BIDS Apps

BIDS Apps are typically docker or singularity images that allow you to seamlessly run many applications without the need to installing all dependencies, and are generally guaranteed to run on your data, provided your data is BIDS compliant. Below is a list of many commonly used BIDS Apps.

Status of the "latest" docker image

Name	Input datatypes	Use raw	Use derivatives	Status latest	Number docker pulls	Image size
afni_proc	func	yes	no
antsCorticalThickness	anat	yes	no
baracus	anat	yes	no
brainiak-srm	func	no	yes
BrainSuite	anat dwi func	yes	no
BROCCOLI		no	no
CPAC	func	yes	no
DPARSF	func	yes	no
example		no	no
freesurfer	func	yes	no
giga_connectome	func	no	yes
HCPPipelines	anat func dwi	yes	no
hyperalignment	func	no	yes
MAGeTbrain	anat	yes	no
mindboggle	anat	yes	no
MRtrix3_connectome	dwi	yes	yes
ndmg	anat dwi	yes	no
nipypelines	func	yes	no
oppni	func	yes	no
PyMVPA	func	no	yes
QAP	anat func	yes	no
rsHRF	func	no	yes
SPM		yes	yes
tracula	dwi	yes	no
bidsMReye	func	no	yes
bidspm	anat func	yes	yes
fmriprep-fake	anat func	yes	no
funcmasker-flex	func	yes	no
gift-bids		no	no
hippunfold	anat	yes	no
micapipe	anat func dwi fmap	yes	no
fmriprep	anat func	yes	no
dmriprep	anat dwi	yes	no
mriqc	anat func	yes	no
nibabies	anat func	yes	no
nirodents	anat func	yes	no
smriprep		yes	no
fmripost-aroma	func	no	yes
fmripost-phase	func	no	yes
fmripost-rapidtide	func	no	yes
BIDSonym	anat	yes	no
aslprep	perf	yes	no
xcp_d	func	no	yes
qsiprep	dwi	yes	no
qsirecon	dwi	no	yes
fitlins	func	no	yes
reproa	anat fmap func	yes	no
connectomemapper3	anat func dwi eeg	yes	yes
multiscalebrainparcellator	anat	yes	no
mialsuperresolutiontoolkit		no	no
BIBSnet	anat	no	no
petdeface	pet anat	no	no

Status of the default branch on the source repository

Name	Status unstable	Updated	Number issues
afni_proc	Status unstable
antsCorticalThickness	Status unstable
baracus	Status unstable
brainiak-srm	Status unstable
BrainSuite	Status unstable
BROCCOLI	Status unstable
CPAC	Status unstable
DPARSF	Status unstable
example	Status unstable
freesurfer	Status unstable
giga_connectome	Status unstable
HCPPipelines	Status unstable
hyperalignment	Status unstable
MAGeTbrain	Status unstable
mindboggle	Status unstable
MRtrix3_connectome	Status unstable
ndmg	Status unstable
nipypelines	Status unstable
oppni	Status unstable
PyMVPA	Status unstable
QAP	Status unstable
rsHRF	Status unstable
SPM	Status unstable
tracula	Status unstable
bidsMReye	Status unstable
bidspm	Status unstable
fmriprep-fake	Status unstable
funcmasker-flex	Status unstable
gift-bids	Status unstable
hippunfold	Status unstable
micapipe	Status unstable
fmriprep	Status unstable
dmriprep	Status unstable
mriqc	Status unstable
nibabies	Status unstable
nirodents	Status unstable
smriprep	Status unstable
fmripost-aroma	Status unstable
fmripost-phase	Status unstable
fmripost-rapidtide	Status unstable
BIDSonym	Status unstable
aslprep	Status unstable
xcp_d	Status unstable
qsiprep	Status unstable
qsirecon	Status unstable
fitlins	Status unstable
reproa	Status unstable
connectomemapper3	Status unstable
multiscalebrainparcellator	Status unstable
mialsuperresolutiontoolkit	Status unstable
BIBSnet	Status unstable
petdeface	Status unstable