- ynic-users

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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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

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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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Temporary closures for essential maintenance
by Antony Morland 02 Sep '16

02 Sep '16

Dear All, A few things to update you on that will be occurring at YNiC over the next couple of weeks. During the weeks commencing 5th September and 12th September we will be performing essential IT maintenance. This is the normal annual procedure to install updates (as specified below). It will impact on access to the centre and its IT provision as follows. 1) We will be closing the centre from 5pm, Monday 6th September through to 9am, Wednesday 7th September. There will be no access to computing during this period. 2) For the week commencing 12th September we will have a ‘soft’ closure. You may come to the centre, but your work may be disrupted by maintenance of hardware and software. It may also be a period during which we have to close the centre at short notice. We should be able to honour scanner bookings during the fortnight, but again there may be instances when we have to cancel them at short notice. OVERVIEW OF UPDATES: We will be updating our desktop and stimulus PC images. This will mean that software versions will change. We make every effort to check that these have minimal impact on researchers’ ability to run their analysis and stimulus code. However, once our updates are made please check your use of software to ensure it still works. Thank you for your patience Tony -- Antony Morland, PhD Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Thank you
by Gary Green 31 Aug '16

31 Aug '16

Dear Colleagues I have just, 7.30pm on the 31st, packed my last box of papers and am about to vacate my office. Tomorrow, Professor Tony Morland will become the new Director of the York Neuroimaging Centre and Professor Alex Wade will be the Deputy Director I am sure you will join me in welcoming them to their new roles and in wishing them a very successful future. I have had a fantastic time as Director for the last 13 years and 9 months. I am moving into new roles to work on newly funded research into molecular imaging in humans and the associated hardware to accomplish it. I could not have done this job with out the staff at YNiC and I would like to publicly acknowledge my sincere thanks for them being such wonderful colleagues. We also could not have done this without you - the Users. You have made it tremendously exciting. A lot of science has been carried out. Over 300 projects with over 700 Users, have scanned over 4000 people. Thank you I am not going far - CHyM and the new clinical imaging facilities in York and Leeds, so I hope to meet you all from time to time. best wishes 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: Compute blade maintenance
by Andre Gouws 30 Aug '16

30 Aug '16

If you're wondering why the cluster is currently unavailable, please see Paul's message below. -------- Forwarded Message -------- Subject: [Staff] Compute blade maintenance Date: Tue, 30 Aug 2016 14:12:09 +0100 From: Paul Elliott <Paul.Elliott(a)ynic.york.ac.uk> To: undisclosed Hi all, I'll shortly be disabling the queues for the cluster so that I can work with HP to resolve the issues with our compute blades after a further blade failure overnight. If anybody has any urgent jobs for the cluster then please let me know and I'll try and work around your jobs. Thanks, Paul. -- Paul Elliott, UNIX Systems Administrator York Neuroimaging Centre (YNiC), University of York _______________________________________________ Staff mailing list Staff(a)ynic.york.ac.uk https://www.ynic.york.ac.uk/mailman/listinfo/staff

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Lighting at YNiC
by Antony Morland 24 Aug '16

24 Aug '16

Hello All, You may have already been alerted to this, but I wanted to let you know that the overhead lighting at YNiC is being replaced today. It is not too disruptive - I am finding it straightforward to work in open plan. However, there may be occasions when you will be asked to move so the two fitters can gain access to a specific ceiling panel. Best wishes Tony -- Antony Morland, PhD Head of the Centre for Neuroscience, Hull-York Medical School. Deputy Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Books
by Gary Green 23 Aug '16

23 Aug '16

Dear colleagues I am having a clear out before I migrate to another place. The table in my room has piles of books that are now probably not going to be read by me again. Feel free to help yourselves. The ones on my shelf I might read again, or need, so please leave these for now. 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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Thursday talk 4pm B020
by Antony Morland 19 Jul '16

19 Jul '16

Hello All, David Pitcher will be giving a presentation on two proposed projects; one TMS and one fMRI. Best wishes Tony -- Antony Morland, PhD Head of the Centre for Neuroscience, Hull-York Medical School. Deputy Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Cluster update
by Paul Elliott 18 Jul '16

