ynic-users September 2015

ynic-users@ynic.york.ac.uk

7 participants
14 discussions

by Beth Jefferies

Dear YNiC users, This is a reminder that the YNiC Science Committee will meet next Monday, 27th April, at 2pm in B002. YNiC users are welcome to come along to this meeting to ask questions and make suggestions about the running of YNiC. If you wish to raise something, please drop me a line ( beth.jefferies(a)york.ac.uk) before the meeting so that I can add it to the agenda. If you are unable to come along but you want to raise a point for discussion, that is fine too - just get in touch. The YNiC Science Committee meets on Monday week 3 of each term at 2pm. With best wishes Beth -- Beth Jefferies Department of Psychology, University of York, UK +44 01904 324368

9 years, 7 months

Fwd: Induction at the Imaging Centre

by Gary Green

Dear all, As of 1st October this year, YNiC is re-introducing an induction procedure for new centre users. This induction will cover various health & safety, organisational and practical issues regarding using the centre. Induction sessions will take around one hour. This induction is mandatory for all new centre users. To ensure this, fobs and IT accounts will not be issued to any new user who has not completed an induction. We have to be able to show the insurers that we have taken action to ensure that all users are aware of the issues involved in using the centre. If you have been using the centre and have not attended an induction event in the past, please do take the opportunity to attend one of the sessions. Dates and registration details can be found at: https://www.ynic.york.ac.uk/information/induction For taught courses (MSc / MPsych), we run a special set of induction sessions in the Autumn term. We would encourage new PhD students to also register to attend these sessions. This year, these sessions take place on Monday 5th October. Please contact <reception(a)ynic.york.ac.uk> if you wish to attend these sessions. Gary Green

9 years, 7 months

YNiC seminar today

by rem

Dear Users This afternoon (from 4 pm in B020) Ellie Cole will give an internal project proposal presentation on "*Concurrent Activity in the Mirror Neuron System and the Mentalizing System*". Everyone is welcome to attend and refreshments will be available after the seminar. Best wishes Rebecca -- ************************************************************************ Dr. Rebecca E. Millman Science Liaison Officer York Neuroimaging Centre The Biocentre York Science Park Heslington YO10 5DG Tel: +44 (0) 1904 567614 Fax: +44 (0) 1904 435356

9 years, 8 months

YNiC Software Upgrade Complete

by Mark Hymers

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

9 years, 8 months

Key holders - action required

by Sarah Finch

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

9 years, 8 months

Fw: important message

by Alexandra Levine

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

9 years, 8 months

YNiC Seminar 17th September

by Sarah Finch

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

9 years, 8 months

YNiC Software Upgrade

by Mark Hymers

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

9 years, 8 months

Fwd: [BIC-announce] Postdoc, PhD and RA positions available at the BIC

by Jonny Smallwood

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.

9 years, 8 months

YNiC Science day tomorrow, 13:30

by James Davey

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

9 years, 8 months

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ynic-users September 2015