Processing pipeline details¶
fmriprep adapts its pipeline depending on what data and metadata are
available and are used as the input.
For example, slice timing correction will be
performed only if the
SliceTiming metadata field is found for the input
A (very) high-level view of the simplest pipeline (for a single-band dataset with only one task, single-run, with no slice-timing information nor fieldmap acquisitions) is presented below:
The anatomical sub-workflow begins by constructing an average image by conforming all found T1w images to RAS orientation and a common voxel size, and, in the case of multiple images, averages them into a single reference template (see Longitudinal processing).
Brain extraction, brain tissue segmentation and spatial normalization¶
Then, the T1w image/average is skull-stripped using ANTs’
which is an atlas-based brain extraction workflow.
Once the brain mask is computed, FSL
fast is utilized for brain tissue segmentation.
Finally, spatial normalization to MNI-space is performed using ANTs’
in a multiscale, mutual-information based, nonlinear registration scheme.
In particular, spatial normalization is done using the ICBM 2009c Nonlinear
Asymmetric template (1×1×1mm) [Fonov2011].
When processing images from patients with focal brain lesions (e.g. stroke, tumor
resection), it is possible to provide a lesion mask to be used during spatial
normalization to MNI-space [Brett2001].
ANTs will use this mask to minimize warping of healthy tissue into damaged
areas (or vice-versa).
Lesion masks should be binary NIfTI images (damaged areas = 1, everywhere else = 0)
in the same space and resolution as the T1 image, and follow the naming convention specified in
BIDS Extension Proposal 3: Common Derivatives
This file should be placed in the
sub-*/anat directory of the BIDS dataset
to be run through
In the case of multiple T1w images (across sessions and/or runs), T1w images are
merged into a single template image using FreeSurfer’s mri_robust_template.
This template may be unbiased, or equidistant from all source images, or
aligned to the first image (determined lexicographically by session label).
For two images, the additional cost of estimating an unbiased template is
trivial and is the default behavior, but, for greater than two images, the cost
can be a slowdown of an order of magnitude.
Therefore, in the case of three or more images,
templates aligned to the first image, unless passed the
flag, which forces the estimation of an unbiased template.
The preprocessed T1w image defines the
In the case of multiple T1w images, this space may not be precisely aligned
with any of the original images.
Reconstructed surfaces and functional datasets will be registered to the
T1w space, and not to the input images.
fmriprep uses FreeSurfer to reconstruct surfaces from T1w/T2w
If enabled, several steps in the
fmriprep pipeline are added or replaced.
All surface preprocessing may be disabled with the
Surface processing will be skipped if the outputs already exist.
In order to bypass reconstruction in
fmriprep, place existing reconstructed
<output dir>/freesurfer prior to the run.
fmriprep will perform any missing
recon-all steps, but will not perform
any steps whose outputs already exist.
If FreeSurfer reconstruction is performed, the reconstructed subject is placed in
<output dir>/freesurfer/sub-<subject_label>/ (see FreeSurfer Derivatives).
Surface reconstruction is performed in three phases.
The first phase initializes the subject with T1w and T2w (if available)
structural images and performs basic reconstruction (
autorecon1) with the
exception of skull-stripping.
Skull-stripping is skipped since the brain mask calculated previously is injected into the appropriate location for FreeSurfer.
For example, a subject with only one session with T1w and T2w images
would be processed by the following command:
$ recon-all -sd <output dir>/freesurfer -subjid sub-<subject_label> \ -i <bids-root>/sub-<subject_label>/anat/sub-<subject_label>_T1w.nii.gz \ -T2 <bids-root>/sub-<subject_label>/anat/sub-<subject_label>_T2w.nii.gz \ -autorecon1 \ -noskullstrip
The second phase imports the brainmask calculated in the T1w/T2w preprocessing
The final phase resumes reconstruction, using the T2w image to assist
in finding the pial surface, if available.
Reconstructed white and pial surfaces are included in the report.
If T1w voxel sizes are less than 1mm in all dimensions (rounding to nearest
.1mm), submillimeter reconstruction is used, unless disabled with
rh.midthickness surfaces are created in the subject
surf/ directory, corresponding to the surface half-way between the gray/white
boundary and the pial surface.
inflated surfaces are also
converted to GIFTI format and adjusted to be compatible with multiple software
packages, including FreeSurfer and the Connectome Workbench.
GIFTI surface outputs are aligned to the FreeSurfer T1.mgz image, which may differ from the T1w space in some cases, to maintain compatibility with the FreeSurfer directory. Any measures sampled to the surface take into account any difference in these images.
Refinement of the brain mask¶
Typically, the original brain mask calculated with
will contain some innaccuracies including small amounts of MR signal from
outside the brain.
Based on the tissue segmentation of FreeSurfer (located in
and only when the Surface Processing step has been
executed, FMRIPREP replaces the brain mask with a refined one that derives
aseg.mgz file as described in
Preprocessing of BOLD files is split into multiple sub-workflows described below.
For the head-motion estimation workflow, only the first echo is submitted as this echo is expected to have the highest contrast between gray and white matter. For T2* map creation, all echos are considered jointly to look at voxel-wise T2* decay.
BOLD reference image estimation¶
This workflow estimates a reference image for a BOLD series. If a single-band reference (“sbref”) image associated with the BOLD series is available, then it is used directly. If not, a reference image is estimated from the BOLD series as follows: When T1-saturation effects (“dummy scans” or non-steady state volumes) are detected, they are averaged and used as reference due to their superior tissue contrast. Otherwise, a median of motion corrected subset of volumes is used.
