Results included in this manuscript come from preprocessing performed
using \emph{fMRIPrep} 24.1.0.dev28+gfe7c9ff8.d20240822
(\citet{fmriprep1}; \citet{fmriprep2}; RRID:SCR\_016216), which is based
on \emph{Nipype} 1.8.6 (\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 T1w image was corrected for intensity non-uniformity (INU)
with \texttt{N4BiasFieldCorrection} \citep{n4}, distributed with ANTs
2.5.1 \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 6.0.7.12, RRID:SCR\_002823,][]{fsl_fast}. Brain
surfaces were reconstructed using \texttt{recon-all} \citep[FreeSurfer
7.3.2, 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}. A T2-weighted image was used to
improve pial surface refinement. Brain surfaces were reconstructed using
\texttt{recon-all} \citep[FreeSurfer 7.3.2,
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
2.5.1), using brain-extracted versions of both T1w reference and the T1w
template. The following template was were selected for spatial
normalization and accessed with \emph{TemplateFlow}
\citep[24.2.0,][]{templateflow}: \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} 0.10.4
\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}.
\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.
\subsubsection{References}\label{references}
\bibliography{/data/derivatives/bootcamp-geneva/fmriprep-24.0.0/logs/CITATION.bib}
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keywords = {Motion, Correction, Methods, Rs-fMRI},
pages = {74--82},
}
