OSRfmriprep/logs/CITATION.tex

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\begin{document}

Results included in this manuscript come from preprocessing performed
using \emph{fMRIPrep} 20.1.0 (\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]
A total of 2 T1-weighted (T1w) images were found within the input BIDS
dataset. All of them were corrected for intensity non-uniformity (INU)
with \texttt{N4BiasFieldCorrection} \citep{n4}, distributed with ANTs
2.2.0 \citep[RRID:SCR\_004757]{ants}. 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}. A T1w-reference map was computed after
registration of 2 T1w images (after INU-correction) using
\texttt{mri\_robust\_template} \citep[FreeSurfer 6.0.1,][]{fs_template}.
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
2.2.0), 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{]},
\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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\end{document}