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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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