apps.yml

---
apps:
  # template for adding an app
  # - gh: "github_usename/github_repo_name"
  #   dh: "dockerhub_usename/dockerhub_repo_name"
  #   description: "short description of the app"
  #   status: unmaintained
  #   ds_type:
  #     - raw
  #     - derivative
  #   datatype:
  #     - anat
  #     - func
  #     - dwi
  #     - fmap
  #     - eeg
  #   ci: Continuous integration service.
  #       Defaults to "circleci"
  #       Can be any of:
  #         - "gh"
  #         - "travis"
  #         - "circleci"
  #         - "none"
  #   branch: Default branch of the repo. Defaults to "master"
  #   workflow: Name of the test workflow.


  ## --- apps that are part of the bids apps github organization
  # sorted by status and then alphabetically by app name

  ### --- active apps

-   gh: bids-apps/afni_proc
    status: active
    dh: bids/afni_proc
    ds_type:
    -   raw
    datatype:
    -   func
    description: prototype AFNI bids app implementing participant level preprocessing with afni_proc.py

-   gh: bids-apps/antsCorticalThickness
    status: active
    dh: bids/antscorticalthickness
    ds_type:
    -   raw
    datatype:
    -   anat
    description: BIDS App for calculating cortical thickness using ANTs

-   gh: bids-apps/baracus
    status: active
    dh: bids/baracus
    ds_type:
    -   raw
    datatype:
    -   anat
    description: Predicts brain age, based on data from Freesurfer 5.3

-   gh: bids-apps/brainiak-srm
    status: active
    dh: bids/brainiak-srm
    ds_type:
    -   derivative
    datatype:
    -   func
    description: This is the BIDS-app version of the Shared Response Model (SRM) of BrainIAK

-   gh: bids-apps/BrainSuite
    status: active
    dh: bids/brainsuite
    ds_type:
    -   raw
    datatype:
    -   anat
    -   dwi
    -   func
    description: "BrainSuite's structural, diffusion, and functional MRI processing pipelines with QC functionalities. "

-   gh: bids-apps/BROCCOLI
    status: active
    dh: bids/broccoli
    comment: 'missing test data: https://github.com/bids-apps/BROCCOLI/issues/13'
    description: BIDS App for BROCCOLI

-   gh: bids-apps/CPAC
    status: active
    dh: bids/cpac
    ds_type:
    -   raw
    datatype:
    -   func
    description: BIDS Application for the Configurable Pipeline for the Analysis of Connectomes (C-PAC)

-   gh: bids-apps/DPARSF
    status: active
    dh: bids/dparsf
    ds_type:
    -   raw # ??
    datatype:
    -   func
    description: Docker version of DPARSF, also deployed at OpenNeuro.org

-   gh: bids-apps/example
    status: active
    dh: bids/example
    description: This an example app that can serve as a template.

-   gh: bids-apps/freesurfer
    status: active
    dh: bids/freesurfer
    ds_type:
    -   raw
    datatype:
    -   func
    description: BIDS app wrapping recon-all from FreeSurfer

-   gh: bids-apps/giga_connectome
    status: active
    dh: bids/giga_connectome
    ci: gh
    branch: main
    workflow: test
    ds_type:
    -   derivative
    datatype:
    -   func
    description: This is a BIDS-App to extract signal from a parcellation with nilearn, typically useful in a context of resting-state data processing.

-   gh: bids-apps/HCPPipelines
    status: active
    dh: bids/hcppipelines
    ds_type:
    -   raw
    datatype:
    -   anat
    -   func
    -   dwi
    description: A BIDS App for minimal preprocessing using the HCP Pipelines

-   gh: bids-apps/hyperalignment
    status: active
    dh: bids/hyperalignment
    ds_type:
    -   derivative
    datatype:
    -   func
    description: Hyperalignment is a functional alignment method that aligns subjects' brain data in a high-dimensional space of voxels/features.

