Defining standard and nonstandard spaces where data will be resampled
The command line interface of fMRIPrep allows resampling the preprocessed data
onto other output spaces.
That is achieved using the
--output-spaces argument, where standard and
nonstandard spaces can be inserted.
fMRIPrep will reduce the amount of output spaces to just spaces listed in
even if other options require resampling the preprocessed data into intermediary spaces.
TemplateFlow is a software library and a repository of neuroimaging templates that allows end-user applications such as fMRIPrep to flexibly query and pull template and atlas information. In other words, TemplateFlow enables fMRIPrep to access a wide range of templates (and also custom templates, see below). Therefore, TemplateFlow is central to define fMRIPrep’s interface regarding template and atlas prior-knowledge. For more general information about TemplateFlow, visit TemplateFlow.org.
When using fMRIPrep in a workflow that will investigate effects that span across
analytical groupings, neuroimagers typically resample their data on to a standard,
stereotactic coordinate system.
The most extended standard space for fMRI analyses is generally referred to MNI.
For instance, to instruct fMRIPrep to use the MNI template brain distributed with
FSL as coordinate reference the option will read as follows:
By default, fMRIPrep uses
MNI152NLin2009cAsym as spatial-standardization reference.
Valid template identifiers (
MNI152NLin2009cAsym, etc.) come from
the TemplateFlow repository.
Therefore, fMRIPrep will run nonlinear registration processes against the template
T1w image corresponding to all the standard spaces supplied with the argument
By default, fMRIPrep will resample the preprocessed data on those spaces (labeling the
corresponding outputs with the space-<template-identifier> BIDS entity) but keeping
the original resolution of the BOLD data to produce smaller files, more consistent with
the original data gridding.
However, many users will be interested in utilizing a coarse gridding (typically 2mm isotropic)
of the target template.
Such a behavior can be achieved applying modifiers to the template identifier, separated by
--output-spaces MNI152NLin6Asym:res-2 MNI152NLin2009cAsym will generate
preprocessed BOLD 4D files on two standard spaces (
MNI152NLin2009cAsym) with the template’s 2mm isotropic resolution for
the data on
MNI152NLin6Asym space and the original BOLD resolution
(say, e.g., 2x2x2.5 [mm]) for the case of
This is equivalent to saying
--output-spaces MNI152NLin6Asym:res-2 MNI152NLin2009cAsym:res-native.
Please remember that the
resolution entity of TemplateFlow is an index,
res-2 does not necessarily mean 2mm3 - although, it
coincidentally does in the example above.
However, it may not be the case.
MNI152NLin6Asym:res-3 contains a template with
isotropic voxels of 0.5mm3.
Other possible modifiers are, for instance, the
--output-spaces MNIPediatricAsym:res-1:cohort-2 selects
cohort-2 which, for the
template, corresponds to the prepuberty phase
(4.5–8.5 years old).
Space modifiers such as
res are combinatorial:
--output-spaces MNIPediatricAsym:cohort-1:cohort-2:res-native:res-1 will
generate conversions for the following combinations:
1and “native” resolution (meaning, the original BOLD resolution),
1of the template,
2and “native” resolution (meaning, the original BOLD resolution), and
1of the template.
Please mind that the selected resolutions specified must exist within TemplateFlow.
When specifying surface spaces (e.g.,
fsaverage), the legacy identifiers from
FreeSurfer will be supported (e.g.,
fsaverage5) although the use of the density
modifier would be preferred (i.e.,
Custom standard spaces
To make your custom templates visible by fMRIPrep, and usable via
--output-spaces argument, please store your template under
TemplateFlow’s home directory.
The default TemplateFlow’s home directory is
and that can path can be arbitrarily changed by setting
$TEMPLATEFLOW_HOME environment variable.
A minimal example of the necessary files for a template called
MyCustom (and therefore callable via, e.g.,
$TEMPLATEFLOW_HOME/ tpl-MyCustom/ template_description.json tpl-MyCustom_res-1_T1w.nii.gz tpl-MyCustom_res-1_desc-brain_mask.nii.gz tpl-MyCustom_res-2_T1w.nii.gz tpl-MyCustom_res-2_desc-brain_mask.nii.gz
For further information about how custom templates must be organized and corresponding naming, please check the TemplateFlow tutorials.
--output-spaces accepts identifiers of spatial references
that do not generate standardized coordinate spaces:
anat: data are resampled into the individual’s anatomical reference generated with the T1w and T2w images available within the BIDS structure.
fsnative: similarly to the
anatspace for volumetric references, including the
fsnativespace will instruct fMRIPrep to sample the original BOLD data onto FreeSurfer’s reconstructed surfaces for this individual.
sbrefcan be used to generate BOLD data in their original grid, after slice-timing, head-motion, and susceptibility-distortion corrections. These keywords are experimental, and expected to change because additional nonstandard spaces are currently being discussed here.
Modifiers are not allowed when providing nonstandard spaces.
Preprocessing blocks depending on standard templates
Some modules of the pipeline (e.g., the ICA-AROMA denoising, the generation of
HCP compatible grayordinates files, or the fieldmap-less distortion correction)
operate in specific template spaces.
When selecting those modules to be included (using any of the following flags:
--use-syn-sdc) will modify the list of
internal spaces to include the space identifiers they require, should the
identifier not be found within the
--output-spaces list already.
In other words, running fMRIPrep with
--use-syn-sdc will expand the list of resampling spaces to be
However, these spaces that are added implicitly will not be saved to
the derivatives directory.