YNiC Software Upgrade

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