-   gh: bids-apps/MAGeTbrain
    status: active
    dh: bids/magetbrain
    ds_type:
    -   raw
    datatype:
    -   anat
    description:

-   gh: bids-apps/mindboggle
    status: active
    dh: bids/mindboggle
    ds_type:
    -   raw
    datatype:
    -   anat
    description: Improve the accuracy, precision, and consistency of automated labeling and shape analysis of human brain image data

-   gh: bids-apps/MRtrix3_connectome
    status: active
    dh: bids/mrtrix3_connectome
    ds_type:
    -   raw
    -   derivative
    datatype:
    -   dwi
    description: Generate subject connectomes from raw BIDS data & perform inter-subject connection density normalization, using  the MRtrix3 software package.

-   gh: bids-apps/ndmg
    status: active
    dh: bids/ndmg
    ds_type:
    -   raw
    datatype:
    -   anat
    -   dwi
    description: BIDS app for NeuroData's MRI to Graphs pipeline

-   gh: bids-apps/nipypelines
    status: active
    dh: bids/nipypelines
    ds_type:
    -   raw
    datatype:
    -   func
    description: Preprocess functional tasks in a BIDS dataset.

-   gh: bids-apps/oppni
    status: active
    dh: bids/oppni
    ds_type:
    -   raw
    datatype:
    -   func
    description: runs fast optimization of preprocessing pipelines for BOLD fMRI

-   gh: bids-apps/PyMVPA
    status: active
    dh: bids/pymvpa
    ds_type:
    -   derivative
    datatype:
    -   func
    description: runs MVPA and RSA analysis BIDS bold derivative data

-   gh: bids-apps/QAP
    status: active
    dh: bids/qap
    ds_type:
    -   raw
    datatype:
    -   anat
    -   func
    description: PCP Quality Assessment Protocol

-   gh: bids-apps/rsHRF
    status: active
    dh: bids/rshrf
    ds_type:
    -   derivative
    datatype:
    -   func
    comment: does not run on typical fmriprep data
    description: Resting state HRF estimation from BOLD-fMRI signal

-   gh: bids-apps/SPM
    status: active
    dh: bids/spm
    ds_type:
    -   raw
    -   derivative
    description: BIDS App containing an instance of the SPM software.

-   gh: bids-apps/tracula
    status: active
    dh: bids/tracula
    ds_type:
    -   raw
    datatype:
    -   dwi
    description: implements Freesurfer's TRACULA (TRActs Constrained by UnderLying Anatomy) tool for cross-sectional as well as longitudinal (multi session)
        input data.

  ### --- unmaintained apps

-   gh: bids-apps/aa
    status: unmaintained
    dh: bids/aa
    ds_type:
    -   raw
    -   derivative
    description: BIDS App containing an instance of the Automatic Analysis

-   gh: bids-apps/FibreDensityAndCrosssection
    status: unmaintained
    dh: bids/fibredensityandcrosssection
    ds_type:
    -   mri
    datatype:
    -   dmri
    description:

-   gh: bids-apps/niak
    status: unmaintained
    dh: bids/niak
    description: Pipeline for preprocessing of fMRI and structural MRI scans

-   gh: bids-apps/rs_signal_extract
    status: unmaintained
    dh: bids/rs_signal_extract
    ds_type:
    -   derivative
    datatype:
    -   func
    description: BIDS App for resting state signal extraction using nilearn.

# apps hosted somewhere else
# sorted alphabetically by DockerHub (dh)
-   gh: cpp-lln-lab/bidsMReye
    status: active
    dh: cpplab/bidsmreye
    ci: gh
    branch: main
    workflow: system_tests
    ds_type:
    -   derivative
    datatype:
    -   func
    description: BIDS app using deepMReye to decode eye motion for fMRI time series data.

