fmriprep

Package Info

KeyValue
App version21.0.2
XNAT wrapper version1.22
Base imagenipreps/fmriprep:21.0.2
Info URLhttps://fmriprep.org

Required licenses

Source fileMounted atInfo
freesurfer.txt/opt/freesurfer/license.txt

Commands

fmriprep

fMRIPrep is a functional magnetic resonance imaging (fMRI) data preprocessing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting. It performs basic processing steps (coregistration, normalization, unwarping, noise component extraction, segmentation, skullstripping etc.) providing outputs that can be easily submitted to a variety of group level analyses, including task-based or resting-state fMRI, graph theory measures, surface or volume-based statistics, etc. Optional flags that can be provided to the fmriprep_flags parameter: [–anat-only] [–boilerplate_only] [–md-only-boilerplate] [–error-on-aroma-warnings] [-v] [–ignore {fieldmaps,slicetiming,sbref,t2w,flair} [{fieldmaps,slicetiming,sbref,t2w,flair} …]] [–output-spaces [OUTPUT_SPACES [OUTPUT_SPACES …]]] [–me-output-echos] [–bold2t1w-init {register,header}] [–bold2t1w-dof {6,9,12}] [–force-bbr] [–force-no-bbr] [–medial-surface-nan] [–slice-time-ref SLICE_TIME_REF] [–random-seed _RANDOM_SEED] [–use-aroma] [–aroma-melodic-dimensionality AROMA_MELODIC_DIM] [–return-all-components] [–fd-spike-threshold REGRESSORS_FD_TH] [–dvars-spike-threshold REGRESSORS_DVARS_TH] [–skull-strip-template SKULL_STRIP_TEMPLATE] [–skull-strip-fixed-seed] [–skull-strip-t1w {auto,skip,force}] [–fmap-bspline] [–fmap-no-demean] [–topup-max-vols TOPUP_MAX_VOLS] [–use-syn-sdc [{warn,error}]] [–force-syn] [–no-submm-recon] [–cifti-output [{91k,170k}] | –fs-no-reconall] [–resource-monitor] [–reports-only] [–config-file FILE] [–write-graph] [–stop-on-first-crash] [–notrack] [–debug {compcor,fieldmaps,all} [{compcor,fieldmaps,all} …]] [–sloppy]

KeyValue
Short descriptionfMRIPrep: a functional fMRI data preprocessing pipeline
Workflowarcana.tasks.bids:bids_app
Version1a1
Executable/opt/conda/bin/fmriprep
Operates onSession

Inputs

PathInput formatStored formatDescription
T1wmedimage:NiftiGzXmedimage:DicomT1-weighted anatomical scan
T2wmedimage:NiftiGzXmedimage:DicomT2-weighted anatomical scan
fMRImedimage:NiftiGzXmedimage:Dicomfunctional MRI

Outputs

NameOutput formatStored formatDescription
fmriprepcommon:Directoryformat

Parameters

NameData type
fmriprep_flagsstring
json_editsstring