Results included in this manuscript come from preprocessing
performed using *fMRIPrep* 20.2.3
(@fmriprep1; @fmriprep2; RRID:SCR_016216),
which is based on *Nipype* 1.6.1
(@nipype1; @nipype2; RRID:SCR_002502).

Anatomical data preprocessing

: A total of 1 T1-weighted (T1w) images were found within the input
BIDS dataset.The T1-weighted (T1w) image was corrected for intensity non-uniformity (INU)
with `N4BiasFieldCorrection` [@n4], distributed with ANTs 2.3.3 [@ants, RRID:SCR_004757], and used as T1w-reference throughout the workflow.
The T1w-reference was then skull-stripped with a *Nipype* implementation of
the `antsBrainExtraction.sh` workflow (from ANTs), using OASIS30ANTs
as target template.
Brain tissue segmentation of cerebrospinal fluid (CSF),
white-matter (WM) and gray-matter (GM) was performed on
the brain-extracted T1w using `fast` [FSL 5.0.9, RRID:SCR_002823,
@fsl_fast].
Brain surfaces were reconstructed using `recon-all` [FreeSurfer 6.0.1,
RRID:SCR_001847, @fs_reconall], and the brain mask estimated
previously was refined with a custom variation of the method to reconcile
ANTs-derived and FreeSurfer-derived segmentations of the cortical
gray-matter of Mindboggle [RRID:SCR_002438, @mindboggle].
Volume-based spatial normalization to one standard space (MNI152NLin2009cAsym) was performed through
nonlinear registration with `antsRegistration` (ANTs 2.3.3),
using brain-extracted versions of both T1w reference and the T1w template.
The following template was selected for spatial normalization:
*ICBM 152 Nonlinear Asymmetrical template version 2009c* [@mni152nlin2009casym, RRID:SCR_008796; TemplateFlow ID: MNI152NLin2009cAsym],

Functional data preprocessing

: For each of the 1 BOLD run found per subject (across all
tasks and sessions), the following preprocessing was performed.
First, a reference volume and its skull-stripped version were generated
 using a custom
methodology of *fMRIPrep*.
Susceptibility distortion correction (SDC) was omitted.
The BOLD reference was then co-registered to the T1w reference using
`bbregister` (FreeSurfer) which implements boundary-based registration [@bbr].
Co-registration was configured with six degrees of freedom.
Head-motion parameters with respect to the BOLD reference
(transformation matrices, and six corresponding rotation and translation
parameters) are estimated before any spatiotemporal filtering using
`mcflirt` [FSL 5.0.9, @mcflirt].
The BOLD time-series (including slice-timing correction when applied)
were resampled onto their original, native space by applying
the transforms to correct for head-motion.
These resampled BOLD time-series will be referred to as *preprocessed
BOLD in original space*, or just *preprocessed BOLD*.
The BOLD time-series were resampled into standard space,
generating a *preprocessed BOLD run in MNI152NLin2009cAsym space*.
First, a reference volume and its skull-stripped version were generated
 using a custom
methodology of *fMRIPrep*.
Several confounding time-series were calculated based on the
*preprocessed BOLD*: framewise displacement (FD), DVARS and
three region-wise global signals.
FD was computed using two formulations following Power (absolute sum of
relative motions, @power_fd_dvars) and Jenkinson (relative root mean square
displacement between affines, @mcflirt).
FD and DVARS are calculated for each functional run, both using their
implementations in *Nipype* [following the definitions by @power_fd_dvars].
The three global signals are extracted within the CSF, the WM, and
the whole-brain masks.
Additionally, a set of physiological regressors were extracted to
allow for component-based noise correction [*CompCor*, @compcor].
Principal components are estimated after high-pass filtering the
*preprocessed BOLD* time-series (using a discrete cosine filter with
128s cut-off) for the two *CompCor* variants: temporal (tCompCor)
and anatomical (aCompCor).
tCompCor components are then calculated from the top 2% variable
voxels within the brain mask.
For aCompCor, three probabilistic masks (CSF, WM and combined CSF+WM)
are generated in anatomical space.
The implementation differs from that of Behzadi et al. in that instead
of eroding the masks by 2 pixels on BOLD space, the aCompCor masks are
subtracted a mask of pixels that likely contain a volume fraction of GM.
This mask is obtained by dilating a GM mask extracted from the FreeSurfer's *aseg* segmentation, and it ensures components are not extracted
from voxels containing a minimal fraction of GM.
Finally, these masks are resampled into BOLD space and binarized by
thresholding at 0.99 (as in the original implementation).
Components are also calculated separately within the WM and CSF masks.
For each CompCor decomposition, the *k* components with the largest singular
values are retained, such that the retained components' time series are
sufficient to explain 50 percent of variance across the nuisance mask (CSF,
WM, combined, or temporal). The remaining components are dropped from
consideration.
The head-motion estimates calculated in the correction step were also
placed within the corresponding confounds file.
The confound time series derived from head motion estimates and global
signals were expanded with the inclusion of temporal derivatives and
quadratic terms for each [@confounds_satterthwaite_2013].
Frames that exceeded a threshold of 0.5 mm FD or
1.5 standardised DVARS were annotated as motion outliers.
All resamplings can be performed with *a single interpolation
step* by composing all the pertinent transformations (i.e. head-motion
transform matrices, susceptibility distortion correction when available,
and co-registrations to anatomical and output spaces).
Gridded (volumetric) resamplings were performed using `antsApplyTransforms` (ANTs),
configured with Lanczos interpolation to minimize the smoothing
effects of other kernels [@lanczos].
Non-gridded (surface) resamplings were performed using `mri_vol2surf`
(FreeSurfer).


