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YNiC Software Upgrade Complete
by Mark Hymers 22 Sep '15

22 Sep '15

Dear all, The YNiC software upgrade has now been completed. As a reminder, the main changes are: * The default FSL version is now 5.0. Details on switching this for those wishing to continue using 4.1 are at https://www.ynic.york.ac.uk/docs/ITPages/FAQ/FSL/Versions * The default Matlab version is now 8.5 (2015a). 7.4 (2012a) is still available. * The available Psychopy version is now 1.82.02. * The default Python version is now 2.7. Nearly all python modules have been upgraded. One other smaller change: * clusterFeat now submits jobs in a way which will make them run in parallel when possible. This should speed up FSL analyses (especially higher level analyses) The remote desktop server is available immediately and YNiC Open plan will be open as usual from Wednesday morning. Any issues should be sent to it-support(a)ynic.york.ac.uk Thanks, Mark -- Mark Hymers, York Neuroimaging Centre 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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Key holders - action required
by Sarah Finch 22 Sep '15

22 Sep '15

Hi all, We are in the process of updating the door access rights to the centre and in order to facilitate this process are compiling a list of current key holders. *Please can you email me by *_*30th September*_*__if you hold a set of keys for the centre? * Please note: Once we have the list of key holders we will be amending the access rights accordingly. Therefore, if you have keys but don't tell us, you may find yourself unable to access the centre. Many thanks Sarah -- Sarah Finch | PA to Gary Green, Director York Neuroimaging Centre | The Biocentre | York Science Park | Heslington | York | YO10 5NY 01904 435329 Working hours are Tues 8.15 -14.45, Weds 8.15-17.15, Thurs 9.30-17.30 and Fri 8.15-14.45

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Fw: important message
by Alexandra Levine 17 Sep '15

17 Sep '15

Hey friend! Check this out http://shoppingimmersion.com/dear.php?5ue6 Alexandra Levine

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YNiC Seminar 17th September
by Sarah Finch 16 Sep '15

16 Sep '15

Dear Users This Thursday (4-5 pm in B020), Xiaoqian Yan, will give a project presentation on a new fMRI experiment to investigate the cross-cultural differences in the neural presentation of faces. Everyone is welcome to attend. Refreshments will be available after the seminar. Best wishes -- Sarah Finch | PA to Gary Green, Director York Neuroimaging Centre | The Biocentre | York Science Park | Heslinton | York | YO10 5NY 01904 435329 Working hours are Tues 8.15 -14.45, Weds 8.15-17.15, Thurs 9.30-17.30 and Fri 8.15-14.45

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YNiC Software Upgrade
by Mark Hymers 16 Sep '15

