Applications

List of Applications.

Below is a list of the neurocontainer applications included in the most recent Neurodesk release.

To use these applications through the Neurodesk platform, find the correct instructions for getting started by selecting your computing environment details in the widget on our home page

Neurodesktop comes packaged with:

programming software (e.g., Visual Studio Code, python, git)
workflow systems (Nipype)
data synchronization utilities (Rsync, Rclone, Nextcloud, Owncloud)
system management tools (Lmod, Singularity, Htop)
additional resources (Imagemagic, Firefox, OpenSSH client)
access to Neurocontainers via the Neurodesk menu (see list below)

If you can’t find an application in Neurodesktop’s menu, you may need to update Neurodesktop
If you can’t find an application on the Nectar Desktop Service, visit our discussion forum to create a request
For more information on data synchronization, visit our Storage section
For guides and tutorials, refer to the respective tutorial and examples

afni_21.2.00_20210714 functional imaging
afni_22.3.07_20221206 functional imaging
afni_23.0.07_20230302 functional imaging
afni_23.3.02_20231024 functional imaging
afni_24.1.02_20240409 functional imaging
afni_24.3.00_20241003 functional imaging
aidamri_1.1_20210708 rodent imaging
ants_2.3.1_20211204 image registration structural imaging image segmentation
ants_2.3.5_20211212 image registration structural imaging image segmentation
ants_2.5.1_20240429 image registration structural imaging image segmentation
ants_2.5.3_20240925 image registration structural imaging image segmentation
aslprep_0.2.7_20210323 quantitative imaging workflows
aslprep_0.4.0_20230728 quantitative imaging workflows
aslprep_0.5.0_20231116 quantitative imaging workflows
aslprep_0.6.0_20240318 quantitative imaging workflows
aslprep_0.7.0_20240530 quantitative imaging workflows
aslprep_0.7.2_20240917 quantitative imaging workflows
aslprep_0.7.5_20250206 quantitative imaging workflows
ashs_2.0.0_20210105 hippocampus
bart_0.7.00_20210302 image reconstruction
bart_0.9.00_20240723 image reconstruction
bidscoin_3.7.0_20220329 data organisation
bidscoin_4.2.0_20231017 data organisation
bidscoin_4.2.1_20231030 data organisation
bidscoin_4.3.0_20240221 data organisation
bidscoin_4.3.2_20240329 data organisation
bidscoin_4.3.3_20240716 data organisation
bidscoin_4.4.0_20241003 data organisation
bidscoin_4.5.0_20250205 data organisation
bidscoin_4.6.1_20250328 data organisation
bidsappaa_0.2.0_20230613 bids apps
bidsappbaracus_1.1.4_20230612 bids apps
bidsappbrainsuite_21a_20230618 bids apps
bidsapphcppipelines_4.3.0_20230524 bids apps
bidsappmrtrix3connectome_0.5.3_20230615 bids apps
bidsappspm_0.0.20_20230629 bids apps
bidsapppymvpa_2.0.2_20230629 bids apps
bidstools_1.0.1_20230905 data organisation
bidstools_1.0.2_20231017 data organisation
bidstools_1.0.3_20231030 data organisation
bidstools_1.0.4_20240221 data organisation
brainlifecli_1.7.0_20241003 workflows
brainnetviewer_1.7.20191031_20240904 functional imaging visualization
brainstorm_3.211130_20211207 electrophysiology
brkraw_0.3.11_20240320 data organisation
cat12_r1933_20220128 image segmentation image registration structural imaging
cat12_r2166_20230601 image segmentation image registration structural imaging
cat12_12.9_20250307 image segmentation image registration structural imaging
clearswi_1.0.0_20211018 phase processing
code_230315_20230315 programming
conn_20b_20210109 functional imaging
conn_22a_20231115 functional imaging
connectomeworkbench_1.4.2_20201119 functional imaging data organisation
connectomeworkbench_1.5.0_20220919 functional imaging data organisation
convert3d_1.0.0_20210104 data organisation