-   gh: cpp-lln-lab/bidspm
    status: active
    dh: cpplab/bidspm
    ci: gh
    branch: main
    workflow: tests
    ds_type:
    -   raw
    -   derivative
    datatype:
    -   anat
    -   func
    description: an SPM centric BIDS app

-   gh: djarecka/fmriprep-fake
    status: active
    dh: djarecka/fmriprep_fake
    ds_type:
    -   raw
    datatype:
    -   anat
    -   func
    ci: none
    description:

-   gh: khanlab/funcmasker-flex
    status: active
    dh: khanlab/funcmasker-flex
    ci: gh
    branch: main
    workflow: test
    ds_type:
    -   raw
    datatype:
    -   func
    description: BIDS App for U-net brain masking of fetal bold MRI

-   gh: trendscenter/gift-bids
    status: active
    dh: trends/gift-bids
    ci: none
    description:

-   gh: khanlab/hippunfold
    status: active
    dh: khanlab/hippunfold
    ds_type:
    -   raw
    datatype:
    -   anat
    ci: none
    description: BIDS App for Hippunfold (automated hippocampal unfolding and subfield segmentation)

-   gh: MICA-MNI/micapipe
    status: active
    dh: micalab/micapipe
    ds_type:
    -   raw
    datatype:
    -   anat
    -   func
    -   dwi
    -   fmap
    ci: none
    description: micapipe from the Multimodal imaging and connectome analysis lab (https://mica-mni.github.io) at the Montreal Neurological Institute. Read
        The Docs documentation below

-   gh: nipreps/fmriprep
    status: active
    dh: nipreps/fmriprep
    ds_type:
    -   raw
    datatype:
    -   anat
    -   func
    description: fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention,
        thereby ensuring the reproducibility of the results.

-   gh: nipreps/dmriprep
    status: active
    dh: nipreps/dmriprep
    ds_type:
    -   raw
    datatype:
    -   anat
    -   dwi
    description: dMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse dMRI data. The transparent workflow dispenses of manual intervention,
        thereby ensuring the reproducibility of the results.

-   gh: nipreps/mriqc
    status: active
    dh: nipreps/mriqc
    ds_type:
    -   raw
    datatype:
    -   anat
    -   func
    description: Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain

-   gh: nipreps/nibabies
    status: active
    dh: nipreps/nibabies
    ds_type:
    -   raw
    datatype:
    -   anat
    -   func
    description: Processing tools for magnetic resonance images of infant brains

-   gh: nipreps/nirodents
    status: active
    dh: nipreps/nirodents
    ds_type:
    -   raw
    datatype:
    -   anat
    -   func
    description:

-   gh: nipreps/smriprep
    status: active
    dh: nipreps/smriprep
    ds_type:
    -   raw
    description: Structural MRI PREProcessing (sMRIPrep) workflows for NIPreps (NeuroImaging PREProcessing tools)

-   gh: nipreps/fmripost-aroma
    status: active
    dh: nipreps/fmripost-aroma
    ds_type:
    -   derivative
    datatype:
    -   func
    description: Functional MRI postprocessing with ICA-AROMA

-   gh: nipreps/fmripost-phase
    status: active
    dh: nipreps/fmripost-phase
    ds_type:
    -   derivative
    datatype:
    -   func
    description: Postprocessing of complex-valued fMRI data

-   gh: nipreps/fmripost-rapidtide
    status: active
    dh: nipreps/fmripost-rapidtide
    ds_type:
    -   derivative
    datatype:
    -   func
    description: Functional MRI postprocessing with Rapidtide

-   gh: PeerHerholz/BIDSonym
    status: active
    dh: peerherholz/bidsonym
    ci: travis
    branch: master
    ds_type:
    -   raw
    datatype:
    -   anat
    description: a BIDS app for pseudo-anonymization of neuroimaging data

-   gh: PennLINC/aslprep
    dh: pennlinc/aslprep
    description: Preprocessing of arterial spin labeling data
    status: active
    ds_type:
    -   raw
    datatype:
    -   perf
    ci: circleci
    branch: main