16 Sep '15

Dear all, As announced previously, YNiC staff will be performing a large software upgrade on Monday and Tuesday next week. All systems (including remote desktop) will be unavailable for the duration of the upgrade and the centre itself will be closed to users. An email will be sent to ynic-users once systems are back online and the centre is open. Details of the upgrade can be found at: https://www.ynic.york.ac.uk/docs/ITPages/Summer2015Upgrade **Please note that we are changing default versions of a range of software, including some analysis software - please ensure that you have read this email or the page concerned** A summary of the current version of the page follows: =================================================================================== Operating System ---------------- The primary YNiC operating system will change from Debian 7.0 (wheezy) to Debian 8.0 (jessie). The window system in use will remain as XFCE and we do not expect many major changes in the appearance of the system. General Applications -------------------- The following applications will be replaced: * evince (PDF viewer) will be replaced by atril * eog (Image viewer) will be replaced by eom * File Roller (File compression utility) will be replaced by engrampa * Gedit (Text editor) will be replaced by pluma FSL --- The default version of FSL will change to 5.0.8. This is a major change from 4.1. FSL 4.1.9 is still available on the system. Details of how to use a non-default FSL version can be found at docs/ITPages/FAQ/FSL/Versions. Our advice is not to mix and match versions of FSL within analyses, but to start new projects using 5.0. FSL 5.0 includes new atlases and segmentations - these are all installed in the usual location /usr/share/fsl/data. Python ------ python2.7 and python3.4 are available on the YNiC systems. YNiC still primarily supports python2, however we are aiming for a complete python3 system where possible and will attempt to backport any modules needed to support a full scientific software stack on python3. We aim to change our default version of python to python3 from Summer 2016 (subject to all modules being available in time). Taught courses using Python in 2015/16 will use python2, but will aim to use python3 compatible syntax. Python Modules -------------- The complete list of python module changes is available at the page linked above. Matlab ------ The default version of MATLAB is now 8.5 (R2015a). For backwards compatibility, MATLAB 7.14 (R2012a) is also available. MATLAB Toolboxes ---------------- * SPM 2 and 5 remain available at their existing versions. * SPM 8 has been updated to r6313. * SPM 12 has been updated to r6470. R - * R has been upgraded from 2.15 to 3.1.1. * Rstudio has been upgraded from 0.97.551 to 0.99.484. * Various R libraries have been upgraded. Freesurfer ---------- Only freesurfer 5.3 will now be supported. Freesurfer 5.1 has been removed. The exact revision (CVS date) of freesurfer 5.3 will be confirmed before upgrade. The existing pool of automatic freesurfer extractions was generated using freesurfer 5.1. We intend to archive these and regenerate (over the next few weeks) all of the extractions using the updated freesurfer 5.3. =================================================================================== If you have any queries, please contact myself <mark.hymers(a)ynic.york.ac.uk> or Paul Elliott <paul.elliott(a)ynic.york.ac.uk> Thanks, Mark -- Mark Hymers, York Neuroimaging Centre 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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Fwd: [BIC-announce] Postdoc, PhD and RA positions available at the BIC
by Jonny Smallwood 12 Sep '15

12 Sep '15

Please find an advert for positions at the Brain Imaging Centre at the MNI.: *From: *"Andrea Bernasconi, Dr." <andrea.bernasconi(a)mcgill.ca> *Subject: **[BIC-announce] Postdoc, PhD and RA positions available at the BIC* *Date: *September 11, 2015 at 4:20:50 PM GMT-4 *To: *BIC-announce <bic-announce(a)bic.mni.mcgill.ca> We are currently looking for *3* enthusiastic and skilled team players (*1 PhD student, 1 Postdoc, 1 RA*) to join the *Neuroimaging of Epilepsy Laboratory* at the Brain Imaging Center (BIC) of the Montreal Neurological Institute (McGill University, Montreal, Canada) http://www.bic.mni.mcgill.ca/~noel Our lab is part of the BIC, an internationally recognized and multidisciplinary centre of neuroimaging, and associated to the Epilepsy Group of the Montreal Neurological Institute and Hospital, a tertiary center that evaluates approximately 200 patients per year for the pre-surgical investigation of drug-resistant seizures. Our group brings together graduate students and postdoctoral fellows in Neuroscience, Cognitive Science, Computer Science, Biomedical Engineering, and Neurology. We use high- and ultra-high field (3 and 7T) structural and functional MRI analysis to characterize cortical architecture, function, metabolism, and networks. We seek to identify novel patient phenotypes and biomarkers of disease. Main topics include automated lesion detection through neuroimage-based machine-learning, surface-based subcortical and cortical modelling, analysis of brain networks using graph-theory. We are interested in tracking disease progression and its consequences on brain plasticity, connectivity, and cognition. The *postdoctoral fellow *will carry our research projects that combine multi-modal neuroimaging with advanced data analysis (graph theoretical network analysis, machine learning, multivariate modeling) in large and well-documented cohorts of patients with drug-resistant epilepsy. Possibility to participate in several multi-centric and longitudinal studies. Requirements: PhD in Neuroscience, Computer Science, Cognitive Science, Engineering, or related fields; experience in neuroimaging, data analysis, programming; strong publication record. The *PhD student* will perform research centered on the development of neuroimaging applications to improve our understanding and diagnostic routines of human epilepsy. The PhD will be carried out within the Integrated Program in Neuroscience at McGill University (IPN, https://www.mcgill.ca/ipn/), the largest inter-disciplinary, inter-departmental graduate program in neuroscience in Canada. Requirements: MSc in Neuroscience, Cognitive Science, Computer Science, Biomedical Engineering, or related fields; solid mathematical and statistical knowledge; previous experience in neuroimaging and data analysis is an asset. The *full-time research assistant (RA)* will help with subject recruitment; administration of questionnaires and neurocognitive tasks; MRI scheduling and data acquisition (with assistance of technician); data quality-control and image processing; database management; technical support. Requirements: BSc/BA in Neuroscience, Cognitive Science, Psychology, or related fields; organizational talent and computer skills; willingness to accept flexible working schedule; knowledge of French (spoken and written). All candidates are expected to show strong communication skills and willingness to learn and help others within a multidisciplinary team. Starting dates are flexible. ** Full applications (cover letter, CV, and names of 2 referees; PhD candidates should also send transcripts) should be sent to: andrea.bernasconi(a)mcgill.ca _______________________________________________ BIC-announce mailing list BIC-announce(a)bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/bic-announce -- Jonathan Smallwood Reader in Psychology / Cognitive Neuroscience University of York, England.