The reference image is then used to calculate a brain mask for the
BOLD signal using the
Further, the reference is fed to the head-motion estimation
workflow and the registration workflow to map
BOLD series into the T1w image of the same subject.
Using the previously estimated reference scan,
mcflirt is used to estimate head-motion.
As a result, one rigid-body transform with respect to
the reference image is written for each BOLD
Additionally, a list of 6-parameters (three rotations,
three translations) per time-step is written and fed to the
For a more accurate estimation of head-motion, we calculate its parameters
before any time-domain filtering (i.e. slice-timing correction),
as recommended in [Power2017].
Slice time correction¶
SliceTiming field is available within the input dataset metadata,
this workflow performs slice time correction prior to other signal resampling
Slice time correction is performed using AFNI
All slices are realigned in time to the middle of each TR.
Slice time correction can be disabled with the
command line argument.
If a BOLD series has fewer than
5 usable (steady-state) volumes, slice time correction will be disabled
for that run.
T2* Driven Coregistration¶
--t2s-coreg command line argument is supplied with multi-echo
BOLD data, a T2* map is generated.
This T2* map is then used in place of the BOLD reference image
to register the BOLD series to the T1w image of the same subject.
Susceptibility Distortion Correction (SDC)¶
One of the major problems that affects EPI data is the spatial distortion caused by the inhomogeneity of the field inside the scanner. Please refer to Susceptibility Distortion Correction (SDC) for details on the available workflows.
Pre-processed BOLD in native space¶
A new preproc BOLD series is generated from the slice-timing corrected or the original data (if STC was not applied) in the original space. All volumes in the BOLD series are resampled in their native space by concatenating the mappings found in previous correction workflows (HMC and SDC if excecuted) for a one-shot interpolation process. Interpolation uses a Lanczos kernel.
EPI to T1w registration¶
The alignment between the reference EPI image
of each run and the reconstructed subject using the gray/white matter boundary
?h.white surfaces) is calculated by the
If FreeSurfer processing is disabled, FSL
flirt is run with the
BBR cost function, using the
fast segmentation to establish the gray/white matter boundary.
After BBR is run, the resulting affine transform will be compared to the initial transform found by FLIRT.
Excessive deviation will result in rejecting the BBR refinement and accepting the original, affine registration.
EPI to MNI transformation¶
This sub-workflow concatenates the transforms calculated upstream (see Head-motion estimation, Susceptibility Distortion Correction (SDC) –if fieldmaps are available–, EPI to T1w registration, and a T1w-to-MNI transform from T1w/T2w preprocessing) to map the EPI image to standard MNI space. It also maps the T1w-based mask to MNI space.
Transforms are concatenated and applied all at once, with one interpolation (Lanczos) step, so as little information is lost as possible.
The output space grid can be specified using the
This option accepts the following (
'native': the original resolution of the BOLD image will be used.
'1mm': uses the 1:math:times`1:math:times`1 [mm] version of the template.
'2mm': uses the 2:math:times`2:math:times`2 [mm] version of the template.
- Path to arbitrary reference file: the output will be resampled on a grid with same resolution as this reference.
EPI sampled to FreeSurfer surfaces¶
If FreeSurfer processing is enabled, the motion-corrected functional series (after single shot resampling to T1w space) is sampled to the surface by averaging across the cortical ribbon. Specifically, at each vertex, the segment normal to the white-matter surface, extending to the pial surface, is sampled at 6 intervals and averaged.
Surfaces are generated for the “subject native” surface, as well as transformed to the
fsaverage template space.
All surface outputs are in GIFTI format.
Given a motion-corrected fMRI, a brain mask,
mcflirt movement parameters and a
segmentation, the discover_wf sub-workflow calculates potential
confounds per volume.
Calculated confounds include the mean global signal, mean tissue class signal,
tCompCor, aCompCor, Frame-wise Displacement, 6 motion parameters, DVARS, and, if
--use-aroma flag is enabled, the noise components identified by ICA-AROMA
(those to be removed by the “aggressive” denoising strategy).
Particular details about ICA-AROMA are given below.
When one of the –output-spaces selected is in MNI space, ICA-AROMA denoising
can be automatically appended to the workflow.
The number of ICA-AROMA components depends on a dimensionality estimate made by MELODIC.
For datasets with a very short TR and a large number of timepoints, this may result
in an unusually high number of components.
By default, dimensionality is limited to a maximum of 200 components.
To override this upper limit one may specify the number of components to be extracted
Further details on the implementation are given within the workflow generation function (
Note: non-aggressive AROMA denoising is a fundamentally different procedure from its “aggressive” counterpart and cannot be performed only by using a set of noise regressors (a separate GLM with both noise and signal regressors needs to be used). Therefore instead of regressors FMRIPREP produces non-aggressive denoised 4D NIFTI files in the MNI space:
Additionally, the MELODIC mix and noise component indices will
be generated, so non-aggressive denoising can be manually performed in the T1w space with
fsl_regfilt -i sub-<subject_label>_task-<task_id>_bold_space-T1w_preproc.nii.gz \ -f $(cat sub-<subject_label>_task-<task_id>_bold_AROMAnoiseICs.csv) \ -d sub-<subject_label>_task-<task_id>_bold_MELODICmix.tsv \ -o sub-<subject_label>_task-<task_id>_bold_space-<space>_AromaNonAggressiveDenoised.nii.gz
Note: The non-steady state volumes are removed for the determination of components in melodic.
*MELODICmix.tsv may have zero padded rows to account for the volumes not used in
melodic’s estimation of components.
A visualization of the AROMA component classification is also included in the HTML reports.