-   gh: PennLINC/xcp_d
    dh: pennlinc/xcp_d
    description: Post-processing of fMRIPrep, nibabies, HCP, and DCAN BOLD derivatives for functional connectivity analysis
    status: active
    ds_type:
    -   derivative
    datatype:
    -   func
    ci: circleci
    branch: main

-   gh: PennLINC/qsiprep
    status: active
    dh: pennbbl/qsiprep
    ds_type:
    -   raw
    datatype:
    -   dwi
    description: Preprocessing of diffusion MRI
    ci: circleci
    branch: master

-   gh: PennLINC/qsirecon
    status: active
    dh: pennlinc/qsirecon
    ds_type:
    -   derivative
    datatype:
    -   dwi
    description: Reconstruction of preprocessed diffusion MRI
    ci: circleci
    branch: main

-   gh: poldracklab/fitlins
    status: active
    dh: poldracklab/fitlins
    branch: dev
    ds_type:
    -   derivative
    datatype:
    -   func
    description: Fit Linear Models to BIDS Datasets

-   gh: reprostat/reproa
    dh: reprostat/reproa
    status: active
    branch: master
    ds_type:
    -   raw
    datatype:
    -   anat
    -   fmap
    -   func
    description: BIDS App containing an instance of the ReproAnalysis (reproa) software (core only) running under Octave with minimum dependencies.

-   gh: connectomicslab/connectomemapper3
    status: active
    dh: sebastientourbier/connectomemapper-bidsapp
    ds_type:
    -   raw
    -   derivative
    datatype:
    -   anat
    -   func
    -   dwi
    -   eeg
    description: Connectome Mapper 3 is a BIDS App that implements full anatomical, diffusion, resting/state functional MRI, and recently EEG processing
        pipelines, from raw T1 / DWI / BOLD , and preprocessed EEG data to multi-resolution brain parcellation with corresponding connection matrices.

-   gh: sebastientourbier/multiscalebrainparcellator
    status: active
    dh: sebastientourbier/multiscalebrainparcellator
    ds_type:
    -   raw
    datatype:
    -   anat
    description: Multi-Scale Brain Parcellator, part of the Connectome Mapping Toolkit (CMTK), is a BIDS App that implements a full anatomical MRI processing
        pipeline, from raw T1w data to structural brain parcellation at five different scales.

-   gh: Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit
    status: active
    dh: sebastientourbier/mialsuperresolutiontoolkit
    description: The Medical Image Analysis Laboratory Super-Resolution ToolKit (MIALSRTK) consists of a set of C++ and Python processing and workflow tools
        necessary to perform motion-robust super-resolution fetal MRI reconstruction in the BIDS Apps framework.

-   gh: DCAN-Labs/BIBSnet
    status: active
    dh: dcanumn/bibsnet
    datatype:
    -   anat
    description: Utility for creating a nnU-Net anatomical MRI segmentation and mask with a infant brain trained model for the purposes of circumventing
        JLF within Nibabies.

-   gh: openneuropet/petdeface
    status: active
    dh: openneuropet/petdeface
    datatype:
    -   pet
    -   anat
    description: A nipype implementation of MiDeface used to deface PET and MR data as well as co-register the two modalities.
    branch: main
    ci: aws_codebuild
    badge: https://codebuild.us-east-1.amazonaws.com/badges?uuid=eyJlbmNyeXB0ZWREYXRhIjoiYzdXV0tYSkQzTVNkcG04cHA2S055UXlKRlZTU1VONThUMVRoZVcwU3l1aHFhdVBlNDNaRGVCYzdWM1Q0WjYzQ1lRU2ZTSHpmSERPWFRkVXVyb3k3RTZBPSIsIml2UGFyYW1ldGVyU3BlYyI6IjRCZFFIQnNGT2lKcDA1VG4iLCJtYXRlcmlhbFNldFNlcmlhbCI6MX0%3D&branch=main