Sherlock/fmriprep/logs/CITATION.tex

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\begin{document}

Results included in this manuscript come from preprocessing performed
using \emph{fMRIPrep} 20.0.6 (\citet{fmriprep1}; \citet{fmriprep2};
RRID:SCR\_016216), which is based on \emph{Nipype} 1.4.2
(\citet{nipype1}; \citet{nipype2}; RRID:SCR\_002502).

\begin{description}
\item[Anatomical data preprocessing]
The T1-weighted (T1w) image was corrected for intensity non-uniformity
(INU) with \texttt{N4BiasFieldCorrection} \citep{n4}, distributed with
ANTs 2.2.0 \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}.
Volume-based spatial normalization to one standard space
(MNI152NLin2009cAsym) was performed through nonlinear registration with
\texttt{antsRegistration} (ANTs 2.2.0), 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 3 BOLD runs 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{flirt} \citep[FSL 5.0.9,][]{flirt} with the
boundary-based registration \citep{bbr} cost-function. Co-registration
was configured with nine degrees of freedom to account for distortions
remaining in the BOLD reference. 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 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 5\% variable voxels within a mask covering the
subcortical regions. This subcortical mask is obtained by heavily
eroding the brain mask, which ensures it does not include cortical GM
regions. For aCompCor, components are calculated within the intersection
of the aforementioned mask and the union of CSF and WM masks calculated
in T1w space, after their projection to the native space of each
functional run (using the inverse BOLD-to-T1w transformation).
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}}

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