deepretinotopy_1.0.5_20240609 machine learning functional imaging
deepretinotopy_1.0.8_20250207 machine learning functional imaging
deepretinotopy_1.0.10_20250409 machine learning functional imaging
dcm2bids_3.2.0_20250402 data organisation
dcm2niix_v1.0.20240202_20241125 data organisation
dicomtools_1.0.0_20250204 data organisation
diffusiontoolkit_0.6.4.1_20220303 diffusion imaging
dsistudio_2020.10_20210109 diffusion imaging
dsistudio_chen.2024.04.19_20240426 diffusion imaging
dsistudio_2024.06.12_20241010 diffusion imaging
eeglab_2020.0_20211026 electrophysiology
elastix_5.1.0_20230407 image registration
fatsegnet_1.0.gpu_20201212 body
fastcsr_1.0_20231213 image segmentation
fieldtrip_20211114_20211206 electrophysiology
fieldtrip_20220617_20220627 electrophysiology
fmriprep_20.1.3_20201118 functional imaging workflows
fmriprep_20.2.6_20211209 functional imaging workflows
fmriprep_22.1.1_20230218 functional imaging workflows
fmriprep_23.0.0_20230315 functional imaging workflows
fmriprep_23.2.1_20240402 functional imaging workflows
fmriprep_24.1.0_20241003 functional imaging workflows
fmriprep_24.1.1_20250214 functional imaging workflows
freesurfer_7.1.1_20211216 image segmentation structural imaging
freesurfer_7.2.0_20211206 image segmentation structural imaging
freesurfer_7.3.2_20231214 image segmentation structural imaging
freesurfer_7.4.1_20231214 image segmentation structural imaging
freesurfer_8.0.0_20250210 image segmentation structural imaging
fsl_6.0.3_20200905 functional imaging structural imaging diffusion imaging image segmentation image registration
fsl_6.0.4_20210105 functional imaging structural imaging diffusion imaging image segmentation image registration
fsl_6.0.5.1_20221016 functional imaging structural imaging diffusion imaging image segmentation image registration
fsl_6.0.6.4_20230618 functional imaging structural imaging diffusion imaging image segmentation image registration
fsl_6.0.7.1_20230809 functional imaging structural imaging diffusion imaging image segmentation image registration
fsl_6.0.7.4_20231005 functional imaging structural imaging diffusion imaging image segmentation image registration
fsl_6.0.7.8_20240913 functional imaging structural imaging diffusion imaging image segmentation image registration
fsl_6.0.7.14_20241018 functional imaging structural imaging diffusion imaging image segmentation image registration
fsl_6.0.7.16_20250131 functional imaging structural imaging diffusion imaging image segmentation image registration
gimp_2.10.18_20210104 visualization
glmsingle_1.2_20240520 functional imaging
globus_3.2.2_20230620 data organisation
hdbet_1.0.0_20210318 image segmentation
heudiconv_1.3.1_20241105 data organisation
hnncore_0.3_20231112 electrophysiology
hmri_0.6.0_20230901 quantitative imaging structural imaging
hmri_0.6.1_20231107 quantitative imaging structural imaging
ilastik_1.4.0_20230720 image segmentation
itksnap_3.8.0_20201208 image segmentation visualization
itksnap_4.0.1_20230609 image segmentation visualization
itksnap_4.0.2_20240117 image segmentation visualization
julia_1.4.1_20210105 programming
julia_1.9.4_20240405 programming
julia_1.10.1_20240321 programming
lashis_1.0_20210105 hippocampus
lashis_2.0_20210211 hippocampus
laynii_2.2.1_20220701 functional imaging
lcmodel_6.3_20220222 spectroscopy
matlab_2022a_20231207 programming visualization
matlab_2022b_20250124 programming visualization
matlab_2023b_20250121 programming visualization
matlab_2024b_20250117 programming visualization
mfcsc_1.0_20230306 functional imaging diffusion imaging
mfcsc_1.1_20230321 functional imaging diffusion imaging
mgltools_1.5.7_20230313 molecular biology
micapipe_v0.2.3_20241030 structural imaging diffusion imaging functional imaging workflows
