Usage

Execution and the BIDS format

The fmriprep workflow takes as principal input the path of the dataset that is to be processed. The only requirement to the input dataset is that it has a valid BIDS (Brain Imaging Data Structure) format. This can be easily checked online using the BIDS Validator.

The exact command to run fmriprep depends on the Installation method. The common parts of the command follow the BIDS-Apps definition. Example:

fmriprep data/bids_root/ out/ participant -w work/

Command-Line Arguments

FMRIPREP: fMRI PREProcessing workflows

usage: fmriprep [-h] [-v]
                [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
                [-s SESSION_ID] [-r RUN_ID] [-t TASK_ID] [--debug]
                [--nthreads NTHREADS] [--n_cpus NTHREADS]
                [--omp-nthreads OMP_NTHREADS] [--mem_mb MEM_MB]
                [--use-plugin USE_PLUGIN]
                [--ignore {fieldmaps,slicetiming} [{fieldmaps,slicetiming} ...]]
                [--bold2t1w-dof {6,9,12}]
                [--output-space {T1w,MNI152NLin2009cAsym,fsnative,fsaverage,fsaverage6,fsaverage5} [{T1w,MNI152NLin2009cAsym,fsnative,fsaverage,fsaverage6,fsaverage5} ...]]
                [--skull-strip-ants] [--no-skull-strip-ants] [--fmap-bspline]
                [--fmap-no-demean] [--no-freesurfer] [--no-submm-recon]
                [-w WORK_DIR] [--reports-only] [--write-graph]
                bids_dir output_dir {participant}

Positional Arguments

bids_dir the root folder of a BIDS valid dataset (sub-XXXXX folders should be found at the top level in this folder).
output_dir the output path for the outcomes of preprocessing and visual reports
analysis_level

Possible choices: participant

processing stage to be run, only “participant” in the case of FMRIPREP (see BIDS-Apps specification).

Named Arguments

-v, –version show program’s version number and exit

Options for filtering BIDS queries

–participant_label
 one or more participant identifiers (the sub- prefix can be removed)
-s, –session-id
 select a specific session to be processed
-r, –run-id select a specific run to be processed
-t, –task-id select a specific task to be processed

Options to handle performance

–debug run debug version of workflow
–nthreads maximum number of threads across all processes
–n_cpus total number of CPUs to use (alias for –nthreads)
–omp-nthreads maximum number of threads per-process
–mem_mb upper bound memory limit for FMRIPREP processes
–use-plugin nipype plugin configuration file

Workflow configuration

–ignore

Possible choices: fieldmaps, slicetiming

ignore selected aspects of the input dataset to disable corresponding parts of the workflow

–bold2t1w-dof

Possible choices: 6, 9, 12

Degrees of freedom when registering BOLD to T1w images. 9 (rotation, translation, and scaling) is used by default to compensate for field inhomogeneities.

–output-space

Possible choices: T1w, MNI152NLin2009cAsym, fsnative, fsaverage, fsaverage6, fsaverage5

volume and surface spaces to resample functional series into

Specific options for ANTs registrations

–skull-strip-ants
 use ANTs-based skull-stripping (default, slow))
–no-skull-strip-ants
 don’t use ANTs-based skull-stripping (use AFNI instead, fast)

Specific options for handling fieldmaps

–fmap-bspline fit a B-Spline field using least-squares (experimental)
–fmap-no-demean
 do not remove median (within mask) from fieldmap

Specific options for FreeSurfer preprocessing

–no-freesurfer
 disable FreeSurfer preprocessing
–no-submm-recon
 disable sub-millimeter (hires) reconstruction

Other options

-w, –work-dir path where intermediate results should be stored
–reports-only only generate reports, don’t run workflows. This will only rerun report aggregation, not reportlet generation for specific nodes.
–write-graph Write workflow graph.

Debugging

Logs and crashfiles are outputted into the <output dir>/logs directory. Information on how to customize and understand these files can be found on the nipype debugging page.

Support and communication

The documentation of this project is found here: http://fmriprep.readthedocs.org/en/latest/.

If you have a problem or would like to ask a question about how to use fmriprep, please submit a question to NeuroStars.org with an fmriprep tag. NeuroStars.org is a platform similar to StackOverflow but dedicated to neuroinformatics.

All previous fmriprep questions are available here: http://neurostars.org/tags/fmriprep/

To participate in the fmriprep development-related discussions please use the following mailing list: http://mail.python.org/mailman/listinfo/neuroimaging Please add [fmriprep] to the subject line when posting on the mailing list.

All bugs, concerns and enhancement requests for this software can be submitted here: https://github.com/poldracklab/fmriprep/issues.