All apps

bids-apps/aa
bids-apps/afni_proc
bids-apps/antsCorticalThickness
bids-apps/baracus
bids-apps/brainiak-srm
bids-apps/BROCCOLI
bids-apps/CPAC
bids-apps/DPARSF
bids-apps/example
bids-apps/freesurfer
bids-apps/HCPPipelines
bids-apps/hyperalignment
bids-apps/MAGeTbrain
bids-apps/mindboggle
bids-apps/MRtrix3_connectome
bids-apps/ndmg
bids-apps/niak
bids-apps/nipypelines
bids-apps/oppni
bids-apps/PyMVPA
bids-apps/QAP
bids-apps/rs_signal_extract
bids-apps/rsHRF
bids-apps/SPM
bids-apps/tracula
cpp-lln-lab/bidsMReye
cpp-lln-lab/bidspm
khanlab/funcmasker-flex
trendscenter/gift-bids
khanlab/hippunfold
MICA-MNI/micapipe
nipreps/fmriprep
nipreps/dmriprep
nipreps/mriqc
nipreps/nibabies
nipreps/nirodents
nipreps/smriprep
PeerHerholz/BIDSonym
PennLINC/qsiprep
connectomicslab/connectomemapper3
sebastientourbier/multiscalebrainparcellator
Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit

Unmaintainted apps

bids-apps/FibreDensityAndCrosssection

Apps sorted by input type

For BIDS raw datasets: anat data

bids-apps/antsCorticalThickness
bids-apps/baracus
bids-apps/HCPPipelines
bids-apps/MAGeTbrain
bids-apps/mindboggle
bids-apps/ndmg
bids-apps/QAP
cpp-lln-lab/bidspm
nipreps/fmriprep
nipreps/dmriprep
nipreps/mriqc
nipreps/nibabies
nipreps/nirodents
PeerHerholz/BIDSonym
connectomicslab/connectomemapper3
sebastientourbier/multiscalebrainparcellator

For BIDS raw datasets: func data

bids-apps/afni_proc
bids-apps/CPAC
bids-apps/DPARSF
bids-apps/freesurfer
bids-apps/HCPPipelines
bids-apps/nipypelines
bids-apps/oppni
bids-apps/QAP
cpp-lln-lab/bidspm
khanlab/funcmasker-flex
nipreps/fmriprep
nipreps/mriqc
nipreps/nibabies
nipreps/nirodents
connectomicslab/connectomemapper3

For BIDS raw datasets: dwi data

bids-apps/HCPPipelines
bids-apps/MRtrix3_connectome
bids-apps/ndmg
bids-apps/tracula
nipreps/dmriprep
connectomicslab/connectomemapper3

For BIDS derivative datasets: anat data

cpp-lln-lab/bidspm
connectomicslab/connectomemapper3

For BIDS derivative datasets: func data

bids-apps/brainiak-srm
bids-apps/hyperalignment
bids-apps/PyMVPA
bids-apps/rs_signal_extract
bids-apps/rsHRF
cpp-lln-lab/bidsMReye
cpp-lln-lab/bidspm
connectomicslab/connectomemapper3

For BIDS derivative datasets: dwi data

bids-apps/MRtrix3_connectome
connectomicslab/connectomemapper3