Many internal operations of *fMRIPrep* use
*Nilearn* 0.6.2 [@nilearn, RRID:SCR_001362],
mostly within the functional processing workflow.
For more details of the pipeline, see [the section corresponding
to workflows in *fMRIPrep*'s documentation](https://fmriprep.readthedocs.io/en/latest/workflows.html "FMRIPrep's documentation").


### Copyright Waiver

The above boilerplate text was automatically generated by fMRIPrep
with the express intention that users should copy and paste this
text into their manuscripts *unchanged*.
It is released under the [CC0](https://creativecommons.org/publicdomain/zero/1.0/) license.

### References

Results included in this manuscript come from preprocessing performed
using \emph{fMRIPrep} 20.2.3 (\citet{fmriprep1}; \citet{fmriprep2};
RRID:SCR\_016216), which is based on \emph{Nipype} 1.6.1
(\citet{nipype1}; \citet{nipype2}; RRID:SCR\_002502).

\begin{description}
\item[Anatomical data preprocessing]
A total of 1 T1-weighted (T1w) images were found within the input BIDS
dataset.The T1-weighted (T1w) image was corrected for intensity
non-uniformity (INU) with \texttt{N4BiasFieldCorrection} \citep{n4},
distributed with ANTs 2.3.3 \citep[RRID:SCR\_004757]{ants}, and used as
T1w-reference throughout the workflow. The T1w-reference was then
skull-stripped with a \emph{Nipype} implementation of the
\texttt{antsBrainExtraction.sh} workflow (from ANTs), using OASIS30ANTs
as target template. Brain tissue segmentation of cerebrospinal fluid
(CSF), white-matter (WM) and gray-matter (GM) was performed on the
brain-extracted T1w using \texttt{fast} \citep[FSL 5.0.9,
RRID:SCR\_002823,][]{fsl_fast}. Brain surfaces were reconstructed using
\texttt{recon-all} \citep[FreeSurfer 6.0.1,
RRID:SCR\_001847,][]{fs_reconall}, and the brain mask estimated
previously was refined with a custom variation of the method to
reconcile ANTs-derived and FreeSurfer-derived segmentations of the
cortical gray-matter of Mindboggle
\citep[RRID:SCR\_002438,][]{mindboggle}. Volume-based spatial
normalization to one standard space (MNI152NLin2009cAsym) was performed
through nonlinear registration with \texttt{antsRegistration} (ANTs
2.3.3), using brain-extracted versions of both T1w reference and the T1w
template. The following template was selected for spatial normalization:
\emph{ICBM 152 Nonlinear Asymmetrical template version 2009c}
{[}\citet{mni152nlin2009casym}, RRID:SCR\_008796; TemplateFlow ID:
MNI152NLin2009cAsym{]},
\item[Functional data preprocessing]
For each of the 1 BOLD run found per subject (across all tasks and
sessions), the following preprocessing was performed. First, a reference
volume and its skull-stripped version were generated using a custom
methodology of \emph{fMRIPrep}. Susceptibility distortion correction
(SDC) was omitted. The BOLD reference was then co-registered to the T1w
reference using \texttt{bbregister} (FreeSurfer) which implements
boundary-based registration \citep{bbr}. Co-registration was configured
with six degrees of freedom. Head-motion parameters with respect to the
BOLD reference (transformation matrices, and six corresponding rotation
and translation parameters) are estimated before any spatiotemporal
filtering using \texttt{mcflirt} \citep[FSL 5.0.9,][]{mcflirt}. The BOLD
time-series (including slice-timing correction when applied) were
resampled onto their original, native space by applying the transforms
to correct for head-motion. These resampled BOLD time-series will be
referred to as \emph{preprocessed BOLD in original space}, or just
\emph{preprocessed BOLD}. The BOLD time-series were resampled into
standard space, generating a \emph{preprocessed BOLD run in
MNI152NLin2009cAsym space}. First, a reference volume and its
skull-stripped version were generated using a custom methodology of
\emph{fMRIPrep}. Several confounding time-series were calculated based
on the \emph{preprocessed BOLD}: framewise displacement (FD), DVARS and