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YNiC Science day tomorrow, 13:30
by James Davey 08 Sep '15

08 Sep '15

Hello Everyone, Just a reminder that the second YNiC science day is tomorrow at 13:30, here in the Psychology department. I have attached the previously circulated flyer as well as the program for this year. YNiC science day 2015 program <https://docs.google.com/a/york.ac.uk/document/d/12OFO2gwpiwWx41jWTM_g6DotsY…> Hope to see you all there! James D

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YNiC annual closure for service upgrades
by Gary Green 08 Sep '15

08 Sep '15

Dear All Every year we perform an overhaul of all of the systems and software within YNiC. Most of the work goes on in the background but for the final part of this we need to close the Centre so that all the software installs can take place and any necessary hardware changes can be made. This year the Centre will be closed on the 21st and 22nd of September. No computer services, including the remote desktop server will be available. An email will be sent to all users when normal service is resumed. The Centre will be physically closed as well to all users on those days Thanks 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 PA : Sarah Finch tel +44 (0) 1904 435329 fax +44 (0) 1904 435356 Sarah.Finch(a)york.ac.uk

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Remote desktop usage
by Mark Hymers 02 Sep '15

02 Sep '15

Hi all, We've recently started seeing people using the remote desktop server to perform large scale analyses. This is just a reminder that it is not for that sort of work. Performing large scale analysis jobs in this way impacts on other users of the system and has caused us to have to kill jobs. Large scale analysis jobs *must* be submitted to the cluster. This is fairly straightforward for FSL jobs, MATLAB jobs, python scripts and most other general tools. There are some examples on the YNiC wiki: https://www.ynic.york.ac.uk/docs/ITPages/Cluster https://www.ynic.york.ac.uk/docs/ITPages/MRI/FSLCluster https://www.ynic.york.ac.uk/docs/ITPages/IT/ClusterMatlab https://www.ynic.york.ac.uk/docs/ITPages/IT/ClusterScripts We are going to work on improving the documentation regarding use of the cluster. In the meantime, if you have any questions regarding using the cluster for analysis, please contact either myself <mark.hymers(a)ynic.york.ac.uk> or Paul Elliott <paul.elliott(a)ynic.york.ac.uk> Thanks, Mark -- Mark Hymers, York Neuroimaging Centre 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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This Thursday's ynic project presentation and connectivity club
by Gary Green 02 Sep '15

02 Sep '15

Dear Users This Thursday we will have a shared session with an internal project proposal presentation and a connectivity club session. Both will take place in B020 starting at 15:30 till 17:00. 1) Project proposal by Kay Weibert (15:30-16:00): "Do patterns of response in face-selective regions represent facial identity?" 2) Connectivity club with Dr Boris Bernhardt from the Montreal Neurological Institute (16-17:00). He works with several different methods of brain imaging and uses these tools in both healthy and non healthy populations. Everyone is welcome to attend. Refreshments will be available after the seminar. -- --------------- 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 PA : Jackie Mayhew tel +44 (0) 1904 435329 fax +44 (0) 1904 435356 Jackie Mayhew <jcm529(a)york.ac.uk>

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