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

usage: [-h]
                       [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
                       [-v] [-s SESSION_ID] [-r RUN_ID] [--task-id TASK_ID]
                       [-d {anat,func}] [--debug] [--nthreads NTHREADS]
                       [--mem_mb MEM_MB] [--write-graph]
                       [--use-plugin USE_PLUGIN] [-w WORK_DIR]
                       [--ignore {fieldmaps} [{fieldmaps} ...]]
                       [--reports-only] [--skip-native]
                       [--ants-nthreads ANTS_NTHREADS] [--skull-strip-ants]
                       [--no-skull-strip-ants] [--no-freesurfer]
                       bids_dir output_dir {participant}

fMRI Preprocessing workflow

positional arguments:

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit

fMRIprep specific arguments:
  -s SESSION_ID, --session-id SESSION_ID
  -r RUN_ID, --run-id RUN_ID
  --task-id TASK_ID     limit the analysis only ot one task
  -d {anat,func}, --data-type {anat,func}
  --debug               run debug version of workflow
  --nthreads NTHREADS   number of threads
  --mem_mb MEM_MB       try to limit the total amount of requested memory for all workflows to this number
  --write-graph         Write workflow graph.
  --use-plugin USE_PLUGIN
                        nipype plugin configuration file
  -w WORK_DIR, --work-dir WORK_DIR
  --ignore {fieldmaps} [{fieldmaps} ...]
                        In case the dataset includes fieldmaps but you chose not to take advantage of them.
  --reports-only        only generate reports, don't run workflows. This will only rerun report aggregation, not reportlet generation for specific nodes.
  --skip-native         don't output timeseries in native space

specific settings for ANTs registrations:
  --ants-nthreads ANTS_NTHREADS
                        number of threads that will be set in ANTs processes
  --skull-strip-ants    use ANTs-based skull-stripping (default, slow))
                        don't use ANTs-based skull-stripping (use  AFNI instead, fast)

settings for FreeSurfer preprocessing:
  --no-freesurfer       disable FreeSurfer preprocessing


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:

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

All previous fmriprep questions are available here:

To participate in the fmriprep development-related discussions please use the following mailing list: 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: