Release History

Previous releases of neurodesktop

Latest Version: 2024-12-06

2024-12-06

updated QSMxT: v7.2.2
add heudiconv 1.3.1
add mriqc 24.0.2 20241108
add samsrfx v10.003
add palmettobug 0.0.1 20241119
add neurodock/pydesigner
Update dcm2niix version to 20241125
changed CVMFS servers
added -w workaround for docker on apple silicon into dockerfile
add static strace to /opt for container debugging
enabled VNC again and fix RDP auto resizing

2024-10-22

use cloudfront distribution only
workaround for kernel bug on arm64
add ipywidgets ipyvolume jupyterlab_widgets
add fsl 6.0.7.14
add QSMxT v7.2.1

2024-10-16

add jupyter-resource-usage plugin
disable VNC
remove updating of example directory on startup
update jupyter-server-proxy
add more CVMFS servers
Added relion 4.0.1.sm61 20240528
update aslprep to 0.7.0
update deepretinotpy to 1.0.5
add quickshear
add nighres 1.5.1
update bidscoin 4.3.3 and 4.4.0
Added bart 0.9.00
updated QSMxT to 7.1.0
Added mrtrix3src (latest version)
update VesselBoost to ver 1.0.0 by @KMarshallX in #301
add qmrlab
added niimath
updated fsl to 6.0.7.8
update aslprep to 0.7.2
update ants to 2.5.3
updated spinalcordtoolbox to 6.4
Update afni to 24.2.07
add dcm2niix
add micapipe 0.2.3
added brainnetviewer
Added brainlifecli
update fmriprep to 24.1.0
Update dsistudio 2024.06.12
add vmtk 1.5.0

2024-05-25

add new CVMFS CDN servers
add jupyter_scheduler and ipycanvas
update guacamole version to 1.5.5 and tomcat to 9.0.87
add rise extension for presentations
https://github.com/NeuroDesk/neurocommand/releases/tag/2024-05-25
fixed brkraw by @stebo85 in #268
QSMxT: v6.4.1 by @astewartau in #270
update mrtrix3 by @stebo85 in #271
QSMxT: v6.4.2 by @astewartau in #272
QSMxT: v6.4.3 by @astewartau in #274
update bidscoin to 4.3.2 by @stebo85 in #275
update fmriprep by @stebo85 in #277
add julia 1.9.4 by @stebo85 in #280
update dsi_studio by @stebo85 in #283
add glmsingle by @stebo85 in #284
ants 2.5.1 20240429 by @stebo85 in #285
QSMxT: v6.4.4 by @astewartau in #287

2024-03-27

Switched from singularity to apptainer
added (brkraw) and fixed multiple tools (mrtrix3, julia)

2024-01-12

fixed fsl GUI error, when starting fsl in VNC mode (the USER was not exported)
removed c.ServerApp.root_dir setting because it was causing an error when clicking on the Home button. Now it’s not possible to navigate outside of the homedirectory anymore in the side panel.

2023-11-28

fixed a bug where the /proc/cpuinfo file under ARM did not contain a MHz entry, which stopped Matlab from starting up
fixed a bug where the SINGULARITY_BINDPATH was not send in a jupyter notebook file

2023-10-29

bugfix: conda and mamba environments are now initialized correctly when neurodesktop starts up (not just in jupyter)

2023-09-20

the neurodesktop image is now multi-arch and supports x86 and ARM64
fixed recursive link creation in /data
switched to new cvmfs server geolocation DNS steering policy system: cvmfs[1,2,3].neurodesk.org resolve to 3 servers per region which are compared for speed by the client on startup
fixed recursive execution of bash shell inside a singularity container
fixed empty username
switched release tag naming scheme to YYYY-MM-DD instead of YYYYMMDD for better readability

20230628

directories can now be deleted in jupyter interface even if they contain files
moved startup configurations out of .bashrc
removed redundant chown of homedirectory (e.g. affecting windows startup time)
added git extension to juputerlab
more robust handling of CVMFS edge cases

20230531

included neurodesktop version in hostname
removed apt lists
triggered automount externally

20230525

used jupyter based image
fixed environment variables for nipype
fixed RDP upload permission errors
added symlink on home if /data is mounted

20221216

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)

20221129

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)

20220813

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)

20220701

added laynii 2.2.1 - layer fMRI toolbox (contributed by Renzo Huber)
added fieldtrip 20220617 - eeg processing (contributed by David White)

20220329

added bidscoin 3.7.0 (converting data to bids) contributed by Oren
added sigviewer 0.6.4 (viewing electrophysiological data) contributed by Tom
added niftyreg 1.4.0 (image registration tool) contributed by Steffen
added mne 1.0.0 (EEG processing pipeline) contributed by David

20220302

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)

20220222

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

20220128

update of Spinalcordtoolbox to 5.5
update of CAT12 to r1933

20220121

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)

20220111

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

20211220

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

20211207

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

20211028

added EEGLAB

20211018

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)

20210929

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…)

20210923

removed faulty mriqc 0.15.2 container
neurodesk.github.io is now starting page in firefox browser

20210918

added mriqc 0.16.1 and mrtrix 3.0.3

20210917

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

20210916

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

Last modified December 14, 2024: updated version and added inplace update (663dbfa)