123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114 |
- \PassOptionsToPackage{unicode=true}{hyperref} % options for packages loaded elsewhere
- \PassOptionsToPackage{hyphens}{url}
- %
- \documentclass[]{article}
- \usepackage{lmodern}
- \usepackage{amssymb,amsmath}
- \usepackage{ifxetex,ifluatex}
- \usepackage{fixltx2e} % provides \textsubscript
- \ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
- \usepackage[T1]{fontenc}
- \usepackage[utf8]{inputenc}
- \usepackage{textcomp} % provides euro and other symbols
- \else % if luatex or xelatex
- \usepackage{unicode-math}
- \defaultfontfeatures{Ligatures=TeX,Scale=MatchLowercase}
- \fi
- % use upquote if available, for straight quotes in verbatim environments
- \IfFileExists{upquote.sty}{\usepackage{upquote}}{}
- % use microtype if available
- \IfFileExists{microtype.sty}{%
- \usepackage[]{microtype}
- \UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
- }{}
- \IfFileExists{parskip.sty}{%
- \usepackage{parskip}
- }{% else
- \setlength{\parindent}{0pt}
- \setlength{\parskip}{6pt plus 2pt minus 1pt}
- }
- \usepackage{hyperref}
- \hypersetup{
- pdfborder={0 0 0},
- breaklinks=true}
- \urlstyle{same} % don't use monospace font for urls
- \setlength{\emergencystretch}{3em} % prevent overfull lines
- \providecommand{\tightlist}{%
- \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
- \setcounter{secnumdepth}{0}
- % Redefines (sub)paragraphs to behave more like sections
- \ifx\paragraph\undefined\else
- \let\oldparagraph\paragraph
- \renewcommand{\paragraph}[1]{\oldparagraph{#1}\mbox{}}
- \fi
- \ifx\subparagraph\undefined\else
- \let\oldsubparagraph\subparagraph
- \renewcommand{\subparagraph}[1]{\oldsubparagraph{#1}\mbox{}}
- \fi
- % set default figure placement to htbp
- \makeatletter
- \def\fps@figure{htbp}
- \makeatother
- \usepackage[]{natbib}
- \bibliographystyle{plainnat}
- \date{}
- \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}}
- \bibliography{/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/data/boilerplate.bib}
- \end{document}
|