123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166 |
- \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} 20.0.6 (\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}}
- \bibliography{/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/data/boilerplate.bib}
- \end{document}
|