Release History

Previous releases of neurodesktop

20230628

added VNC connection back into docker container because RDP currently causes issues for european keyboards
added freesurfer into AFNI container to get @SUMA_Make_Spec_FS to work (issue: https://github.com/orgs/NeuroDesk/discussions/210#discussioncomment-4337927)
added deepretinotopy tool in version 1.0.0 20221201 (contributed by Xincheng & Fernanda)

updated qsmxt to 1.1.13 (contributed by Ashley)
added nipype 1.8.3 (contributed by Steffen)
added mneextended 1.1.0 (contributed by David)
added new tool category “workflows”
added new CVMFS mirror server in Phoenix
added mimetypes so that nii/minc files now open in the respective applications
matlab licenses can now be saved from the activation GUI
update rstudio to 2022.07.2 (and R version to 4.1.2 with new additional packages, like brms)

updated qsmxt to 1.1.12 (contributed by Ashley)
updated 3D Slicer to 5.0.3 and included MONAI Label (contributed by Xincheng)
added Matlab 2022a (contributed by Oren)
updated AFNI to 22.1.14 (contributed by Steffen)
updated Spinal Cord Toolbox to 5.7 (contributed by Steffen)
updated Oshyx to 0.4 (contributed by Jeryn)
updated freesurfer to 7.3.2 (contributed by Steffen)
added CVMFS mirror server in Perth and cleaned up server list to account for DNS geo location steering (contributed by Steffen)

update of ROMEO (phase unwrapping) to latest version 3.2.8
update of QSMxT (automated end-to-end QSM processing) to latest version 1.1.10
added mritools 3.3.0 (includes clearswi 1.0.1, mcpc3ds 0.1.0, romeo 3.2.8 as compiled binaries)

update for PhysIO toolbox (physiological noise correction for fMRI) to r2021a including the latest SPM r8224
update of lcmodel to include basis sets for 1.5-9.4T
added a memory display plugin to illustrate how much memory is available to the container and how much is consumed
added a version checker to help with identifying if a new version is available
added file upload via guacamole (+ update of guacamole to 1.4) - users can now drag and drop their files onto guacamole and they get copied to the desktop

MNE Python 0.23.4 container including VScode and extensions
VScode container including Python/Julia Extensions and singularity to test “Inception Mode” (Running singularity containers within singularity containers)
update of fsl to 6.0.5.1
added CAT12 (a software that allows estimation of tissue volumes (and additional surface parameters such as cortical thickness, gyrification or fractal dimension) for different volume and surface-based atlas maps)

a deep learning based vessel segmentation algorithm “vesselapp” was added in version 0.3.1
palm - Permutation Analysis of Linear Models - was added in version alpha119
niistat running in octave was added with version 1.0.20191216
MRIcroGL was updated to a version with included python support, so the scripting is now working
rabies - Rodent Automated Bold Improvement of EPI Sequences was added with version 0.3.5
oshyx was updated to 0.3

neurodesktop can now be accessed via native RDP client as well (e.g. for multi-monitor support): https://www.neurodesk.org/docs/getting-started/neurodesktop/windows/#using-an-rdp-client
there is a new Help button in the menu :)
updates of ants 2.3.4 (now includes Scripts as well, including antsCookTemplatePriors.sh) + newly added version 2.3.5
new version of QSMxT 1.1.9 20211219
new version of Spinal Cord Toolbox 5.4
new tools: MRIcroGL and surfice - fantastic viewers for neuroimaging data

Physio toolbox compiled and added to SPM + update of SPM
added brainstorm
new neurodesktop container management scripts for Linux, Mac and Windows: https://github.com/NeuroDesk/neurodesktop
added fieldtrip
Datalad is now in the main image, so datalad run should work
added Oshy-X segmentation tool
updated freesurfer 7.2.0

added Rstudio, R and multiple R packages (plotly, car, tidyverse, …)
added ClearSWI and ROMEO for MRI phase processing (including new Tutorials: https://www.neurodesk.org/tutorials-examples/tutorials/phase_processing/)
added more categories in applications menu (Body, Electrophysiology, Hippocampus, Phase Processing, Rodent Imaging, Shape Analysis, Spine, Statistics)
bugfix: improved startup time of the desktop container (miniconda in homedirectory was causing chmod slowdown)
bugfix: ssh, vnc and rdp servers are now restarted in case the container was stopped and started again (e.g. on Standby)

fixed naming of aidmri to aidamri and added new category “Rodent Imaging”
updated all tool icons and updated neurodesk icon including background image
VScode now stores settings in persistent storage /neurodesktop-storage and with this keeps extensions and settings across different neurodesktop versions
docker layers are now cached, so updating the desktop to the next version is very fast and consumes less disk space locally
default theme of terminal changed from Solarized to Tango as the old theme was hiding information in tools like htop (same font colour on same background…)

included more tools for connecting to cloud storage services (rclone, owncloud, nextcloud, davfs2, globus). For more info: Storage
styling of desktop interface, including background wallpaper and colour scheme in terminal window
new categories in menu system (visualization) and added more categories to tools

This is the first version of the newly renamed and rebuild neurodesktop (previously vnm and neuromachine)
containers are mounted by default from CVMFS, but this can be deactivated by adding -e CVMFS_DISABLE=true to the docker call