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 ...]]
[-t TASK_ID] [--debug] [--nthreads NTHREADS]
[--omp-nthreads OMP_NTHREADS] [--mem_mb MEM_MB]
[--use-plugin USE_PLUGIN] [--anat-only]
[--ignore-aroma-denoising-errors]
[--ignore {fieldmaps,slicetiming} [{fieldmaps,slicetiming} ...]]
[--longitudinal] [--bold2t1w-dof {6,9,12}]
[--output-space {T1w,template,fsnative,fsaverage,fsaverage6,fsaverage5} [{T1w,template,fsnative,fsaverage,fsaverage6,fsaverage5} ...]]
[--template {MNI152NLin2009cAsym}]
[--output-grid-reference OUTPUT_GRID_REFERENCE] [--use-aroma]
[--skull-strip-ants] [--no-skull-strip-ants] [--fmap-bspline]
[--fmap-no-demean] [--use-syn-sdc] [--force-syn]
[--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, --participant-label | |
one or more participant identifiers (the sub- prefix can be removed) | |
-t, --task-id | select a specific task to be processed |
Options to handle performance¶
--debug | run debug version of workflow |
--nthreads, --n_cpus, -n-cpus | |
maximum number of threads across all processes | |
--omp-nthreads | maximum number of threads per-process |
--mem_mb, --mem-mb | |
upper bound memory limit for FMRIPREP processes | |
--use-plugin | nipype plugin configuration file |
--anat-only | run anatomical workflows only |
--ignore-aroma-denoising-errors | |
ignores the errors ICA_AROMA returns when there are no components classified as either noise or signal |
Workflow configuration¶
--ignore | Possible choices: fieldmaps, slicetiming ignore selected aspects of the input dataset to disable corresponding parts of the workflow |
--longitudinal | treat dataset as longitudinal - may increase runtime |
--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, template, fsnative, fsaverage, fsaverage6, fsaverage5
|
--template | Possible choices: MNI152NLin2009cAsym volume template space (default: MNI152NLin2009cAsym) |
--output-grid-reference | |
Grid reference image for resampling BOLD files to volume template space. It determines the field of view and resolution of the output images, but is not used in normalization. |
Specific options for running ICA_AROMA¶
--use-aroma | add ICA_AROMA to your preprocessing stream |
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 SyN distortion correction¶
--use-syn-sdc | EXPERIMENTAL: Use fieldmap-free distortion correction |
--force-syn | EXPERIMENTAL/TEMPORARY: Use SyN correction in addition to fieldmap correction, if available |
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.