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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

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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.

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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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