├── .codespellrc ├── .devcontainer └── devcontainer.json ├── .dockerignore ├── .gitattributes ├── .github ├── .dive-ci.yml ├── FUNDING.yml ├── copilot-instructions.md └── workflows │ ├── auto-build.yml │ ├── auto-update.yml │ ├── build-app.yml │ ├── build-config.json │ ├── full-container-test.yml │ ├── manual-build.yml │ ├── on-opening-issue.yml │ ├── process-issues.yml │ ├── publish-dashboard.yml │ ├── recipes-ci.yml │ ├── test-builder.yml │ ├── test-release-pr.yml │ ├── update-apps-json.yml │ └── validate-recipes.yml ├── .gitignore ├── .python-version ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── dashboard ├── .gitignore ├── README.md ├── build.sh ├── cmd │ └── download_issue_comments │ │ └── main.go ├── env.go ├── github_test_report.go ├── go.mod ├── go.sum ├── main.go ├── parser_test.go └── templates │ ├── base.html │ └── index.html ├── macros └── openrecon │ └── neurodocker.yaml ├── pyproject.toml ├── recipes ├── afib1 │ ├── afib1.py │ ├── build.yaml │ └── test.yaml ├── afni │ ├── README.md │ ├── build.old │ ├── build.yaml │ ├── dependencies.R │ ├── license.txt │ ├── test.tgz │ └── test.yaml ├── aidamri │ ├── README.md │ └── build.sh ├── amico │ └── build.yaml ├── ants │ └── build.yaml ├── apptainer │ └── build.yaml ├── arfiproc │ ├── arfiproc.py │ ├── build.yaml │ └── test.yaml ├── ashs │ ├── Readme.md │ └── build.sh ├── aslprep │ └── build.yaml ├── b0map │ ├── b0map.py │ ├── build.yaml │ └── test.yaml ├── bart │ └── build.yaml ├── batchheudiconv │ └── build.yaml ├── bidsappaa │ ├── README.md │ ├── build.sh │ └── test.sh ├── bidsappbaracus │ ├── README.md │ ├── build.sh │ └── test.sh ├── bidsappbrainsuite │ ├── README.md │ ├── build.sh │ └── test.sh ├── bidsapphcppipelines │ ├── README.md │ ├── build.sh │ └── test.sh ├── bidsappmrtrix3connectome │ └── build.yaml ├── bidsapppymvpa │ ├── README.md │ ├── build.sh │ └── test.sh ├── bidsappspm │ ├── README.md │ ├── build.sh │ └── test.sh ├── bidscoin │ ├── build.yaml │ └── test.yaml ├── bidsme │ └── build.yaml ├── bidstools │ └── build.yaml ├── brainlesion │ └── build.yaml ├── brainlifecli │ └── build.yaml ├── brainnetviewer │ ├── README.md │ ├── bnv.star │ ├── brainnetviewer │ └── build.sh ├── brainstorm │ └── build.yaml ├── brkraw │ ├── README.md │ ├── brkraw.pkg │ └── build.sh ├── builder │ └── build.yaml ├── cartool │ ├── README.md │ ├── build.sh │ ├── license.txt │ └── test.sh ├── cat12 │ └── build.yaml ├── cbsb0stats │ ├── build.yaml │ ├── cbsb0stats.py │ └── test.yaml ├── civet │ └── build.yaml ├── clearswi │ ├── README.md │ ├── build.sh │ ├── install_packages.jl │ └── test.jl ├── clinica │ └── build.yaml ├── clinicadl │ └── build.yaml ├── code │ ├── README.md │ ├── build.sh │ ├── code │ └── module.sh ├── condaenvs │ ├── README.md │ ├── build.sh │ └── install_all.sh ├── conn │ └── build.yaml ├── connectomeworkbench │ ├── README.md │ ├── build.yaml │ └── license.txt ├── convert3d │ ├── README.md │ └── build.yaml ├── cosmomvpa │ ├── .octaverc │ ├── README.md │ ├── build.sh │ └── setup_cosmomvpa.m ├── cpac │ └── build.yaml ├── dafne │ ├── build.yaml │ └── test.yaml ├── datalad │ ├── build.yaml │ └── test.yaml ├── dcm2bids │ ├── build.yaml │ └── test.yaml ├── dcm2niix │ ├── build.yaml │ └── test.yaml ├── deepisles │ └── build.yaml ├── deeplabcut │ └── build.yaml ├── deepretinotopy │ └── build.yaml ├── deepsif │ └── build.yaml ├── delphi │ ├── README.md │ └── build.sh ├── dicomtools │ └── build.yaml ├── diffusiontoolkit │ ├── README.md │ └── build.sh ├── dsistudio │ └── build.yaml ├── eeglab │ └── build.yaml ├── eharmonize │ └── build.yaml ├── elastix │ ├── README.md │ └── build.sh ├── esilpd │ └── build.yaml ├── exploreasl │ └── build.yaml ├── ezbids │ ├── build.yaml │ └── test.yaml ├── fastcsr │ ├── README.md │ ├── build.sh │ ├── fs_license.txt │ ├── license.txt │ └── test.sh ├── fastsurfer │ └── build.yaml ├── fatsegnet │ ├── README.md │ └── build.sh ├── fieldtrip │ └── build.yaml ├── fitlins │ └── build.yaml ├── fmriprep │ ├── build.yaml │ └── test.yaml ├── freesurfer │ ├── build.yaml │ └── test.yaml ├── fsl │ ├── build.yaml │ ├── eddy │ └── test.yaml ├── fsqc │ └── build.yaml ├── gigaconnectome │ └── build.yaml ├── gimp │ ├── README.md │ └── build.sh ├── gingerale │ └── build.yaml ├── glmsingle │ ├── LICENSE │ ├── build.yaml │ └── test.yaml ├── globus │ ├── README.md │ ├── build.sh │ └── test.sh ├── gouhfi │ └── build.yaml ├── halfpipe │ └── build.yaml ├── hcpasl │ └── build.yaml ├── hdbet │ ├── README.md │ └── build.sh ├── heudiconv │ ├── build.yaml │ └── test.yaml ├── hmri │ └── build.yaml ├── hnncore │ ├── build.yaml │ └── test.yaml ├── ilastik │ ├── README.md │ ├── build.sh │ └── test.sh ├── irkernel │ └── build.yaml ├── itksnap │ └── build.yaml ├── jamovi │ ├── README.md │ └── build.sh ├── jidt │ ├── README.md │ ├── build.sh │ ├── dependencies.R │ └── test.sh ├── julia │ └── build.yaml ├── lashis │ ├── Readme.md │ └── build.sh ├── laynii │ └── build.yaml ├── lcmodel │ ├── README.md │ ├── basissets.txt │ ├── build.sh │ ├── controlfiledefault │ ├── datasets.txt │ ├── gui-defaults │ ├── license │ └── setup_lcmodel.sh ├── lesionquantificationtoolkit │ └── build.yaml ├── lesymap │ └── build.yaml ├── linda │ └── build.yaml ├── lipsia │ └── build.yaml ├── lqt │ └── build.yaml ├── lstai │ └── build.yaml ├── matlab │ ├── README.md │ ├── build.sh │ ├── matlab │ └── module.sh ├── megnet │ └── build.yaml ├── metabody │ ├── afni_processing.sh │ ├── build.yaml │ ├── metabody.py │ └── test.yaml ├── mfcsc │ ├── README.md │ ├── app_test.sh │ ├── app_version.sh │ ├── build.sh │ └── fix_bash.sh ├── mgltools │ ├── README.md │ ├── build.sh │ └── test.sh ├── micapipe │ ├── README.md │ ├── build.sh │ ├── license.txt │ └── test.sh ├── minc │ └── build.yaml ├── mipav │ └── build.yaml ├── mitkdiffusion │ ├── README.md │ └── build.sh ├── mne │ └── build.yaml ├── mneextended │ ├── README.md │ ├── build.sh │ ├── code │ └── mne-extended.yml ├── mricrogl │ └── build.yaml ├── mricron │ ├── README.md │ ├── build.sh │ └── build.yaml ├── mriqc │ ├── build.yaml │ └── test.yaml ├── mritools │ └── build.yaml ├── mrsimetabolicconnectome │ └── build.yaml ├── mrsiproc │ ├── README.md │ ├── build.sh │ ├── controlfiledefault │ ├── gui-defaults │ ├── install_packages.jl │ ├── matlab │ ├── setup_lcmodel.sh │ └── update_mrsi.sh ├── mrtrix3 │ ├── build.yaml │ └── test.yaml ├── mrtrix3src │ ├── README.md │ ├── build.sh │ └── test.sh ├── mrtrix3tissue │ ├── README.md │ └── build.sh ├── musclemap │ ├── build.yaml │ ├── enhanceddicom2mrd.py │ ├── musclemap.py │ ├── nifti2mrd.py │ └── test.yaml ├── networkcorrespondancetoolkit │ └── build.yaml ├── neurodock │ └── build.yaml ├── nftsim │ └── build.yaml ├── niftyreg │ └── build.yaml ├── nighres │ ├── build.yaml │ └── test.yaml ├── niimath │ ├── README.md │ └── build.yaml ├── niistat │ ├── README.md │ ├── SPMinOctave.m │ └── build.sh ├── nipype │ └── build.yaml ├── noddi │ └── build.yaml ├── openreconexample │ ├── build.yaml │ ├── openreconexample.py │ └── test.yaml ├── oshyx │ └── build.yaml ├── osprey │ └── build.yaml ├── ospreybids │ └── build.yaml ├── palm │ └── build.yaml ├── palmettobug │ ├── build.yaml │ └── test.yaml ├── pcntoolkit │ └── build.yaml ├── physio │ └── build.yaml ├── prostatefiducialseg │ ├── build.yaml │ ├── prostatefiducialseg.py │ └── test.yaml ├── pydeface │ └── build.yaml ├── qmrlab │ ├── README.md │ ├── build.sh │ ├── qMRLab.sh │ └── qMRLab.star ├── qsiprep │ └── build.yaml ├── qsirecon │ └── build.yaml ├── qsmxt │ ├── build.yaml │ └── qsmxt.py ├── quickshear │ ├── build.yaml │ ├── invertcontrast.py │ └── test.yaml ├── qupath │ └── build.yaml ├── rabies │ └── build.yaml ├── radtract │ ├── README.md │ ├── build.sh │ └── radtract.star ├── relion │ ├── README.md │ ├── build.sh │ ├── ctffind.cpp │ ├── license.txt │ ├── load_topaz.sh │ └── module.sh ├── romeo │ └── build.yaml ├── root │ └── build.yaml ├── rstudio │ ├── build.yaml │ └── test.yaml ├── samri │ ├── README.md │ └── build.sh ├── samsrfx │ └── build.yaml ├── segmentator │ ├── README.md │ ├── build.sh │ ├── build.yaml │ └── test.sh ├── sigviewer │ └── build.yaml ├── slicer │ ├── README.md │ └── build.sh ├── slicersalt │ ├── README.md │ └── build.sh ├── sovabids │ ├── README.md │ ├── build.sh │ ├── code │ └── sovabids.yml ├── spant │ └── build.yaml ├── spinalcordtoolbox │ ├── build.yaml │ ├── nifti2mrd.py │ ├── spinalcordtoolbox.py │ └── test.yaml ├── spm12 │ └── build.yaml ├── spm12bi │ ├── README.md │ └── build.sh ├── spm25 │ └── build.yaml ├── spmpython │ └── build.yaml ├── surfice │ └── build.yaml ├── synthstrip │ ├── README.md │ ├── build.sh │ └── synthstrip.star ├── template │ ├── build.yaml │ └── test.yaml ├── terastitcher │ ├── README.md │ ├── build.sh │ └── test.sh ├── tgvqsm │ ├── README.md │ ├── build.sh │ └── setup.py ├── tinyrange │ └── build.yaml ├── topaz │ ├── README.md │ ├── app_test.sh │ ├── app_version.sh │ ├── build.sh │ ├── build.sh.backup │ └── license.txt ├── trackvis │ ├── README.md │ └── build.sh ├── tractseg │ └── build.yaml ├── vesselboost │ ├── build.yaml │ ├── test.yaml │ └── vesselboost.py ├── vesselvio │ ├── README.md │ ├── build.sh │ ├── fixCentos8.sh │ └── vesselvio ├── vina │ └── build.yaml ├── vmtk │ ├── README.md │ ├── build.sh │ └── vmtk.yml ├── voreen │ ├── README.md │ └── build.sh ├── wftfi │ ├── README.md │ ├── build.sh │ └── environment.yml ├── workshopdemo │ └── build.yaml ├── xcpd │ ├── build.yaml │ └── test.yaml └── xnat │ └── build.yaml ├── releases ├── afni │ ├── 21.2.00.json │ ├── 22.3.07.json │ ├── 23.0.07.json │ ├── 23.3.02.json │ ├── 24.1.02.json │ ├── 24.3.00.json │ └── 25.2.03.json ├── aidamri │ └── 1.1.json ├── amico │ └── 2.1.0.json ├── ants │ ├── 2.3.1.json │ ├── 2.3.5.json │ ├── 2.5.1.json │ ├── 2.5.3.json │ ├── 2.5.4.json │ └── 2.6.0.json ├── apptainer │ └── 1.4.4.json ├── ashs │ └── 2.0.0.json ├── aslprep │ ├── 0.2.7.json │ ├── 0.4.0.json │ ├── 0.5.0.json │ ├── 0.6.0.json │ ├── 0.7.0.json │ ├── 0.7.2.json │ └── 0.7.5.json ├── bart │ ├── 0.7.00.json │ └── 0.9.00.json ├── batchheudiconv │ └── 1.0.0.json ├── bidsappaa │ └── 0.2.0.json ├── bidsappbaracus │ └── 1.1.4.json ├── bidsappbrainsuite │ └── 21a.json ├── bidsapphcppipelines │ └── 4.3.0.json ├── bidsappmrtrix3connectome │ └── 0.5.3.json ├── bidsapppymvpa │ └── 2.0.2.json ├── bidsappspm │ └── 0.0.20.json ├── bidscoin │ ├── 3.7.0.json │ ├── 4.2.0.json │ ├── 4.2.1.json │ ├── 4.3.0.json │ ├── 4.3.2.json │ ├── 4.3.3.json │ ├── 4.4.0.json │ ├── 4.5.0.json │ ├── 4.6.1.json │ └── 4.6.2.json ├── bidsme │ └── 1.9.3.json ├── bidstools │ ├── 1.0.1.json │ ├── 1.0.2.json │ ├── 1.0.3.json │ └── 1.0.4.json ├── brainlifecli │ └── 1.7.0.json ├── brainnetviewer │ └── 1.7.20191031.json ├── brainstorm │ └── 3.211130.json ├── brkraw │ └── 0.3.11.json ├── cat12 │ ├── 12.9.json │ ├── r1933.json │ └── r2166.json ├── clearswi │ └── 1.0.0.json ├── code │ └── 230315.json ├── conn │ ├── 20b.json │ └── 22a.json ├── connectomeworkbench │ ├── 1.4.2.json │ ├── 1.5.0.json │ └── 2.1.0.json ├── convert3d │ ├── 1.0.0.json │ └── 1.1.0.json ├── dcm2bids │ └── 3.2.0.json ├── dcm2niix │ └── v1.0.20240202.json ├── deepretinotopy │ ├── 1.0.10.json │ ├── 1.0.11.json │ ├── 1.0.12.json │ ├── 1.0.14.json │ ├── 1.0.15.json │ ├── 1.0.16.json │ ├── 1.0.18.json │ ├── 1.0.5.json │ └── 1.0.8.json ├── dicomtools │ └── 1.0.0.json ├── diffusiontoolkit │ └── 0.6.4.1.json ├── dsistudio │ ├── 2020.10.json │ ├── 2024.06.12.json │ └── chen.2024.04.19.json ├── eeglab │ └── 2020.0.json ├── elastix │ └── 5.1.0.json ├── fastcsr │ └── 1.0.json ├── fastsurfer │ └── 2.4.2.json ├── fatsegnet │ └── 1.0.gpu.json ├── fieldtrip │ ├── 20211114.json │ └── 20220617.json ├── fmriprep │ ├── 20.1.3.json │ ├── 20.2.6.json │ ├── 22.1.1.json │ ├── 23.0.0.json │ ├── 23.2.1.json │ ├── 24.1.0.json │ ├── 24.1.1.json │ └── 25.1.3.json ├── freesurfer │ ├── 7.1.1.json │ ├── 7.2.0.json │ ├── 7.3.2.json │ ├── 7.4.1.json │ ├── 8.0.0.json │ └── 8.1.0.json ├── fsl │ ├── 6.0.3.json │ ├── 6.0.4.json │ ├── 6.0.5.1.json │ ├── 6.0.6.4.json │ ├── 6.0.7.1.json │ ├── 6.0.7.14.json │ ├── 6.0.7.16.json │ ├── 6.0.7.18.json │ ├── 6.0.7.4.json │ └── 6.0.7.8.json ├── fsqc │ └── 2.1.4.json ├── gigaconnectome │ └── 0.6.0.json ├── gimp │ └── 2.10.18.json ├── gingerale │ └── 3.0.2.json ├── glmsingle │ └── 1.2.json ├── globus │ └── 3.2.2.json ├── halfpipe │ └── 1.2.3.json ├── hdbet │ └── 1.0.0.json ├── heudiconv │ └── 1.3.1.json ├── hmri │ ├── 0.6.0.json │ └── 0.6.1.json ├── hnncore │ └── 0.3.json ├── ilastik │ └── 1.4.0.json ├── itksnap │ ├── 3.8.0.json │ ├── 4.0.1.json │ ├── 4.0.2.json │ ├── 4.2.2.json │ └── 4.4.0.json ├── julia │ ├── 1.10.1.json │ ├── 1.4.1.json │ └── 1.9.4.json ├── lashis │ ├── 1.0.json │ └── 2.0.json ├── laynii │ └── 2.2.1.json ├── lcmodel │ └── 6.3.json ├── lesymap │ └── 0.0.0.9222.json ├── linda │ └── 0.5.1.json ├── matlab │ ├── 2022a.json │ ├── 2022b.json │ ├── 2023b.json │ └── 2024b.json ├── mfcsc │ ├── 1.0.json │ └── 1.1.json ├── mgltools │ └── 1.5.7.json ├── micapipe │ └── v0.2.3.json ├── minc │ ├── 1.9.17.json │ └── 1.9.18.json ├── mitkdiffusion │ └── 1.2.0.json ├── mne │ ├── 0.23.4.json │ ├── 1.0.0.json │ ├── 1.0.3.json │ ├── 1.1.0.json │ └── 1.1.1.json ├── mricrogl │ └── 1.2.20211006.json ├── mricron │ └── 1.0.20190902.json ├── mriqc │ ├── 0.16.1.json │ ├── 22.0.6.json │ └── 24.0.2.json ├── mritools │ └── 3.3.0.json ├── mrsiproc │ ├── 0.0.1.json │ └── 0.1.0.json ├── mrtrix3 │ ├── 3.0.1.json │ ├── 3.0.2.json │ ├── 3.0.3.json │ ├── 3.0.4.json │ ├── 3.0.7.json │ └── latest.json ├── mrtrix3tissue │ └── 5.2.8.json ├── networkcorrespondancetoolkit │ └── 0.3.3.json ├── neurodock │ └── 1.0.0.json ├── nftsim │ └── 1.0.2.json ├── niftyreg │ └── 1.4.0.json ├── nighres │ ├── 1.5.1.json │ └── 1.5.2.json ├── niimath │ ├── 1.0.0.json │ ├── 1.0.20250529.json │ └── 1.0.20250804.json ├── niistat │ └── 1.0.20191216.json ├── nipype │ └── 1.8.3.json ├── oshyx │ └── 0.4.json ├── osprey │ └── 2.9.0.json ├── ospreybids │ └── 4.2.1.json ├── palm │ └── alpha119.json ├── palmettobug │ └── 0.0.3.json ├── pcntoolkit │ └── 0.35.json ├── physio │ └── r2021a.json ├── pydeface │ └── 2.0.2.json ├── qmrlab │ └── 2.4.2.json ├── qsiprep │ ├── 0.20.0.json │ └── 1.0.1.json ├── qsirecon │ └── 1.1.0.json ├── qsmxt │ ├── 5.1.0.json │ ├── 6.3.2.json │ ├── 6.4.4.json │ ├── 7.3.3.json │ ├── 8.0.7.json │ ├── 8.1.0.json │ ├── 8.1.1.json │ ├── 8.1.3.json │ └── 8.2.0.json ├── quickshear │ └── 1.1.0.json ├── qupath │ └── 0.6.0.json ├── rabies │ ├── 0.3.5.json │ └── 0.5.3.json ├── relion │ └── 4.0.1.sm61.json ├── romeo │ ├── 3.2.4.json │ └── 3.2.8.json ├── root │ └── 6.22.02.json ├── rstudio │ ├── 1.4.1106.json │ ├── 2022.07.2.json │ ├── 2023.09.1.json │ └── 2023.12.1.json ├── samsrfx │ └── v10.004.json ├── sigviewer │ └── 0.6.4.json ├── slicer │ ├── 4.11.20200930.json │ └── 5.0.3.json ├── slicersalt │ └── 3.0.0.json ├── sovabids │ └── 0.3.1a0.json ├── spinalcordtoolbox │ ├── 5.4.json │ ├── 5.5.json │ ├── 5.6.json │ ├── 5.7.json │ ├── 5.8.json │ ├── 6.4.json │ └── 7.2.json ├── spm12 │ └── r7771.json ├── spm25 │ └── 25.01.02.json ├── spmpython │ └── 25.1.2.post1.json ├── surfice │ └── 1.0.20210730.json ├── synthstrip │ └── 7.4.1.json ├── tgvqsm │ └── 1.0.0.json ├── topaz │ └── 0.2.5.json ├── trackvis │ └── 0.6.1.json ├── tractseg │ └── 2.9.json ├── vesselapp │ └── 0.3.1.json ├── vesselboost │ ├── 0.9.1.json │ ├── 0.9.4.json │ └── 1.0.0.json ├── vesselvio │ └── 1.1.2.json ├── vina │ └── 1.2.3.json ├── vmtk │ └── 1.5.0.json └── xnat │ └── 1.9.2.1.json ├── requirements.txt ├── tools └── generate_apps_json.py ├── uv.lock └── workflows ├── README.md ├── TESTING.md ├── __init__.py ├── container_tester.py ├── format_test_results.py ├── full_container_test.py ├── generate_test_report.py ├── pr_test_runner.py ├── reporting.py ├── summarize_deploy_results.py ├── test_all.sh ├── test_deploy.sh ├── test_runner.py ├── test_utils.py └── validate_all.sh /.codespellrc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/neurodesk/neurocontainers/HEAD/.codespellrc 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