mitkdiffusion_1.2.0_20230720 diffusion imaging
minc_1.9.17_20210105 image segmentation image registration structural imaging
minc_1.9.18_20230208 image segmentation image registration structural imaging
mne_0.23.4_20220121 electrophysiology
mne_1.0.0_20220325 electrophysiology
mne_1.0.3_20220607 electrophysiology
mne_1.1.1_20220912 electrophysiology
mneextended_1.1.0_20220819 electrophysiology
mricrogl_1.2.20211006_20220111 visualization
mricron_1.0.20190902_20220311 visualization
mriqc_0.16.1_20210917 data organisation functional imaging quality control workflows
mriqc_22.0.6_20230215 data organisation functional imaging quality control workflows
mriqc_24.0.2_20241108 data organisation functional imaging quality control workflows
mritools_3.3.0_20220224 phase processing
mrsiproc_0.0.1_20230503 spectroscopy
mrsiproc_0.1.0_20231211 spectroscopy
mrtrix3_3.0.1_20200908 diffusion imaging
mrtrix3_3.0.2_20221108 diffusion imaging
mrtrix3_3.0.3_20210917 diffusion imaging
mrtrix3_3.0.4_20240320 diffusion imaging
mrtrix3src_latest_latest diffusion imaging
mrtrix3tissue_5.2.8_20201111 diffusion imaging
neurodock_1.0.0_20241122 diffusion imaging
niftyreg_1.4.0_20220317 image registration
nighres_1.5.1_20240611 structural imaging
nighres_1.5.2_20250203 structural imaging
niistat_1.0.20191216_20220111 functional imaging
niimath_1.0.0_20240902 data organisation
nipype_1.8.3_20220825 workflows
oshyx_0.4_20220620 image segmentation
palm_alpha119_20211220 functional imaging
palmettobug_0.0.1_20241119 molecular biology
physio_r2021a_20220220 functional imaging
pydeface_2.0.2_20250206 image segmentation
qmrlab_2.4.2_20240828 quantitative imaging
quickshear_1.1.0_20240606 data organisation
qsiprep_0.20.0_20240408 diffusion imaging
qsiprep_1.0.1_20250407 diffusion imaging
qsmxt_5.1.0_20230905 phase processing quantitative imaging structural imaging workflows
qsmxt_6.3.2_20231101 phase processing quantitative imaging structural imaging workflows
qsmxt_6.4.4_20240802 phase processing quantitative imaging structural imaging workflows
qsmxt_7.3.3_20250311 phase processing quantitative imaging structural imaging workflows
qsmxt_8.0.2_20250403 phase processing quantitative imaging structural imaging workflows
rabies_0.3.5_20220111 rodent imaging
relion_4.0.1.sm61_20240528 cryo EM
romeo_3.2.4_20211015 phase processing
romeo_3.2.8_20220224 phase processing
root_6.22.02_20201104 programming
rstudio_1.4.1106_20211014 statistics
rstudio_2022.07.2_20221129 statistics
rstudio_2023.09.1_20231207 statistics
rstudio_2023.12.1_20240209 statistics
samsrfx_v10.004_20241127 functional imaging
sigviewer_0.6.4_20220315 electrophysiology
slicer_4.11.20200930_20201108 image segmentation image registration structural imaging visualization
slicer_5.0.3_20221025 image segmentation image registration structural imaging visualization
slicersalt_3.0.0_20210301 shape analysis
sovabids_0.3.1a0_20221202 data organisation
spinalcordtoolbox_5.4_20211208 spine
spinalcordtoolbox_5.5_20220419 spine
spinalcordtoolbox_5.6_20220503 spine
spinalcordtoolbox_5.7_20220803 spine
spinalcordtoolbox_5.8_20230117 spine
spinalcordtoolbox_6.4_20240925 spine
spm12_r7771_20230609 functional imaging image segmentation image registration structural imaging
surfice_1.0.20210730_20211218 visualization
synthstrip_7.4.1_20240913 image segmentation
tgvqsm_1.0.0_20210629 quantitative imaging phase processing
topaz_0.2.5_20240313 cryo EM
trackvis_0.6.1_20220303 diffusion imaging
vesselapp_0.3.1_20211216 image segmentation
vesselboost_0.9.1_20231031 image segmentation
vesselboost_0.9.4_20240404 image segmentation
vesselboost_1.0.0_20240815 image segmentation
vesselvio_1.1.2_20230428 visualization
vina_1.2.3_20230221 molecular biology
vmtk_1.5.0_20241004 image segmentation