18 Jul '16

Dear all, Following the cluster failures on Friday we have attempted to replicate the issue over the weekend by loading up all the compute nodes within the cluster to the highest level possible. So far we have not seen any further failures. As such we will shortly return the cluster to service but as the root cause of the original failures are still unknown we may see further sudden and unexpected losses of service. If you submit jobs to the cluster please keep careful track of which jobs you have submitted and ensure that you validate your jobs have run successfully before using any of the output. HP Enterprise (who manufacture and support our hardware) are currently investigating the cause of the failures and we hope to have a full resolution as quickly as possible. Best wishes, Paul. -- Paul Elliott, UNIX Systems Administrator York Neuroimaging Centre (YNiC), University of York

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Cluster issues
by Antony Morland 15 Jul '16

15 Jul '16

Hello All, We are having intermittent faults on some of the blades that make up our cluster. Given that jobs submitted can fail and we also want to ensure no damage is done to the cluster, we are taking it off line for the time being. I am very sorry for inconveniences that may arise. Best wishes Tony -- Antony Morland, PhD Head of the Centre for Neuroscience, Hull-York Medical School. Deputy Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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Operator cover over the summer
by Antony Morland 12 Jul '16

12 Jul '16

Dear All, As you may already know a new Siemens scanner has been installed. Also, we have hired a new radiographer, Jane. These are both very good pieces of news for the centre. However, over the summer we will need to run acceptance testing procedures on the new scanner and also ensure that our radiographers and other YNiC Staff MRI operators are trained to use the new scanner. The acceptance testing and training will impact on our provision of operator covered slots on the GE system. Over this week and last we have not scheduled operator cover, but have resumed normal operator cover form 18th July. We will give as much notice as we can about reductions in operator cover. If during periods when operator cover is reduced and you need a YNiC to scan, please get in touch with us and we will do our best to fit you in. Thanks for your understanding. Best wishes Tony -- Antony Morland, PhD Head of the Centre for Neuroscience, Hull-York Medical School. Deputy Director, York Neuroimaging Centre Department of Psychology, University of York, York YO10 5DD, UK.

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security update
by Ross Devlin 11 Jul '16

11 Jul '16

Hi all, It would appear that we may have a 'fault' associated with the new extension fire doors. They triggered an alarm at the weekend. Therefore until further notice when locking the department in the evening please do not set the alarm in the MRI corridor. Doors should be locked on the computer as per normal and the alarm should be set in MEG and open plan as usual. I will update you all when normal procedures can be resumed. Ross

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security
by Ross Devlin 08 Jul '16

08 Jul '16

Hi all, As the builders are no longer on site, we can now lock the MRI corridor and its enclosed offices and set the alarm at night. There are two additional doors which should be 'locked' on the computer system '1st new extension' and '2nd new extension'. Many thanks Ross

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interesting paper
by Gary Green 29 Jun '16

29 Jun '16

http://www.pnas.org/content/pnas/early/2016/06/27/1602413113.abstract.html?… Functional MRI (fMRI) is 25 years old, yet surprisingly its most common statistical methods have not been validated using real data. Here, we used resting-state fMRI data from 499 healthy controls to conduct 3 million task group analyses. Using this null data with different experimental designs, we estimate the incidence of significant results. In theory, we should find 5% false positives (for a significance threshold of 5%), but instead we found that the most common software packages for fMRI analysis (SPM, FSL, AFNI) can result in false-positive rates of up to 70%. These results question the validity of some 40,000 fMRI studies and may have a large impact on the interpretation of neuroimaging results. They state "Our principal finding is that the parametric statistical methods work well, if conservatively, for voxelwise inference, but not for clusterwise inference. We note that other authors have found RFT clusterwise inference to be invalid in certain settings under stationarity (21, 30) and nonstationarity (13, 33). This present work, however, is the most comprehensive to explore the typical parameters used in task fMRI for a variety of software tools. Our results are also corroborated by similar experiments for structural brain analysis (VBM) (11–13, 39, 40), showing that cluster-based P values are more sensitive to the statistical assumptions. For voxelwise inference, our results are consistent with a previous comparison between parametric and nonparametric methods for fMRI, showing that a nonparametric permutation test can result in more lenient statistical thresholds while offering precise control of false positives (13, 41). " Would be worth discussing at a ynic seminar later in the summer 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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Fixing pesky file permission problems
by Andre Gouws 28 Jun '16

