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
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
- 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
- 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
- ashs_2.0.0_20210105 hippocampus
- bart_0.7.00_20210302 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
- 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
- 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
- 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_1.0.0_20221201 machine learning
- deepretinotopy_1.0.1_20231011 machine learning
- deepretinotopy_1.0.2_20231223 machine learning
- deepretinotopy_1.0.4_20240409 machine learning
- diffusiontoolkit_0.6.4.1_20220303 diffusion imaging
- dsistudio_2020.10_20210109 diffusion imaging
- dsistudio_chen.2024.04.19_20240426 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
- 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
- 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
- gimp_2.10.18_20210104 visualization
- globus_3.2.2_20230620 data organisation
- hdbet_1.0.0_20210318 image segmentation
- 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
- mfcsc_1.0_20230306 functional imaging diffusion imaging
- mfcsc_1.1_20230321 functional imaging diffusion imaging
- mgltools_1.5.7_20230313 molecular biology
- 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
- 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
- mrtrix3tissue_5.2.8_20201111 diffusion imaging
- niftyreg_1.4.0_20220317 image registration
- niistat_1.0.20191216_20220111 functional imaging
- nipype_1.8.3_20220825 workflows
- oshyx_0.4_20220620 image segmentation
- palm_alpha119_20211220 functional imaging
- physio_r2021a_20220220 functional imaging
- qsiprep_0.20.0_20240408 diffusion imaging
- qsmxt_2.1.0_20230509 phase processing quantitative imaging structural imaging workflows
- qsmxt_4.0.1_20230824 phase processing quantitative imaging structural imaging workflows
- 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_6.4.3_20240327 phase processing quantitative imaging structural imaging workflows
- rabies_0.3.5_20220111 rodent imaging
- 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
- 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
- spm12_r7771_20230609 functional imaging image segmentation image registration structural imaging
- surfice_1.0.20210730_20211218 visualization
- tgvqsm_1.0.0_20210629 quantitative imaging phase processing
- 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
- vesselvio_1.1.2_20230428 visualization
- vina_1.2.3_20230221 molecular biology