Package Info

KeyValue
Namefmriprep
TitleFunctional MRI data preprocessing pipeline
Package version23.1.4
Build0
Base imagenipreps/fmriprep:23.1.4
MaintainerThomas G. Close (thomas.close@sydney.edu.au)
Info URLhttps://fmriprep.org
Known issueshttps://github.com/nipreps/fmriprep/issues

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]

Required licenses

NameURLDescription
freesurferhttps://surfer.nmr.mgh.harvard.edu/registration.htmlfMRIPRep uses FreeSurfer tools, which require a license to run.

Command

KeyValue
Taskarcana.bids:bids_app
Operates onsession

Inputs

NameRequired data-typeDefault column data-typeDescription
T1wmedimage/nifti-gz-xmedimage/dicom-seriesT1-weighted anatomical scan
T2wmedimage/nifti-gz-xmedimage/dicom-seriesT2-weighted anatomical scan
boldmedimage/nifti-gz-xmedimage/dicom-seriesfunctional MRI
fmap_magnitude1medimage/nifti-gz-xmedimage/dicom-seriesField map - BIDS Case 1 & 2: magnitude of first echo
fmap_magnitude2medimage/nifti-gz-xmedimage/dicom-seriesField map - BIDS Case 1 & 2: magnitude of second echo
fmap_magnitudemedimage/nifti-gz-xmedimage/dicom-seriesField map - BIDS Case 3: magnitude image used for anatomical reference
fmap_phasediffmedimage/nifti-gz-xmedimage/dicom-seriesField map - BIDS Case 1: phasediff image corresponding to the phase-diff map between echo times
fmap_phase1medimage/nifti-gz-xmedimage/dicom-seriesField map - BIDS Case 2: phase of first echo
fmap_phase2medimage/nifti-gz-xmedimage/dicom-seriesField map - BIDS Case 2: phase of second echo
fmap_fieldmapmedimage/nifti-gz-xmedimage/dicom-seriesField map - BIDS Case 3: directly reconstructed field map
fmap_epimedimage/nifti-gz-xmedimage/dicom-seriesField map - BIDS Case 4: Spin Echo EPI scans with different phase encoding directions to estimate the distortion map corresponding to the nonuniformities of the B0 field

Outputs

NameRequired data-typeDefault column data-typeDescription
fmriprepgeneric/directorygeneric/directoryPreprocessed fMRI data

Parameters

NameData typeDescription
fmriprep_flagsstrCommand line flags passed on directly to fMRIPrep
json_editsstrJQ filters (https://devdocs.io/jq/) to apply to JSON side-cars in order to handle special cases where the dcm2niix fails to produce valid a BIDS