28 Jun '16

We are aware that many of you who use shared project folders often encounter the situation where a file in that folder is not accessible to all members of the group. We have prepared some guidance on how to avoid this happening. In addition, we have prepared a (semi) automated procedure that will any user with access to a group folder to reset the permissions in that folder so that all files can be shared by all users. This procedure involves running a script in a command terminal -- a script that resets the permissions in the entire group directory for all users. For information, please log into the YNiC wiki with your YNiC login and view the guidance at: https://www.ynic.york.ac.uk/docs/ITPages/FilePermissions -- 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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Biocentre fire alarm test
by Gary Green 21 Jun '16

21 Jun '16

Hi All, Apologies for the short notice; however, would you please be advised that following further changes to the fire alarm system within the Biocentre MRI Extension; it will be necessary for me to re-witness the system in operation on Wednesday 22nd June 2016 between the hours of 16.30pm & 18.30pm approximately. 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 may 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 Wednesday afternoon (22/6/16). -- --------------- 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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Two seminars at YNiC this week
by Gary Green 15 Jun '16

15 Jun '16

There will be two ynic seminars this week. First we have an extra seminar by Andy Ioannides from the Lab for Human Brain Dynamiocs, Nicosia. This seminar will be at noon on Wednesday the 15th in BO20 and the title is "Understanding sleep and its implications for specific health conditions" the abstract is below The second seminar is at the normal time of 4pm on Thursday also in BO20 That seminar will be given by Jody Culham from Western and the title is "The treachery of images":Why the brain responds differently to real objects than photos " Her seminar abstract is "Psychologists and neuroimagers commonly study perceptual and cognitive processes using images because of the convenience and ease of experimental control they provide. However, real objects differ from pictures in many ways, including the availability and consistency of depth cues and the potential for interaction. Across a series of neuroimaging experiments, we have shown that the brain responds differently to real objects than pictures, both in terms of the level of activation and the pattern. Now that these results have shown quantitative and qualitative differences in the way the brain processes real objects and images, the next step is to determine which aspects of real objects drive these differences. " ----------------------------- Andy Ioannides abstract is "Some 20 years ago, Michel Jouvet, motivated by the early PET scanning studies of the sleeping brain wrote in the concluding chapter of his book The paradox of sleep - the story of dreaming “… the majority of researchers are waiting with bated breath for the results of studies combining PET scanning, ‘functional’ magnetic resonance imaging (fMRI), magnetoencephalography and tomographic electroencephalography.” The developments in the last two decades have fully vindicated this statement. The talk will first review published work obtained from real time tomographic analysis of the first whole night MEG recordings of sleep that focused on changes in regional brain activations and connectivity between areas related to eye movements and [1] and changes in regional spectral content in each sleep stage and especially during Rapid Eye Movement (REM) sleep [2]. The rest of the talk will present unpublished results from further and more detailed analysis of the same data. focusing on light sleep (NREM1 and NREM2) and discuss the new findings in the context of current ideas about the role of K-complexes and spindles in sleep maintenance and memory consolidation and how these may relate to pathology. " References: [1] Ioannides, A.A., Corsi-Cabrera, M., Fenwick, P.B.C., del Rio Portilla, Y., Laskaris, N.A., Khurshudyan, A., Theofilou, D., Shibata, T., Uchida, S., Nakabayashi, T., Kostopoulos, G.K., 2004. MEG tomography of human cortex and brainstem activity in waking and REM sleep saccades. Cereb. Cortex 14, 56–72. [2] Ioannides, A.A., Kostopoulos, G.K., Liu, L., Fenwick, P.B.C., 2009. MEG identifies dorsal medial brain activations during sleep. Neuroimage 44, 455–468. doi:10.1016/j.neuroimage.2008.09.030 -- --------------- 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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