three region-wise global signals. FD was computed using two formulations
following Power (absolute sum of relative motions,
\citet{power_fd_dvars}) and Jenkinson (relative root mean square
displacement between affines, \citet{mcflirt}). FD and DVARS are
calculated for each functional run, both using their implementations in
\emph{Nipype} \citep[following the definitions by][]{power_fd_dvars}.
The three global signals are extracted within the CSF, the WM, and the
whole-brain masks. Additionally, a set of physiological regressors were
extracted to allow for component-based noise correction
\citep[\emph{CompCor},][]{compcor}. Principal components are estimated
after high-pass filtering the \emph{preprocessed BOLD} time-series
(using a discrete cosine filter with 128s cut-off) for the two
\emph{CompCor} variants: temporal (tCompCor) and anatomical (aCompCor).
tCompCor components are then calculated from the top 2\% variable voxels
within the brain mask. For aCompCor, three probabilistic masks (CSF, WM
and combined CSF+WM) are generated in anatomical space. The
implementation differs from that of Behzadi et al.~in that instead of
eroding the masks by 2 pixels on BOLD space, the aCompCor masks are
subtracted a mask of pixels that likely contain a volume fraction of GM.
This mask is obtained by dilating a GM mask extracted from the
FreeSurfer's \emph{aseg} segmentation, and it ensures components are not
extracted from voxels containing a minimal fraction of GM. Finally,
these masks are resampled into BOLD space and binarized by thresholding
at 0.99 (as in the original implementation). Components are also
calculated separately within the WM and CSF masks. For each CompCor
decomposition, the \emph{k} components with the largest singular values
are retained, such that the retained components' time series are
sufficient to explain 50 percent of variance across the nuisance mask
(CSF, WM, combined, or temporal). The remaining components are dropped
from consideration. The head-motion estimates calculated in the
correction step were also placed within the corresponding confounds
file. The confound time series derived from head motion estimates and
global signals were expanded with the inclusion of temporal derivatives
and quadratic terms for each \citep{confounds_satterthwaite_2013}.
Frames that exceeded a threshold of 0.5 mm FD or 1.5 standardised DVARS
were annotated as motion outliers. All resamplings can be performed with
\emph{a single interpolation step} by composing all the pertinent
transformations (i.e.~head-motion transform matrices, susceptibility
distortion correction when available, and co-registrations to anatomical
and output spaces). Gridded (volumetric) resamplings were performed
using \texttt{antsApplyTransforms} (ANTs), configured with Lanczos
interpolation to minimize the smoothing effects of other kernels
\citep{lanczos}. Non-gridded (surface) resamplings were performed using
\texttt{mri\_vol2surf} (FreeSurfer).
\end{description}

Many internal operations of \emph{fMRIPrep} use \emph{Nilearn} 0.6.2
\citep[RRID:SCR\_001362]{nilearn}, mostly within the functional
processing workflow. For more details of the pipeline, see
\href{https://fmriprep.readthedocs.io/en/latest/workflows.html}{the
section corresponding to workflows in \emph{fMRIPrep}'s documentation}.

\hypertarget{copyright-waiver}{%
\subsubsection{Copyright Waiver}\label{copyright-waiver}}

The above boilerplate text was automatically generated by fMRIPrep with
the express intention that users should copy and paste this text into
their manuscripts \emph{unchanged}. It is released under the
\href{https://creativecommons.org/publicdomain/zero/1.0/}{CC0} license.

\hypertarget{references}{%
\subsubsection{References}\label{references}}

\bibliography{/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/data/boilerplate.bib}

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