact it-support(a)ynic.york.ac.uk Thanks, Mark -- Mark Hymers, Lecturer in Neuroimaging Methods York NeuroImaging Centre and Department of Psychology University of York, UK Please note that my email address is: mark.hymers(a)ynic.york.ac.uk Responses to messages sent to other addresses may be delayed

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Data CD creation of participant data
by Antony Morland 02 Nov '16

02 Nov '16

Hello All, A gentle reminder that we mechanisms in place to allow you to provide MRI images to those participants that request them. Please use this process rather than printing out 'pictures' of brains. Many thanks Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

2 1

Computing cluster
by Andre Gouws 26 Oct '16

26 Oct '16

Many of you will be aware that we have recently experienced a few hardware failures on the YNiC computing cluster. We have now escalated these issues and the manufacturer has committed to attend on site to attempt to resolve the existing issues. Without being too technical, this process is essentially an overhaul of the current cluster and requires two engineers. Obviously, we are doing out utmost to get your cluster up and running again but, considering the scale of the job, please be patient. We will keep you updated. Thanks, -- André ************************************************************************ André Gouws 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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Create CDs of data for your participants
by Antony Morland 24 Oct '16

24 Oct '16

Dear All, We have a system for providing CDs at YNiC. However, such is the number of requests we have to deal with, we now need to rethink how to provide the anatomical scan data to participants. What’s even more frustrating, is that although we have a system that alerts participants that their CD is ready, 58 remain uncollected. We are therefore being asked to allocate considerable resource to generating CDs that the participants subsequently have little or no interest in. Rethink: Moving forward, we will allow researchers to create data CDs for their participants. The researcher will need to provide their own CD and execute a script. The script, 'Create subject CD', can be run from the 'Applications' menu under 'YNiC Utilities'. Please follow the instructions given by the script and note that you (1) have to have the permission of the participant (2) make sure that the participant receives the CD [you may want to record their signature] and (3) you record who you have sent CDs to. Andre is also putting a webpage together to give guidance. https://www.ynic.york.ac.uk/information/mri/MakeASubjectCD Requests to YNiC for data CDs will no longer be met after 1/11/2016. Thank you Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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YNiC seminar today
by Junior Whiteley 20 Oct '16

20 Oct '16

Dear Users, Today we will be graced with the presence of Dr Helen Nutall from the Psychology Department at Lancaster University. She will be giving a talk entitled: "Sensorimotor processing in perception of degraded speech" The talk will be held in room B020 in the Psycholgy Department, at 4pm. All are welcome and refreshments will be served afterwards. Best, Junior -- Junior Whiteley York Neuroimaging Centre junior.whiteley(a)ynic.york.ac.uk

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Consent and screening
by Antony Morland 10 Oct '16

10 Oct '16

Hello All, It has been noted that investigators are sometimes asking potential participants screening questions in reception and other areas where confidential answers may be overheard. Please make appropriate arrangements to ensure the confidentiality of your participants responses. Many thanks Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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No Thursday talk this week
by Antony Morland 06 Oct '16

06 Oct '16

Hello everyone, To avoid confusion for those recently joining the ynic user community, Thursday seminars are announced, usually early in the week. This week there is no seminar. Best wishes Tony

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YNiC Open Plan teaching times for Autumn Term 2016
by Mark Hymers 03 Oct '16

03 Oct '16

Hi all, At the following times during this term, YNiC open plan will be closed for teaching. Please note that if any YNiC open plan computers have been left logged on at the start of the teaching sessions, they will be automatically logged out. Week 2: * Tuesday 4th October 1200-1600 * Thursday 6th October 0900-1300 Week 3: * Monday 10th October 1200-1600 Week 4: * Monday 17th October: 1200-1600 Week 7: * Monday 7th November: 1200-1600 Week 9: * Monday 21st November: 1200-1600 Timings for the Spring term will be sent around in December. Thanks, Mark -- Mark Hymers, Lecturer in Neuroimaging Methods York NeuroImaging Centre and Department of Psychology University of York, UK Please note that my email address is: mark.hymers(a)ynic.york.ac.uk Responses to messages sent to other addresses may be delayed

1 0

Update
by Antony Morland 09 Sep '16

09 Sep '16

Dear All, Many of the routine updates to our IT provision have been successfully completed. We will complete the remaining jobs next week. These involve the stimulus PCs. The cluster is currently down. This is an issue that is unrelated to the routine updates and is being dealt with by HP engineers. Thanks, Paul, for installing these important updates. As I wrote previously, please report any issues that arise in your use of the IT system here (other than the cluster issue, which we know about). This will help us resolve them speedily. Best wishes Tony -- Antony Morland, PhD. Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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