Hi everyone
During the YNiC closure the following updates and changes will be made to
the available software:
*FSLView*
- This will be the last YNiC desktop build which contains FSLView. It
is deprecated and we are already pulling various tricks to make it work.
We had initially scheduled its removal for Summer 2018 but we have managed
to keep it going. We now intend to remove it in Summer 2020. This really
is the end of fslview, so please migrate to FSLeyes.
*FSL*
- FSL 5 has been updated from 5.0.9 to 5.0.11 with all new tools also
added (bianca, mist, surface-based tools, film_cifti).
- FSL 6 is now installed (version 6.0.1) but version 5 will remain the
default.
- We will review the default FSL version in Summer 2020 and decide
whether to switch the default to FSL-6 at this time.
*Freesurfer*.
- This will be the last YNiC desktop build which contains Freesurfer
5.3. All projects should now be using 6.0. Please let us know if you are
still using 5.3.
*AFNI*
- AFNI is being reintroduced after a several year absence. We will be
using the latest stable release (20190220), but will configure AFNI in such
a way that multiple versions can be supported at once. Details of how to
use AFNI at YNiC will be added to the documentation pages.
*MATLAB*
- The available versions of Matlab will be 8.5 and 9.6
- Matlab 9.0, 9.2 and 9.4 are no longer available.
- Note that we will not retain 8.5 beyond Summer 2021, so if you are
still using it, you need to migrate your tools as soon as possible. Please
let us know if you are still using 8.5 for some reason.
*SPM*
- SPM 12 has been updated to the latest patch release.
- SPMs 5 and 8 have been removed from the system. These versions are
over a decade old, are not supported upstream, and building them is
becoming harder as compilers become more pedantic about code quality.
- We have retained SPM 2 as it is still buildable and has historically
been used by a couple of other packages (for co-registration etc). SPM 2
will be removed in Summer 2021. If you still have a real need for SPM 2, 5
or 8, please get in touch as soon as possible.
- All new projects should be using SPM 12.
*Connectome Workbench*
- This has been upgraded from 1.2.3 to 1.3.2
*Python 2 / 3*
- This will be last build of the YNIC desktop where Python 2 is fully
supported as it is now deprecated upstream.
- All new code should be written using Python 3. We plan to run a
workshop in the first weeks of term to assist people in migrating code from
Python 2 to 3; this will be especially relevant for those who use Psychopy.
- Python 3.7.3 is now installed, upgraded from 3.5.3.
- We are aware of the following modules used under Python 2 which are
not currently available for python 3:
*python-mvpa2:* Upstream are working on porting this; we will make it
available as soon as possible.
*python-pymc: *We are currently working on python3 compatible packages for
this
Major module updates:
- numpy 1.16.2 (from 1.12.1)
- scipy 1.1.0 (from 0.18.1)
- matplotlib 3.0.2 (from 2.0.0)
- h5py 2.8 (from 2.7)
- mdp is no longer available: you should use sklearn instead
- mpi4py 3.0.2 (from 2.0.0); note that this is a newer version than in
Debian Buster by default
- nibabel 2.3.2 (from 2.1.0)
- nifti -> this is a python 2 module and is deprecated; use nibabel
instead
- pil 5.4.1 (from 4.0)
- pyglet 1.4.1 (from 1.1.4); note that this is a newer version than in
Debian Buster by default
- scikits.audiolab is replaced by soundfile 0.10.1
- sounddevice 0.3.13 is the supported sound presentation module
- vtk: version 7 for Python 3; version 6 for Python 2
- wxpython 4.0 (from 3.0); note that this is a major version change
- Psychopy has been updated to 3.1.5 (from 1.90.0). This involves
changing from Python 2 to Python 3. We recommend that people attend the
Python 2 to 3 migration workshop which will provide a good opportunity for
people to get assistance in updating scripts (where necessary).
*Mathematica*
- Version 10 is no longer available; you should use Mathematica 11.
*Shutter (the screenshot app)*
- This application is no longer available. We recommend Flameshot as
the replacement.
YNiC will be closed from 5pm today (Friday 30th Aug), and will re-open on
Monday 23rd September. Please note that there will be no access to YNiC
open plan, remote desktops, or support, during the closure period.
I hope you all have a pleasant YNiC break, and we'll see you again in a few
weeks!
Kind regards
Lauren
--
Lauren Welbourne, PhD
Senior Research Technician
lauren.welbourne(a)york.ac.uk
York Neuroimaging Centre
University of York
Innovation Way
Heslington
York
YO10 5NY
