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- <li class="nav-item"><a class="nav-link" href="#Summary">Summary</a></li>
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- <div id="Summary" class="mt-5">
- <h1 class="sub-report-title pt-5 ps-4">Summary</h1>
- <div id="datatype-figures_desc-summary_subject-14_suffix-T1w" class="ps-4 pe-4 mb-2">
- <ul class="elem-desc">
- <li>Subject ID: 14</li>
- <li>Structural images: 1 T1-weighted (+ 1 T2-weighted)</li>
- <li>Functional series: 2</li>
- <ul class="elem-desc">
- <li>Task: mixed (1 run)</li>
- <li>Task: rest (1 run)</li>
- </ul>
- <li>Standard output spaces: MNI152NLin2009cAsym</li>
- <li>Non-standard output spaces: </li>
- <li>FreeSurfer reconstruction: Run by fMRIPrep</li>
- </ul>
- </div>
- </div>
- <div id="Anatomical" class="mt-5">
- <h1 class="sub-report-title pt-5 ps-4">Anatomical</h1>
- <div id="datatype-figures_desc-conform_extension-['.html']_subject-14_suffix-T1w" class="ps-4 pe-4 mb-2">
- <h3 class="elem-title">Anatomical Conformation</h3>
- <ul class="elem-desc">
- <li>Input T1w images: 1</li>
- <li>Output orientation: RAS</li>
- <li>Output dimensions: 224x272x288</li>
- <li>Output voxel size: 0.8mm x 0.8mm x 0.8mm</li>
- <li>Discarded images: 0</li>
- </ul>
- </div>
- <div id="datatype-figures_subject-14_suffix-dseg" class="ps-4 pe-4 mb-2">
- <h3 class="run-title mt-3">Brain mask and brain tissue segmentation of the T1w</h3><p class="elem-caption">This panel shows the final, preprocessed T1-weighted image, with contours delineating the detected brain mask and brain tissue segmentations.</p> <div class="reportlet">
- <img class="svg-reportlet" src="./sub-14/figures/sub-14_acq-denoised_dseg.svg" style="width: 100%" />
- </div>
- <small>Get figure file: <a href="./sub-14/figures/sub-14_acq-denoised_dseg.svg" target="_blank">sub-14/figures/sub-14_acq-denoised_dseg.svg</a></small>
- </div>
- <div id="datatype-figures_regex_search-True_space-.*_subject-14_suffix-T1w" class="ps-4 pe-4 mb-2">
- <h3 class="run-title mt-3">Spatial normalization of the anatomical T1w reference</h3><p class="elem-desc">Results of nonlinear alignment of the T1w reference one or more template space(s). Hover on the panels with the mouse pointer to transition between both spaces.</p><p class="elem-caption">Spatial normalization of the T1w image to the <code>MNI152NLin2009cAsym</code> template.</p> <div class="reportlet">
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- </div>
- <small>Get figure file: <a href="./sub-14/figures/sub-14_acq-denoised_space-MNI152NLin2009cAsym_T1w.svg" target="_blank">sub-14/figures/sub-14_acq-denoised_space-MNI152NLin2009cAsym_T1w.svg</a></small>
- </div>
- <div id="datatype-figures_desc-reconall_subject-14_suffix-T1w" class="ps-4 pe-4 mb-2">
- <h3 class="run-title mt-3">Surface reconstruction</h3><p class="elem-caption">Surfaces (white and pial) reconstructed with FreeSurfer (<code>recon-all</code>) overlaid on the participant's T1w template.</p> <div class="reportlet">
- <img class="svg-reportlet" src="./sub-14/figures/sub-14_acq-denoised_desc-reconall_T1w.svg" style="width: 100%" />
- </div>
- <small>Get figure file: <a href="./sub-14/figures/sub-14_acq-denoised_desc-reconall_T1w.svg" target="_blank">sub-14/figures/sub-14_acq-denoised_desc-reconall_T1w.svg</a></small>
- </div>
- </div>
- <div id="About" class="mt-5">
- <h1 class="sub-report-title pt-5 ps-4">About</h1>
- <div id="datatype-figures_desc-about_subject-14_suffix-T1w" class="ps-4 pe-4 mb-2">
- <ul>
- <li>fMRIPrep version: 24.1.0.dev28+gfe7c9ff8.d20240822</li>
- <li>fMRIPrep command: <code>/home/oesteban/.miniconda3/envs/fmriprep/bin/fmriprep /data/datasets/bootcamp/bidsdata /data/derivatives/bootcamp-geneva/fmriprep-24.0.0/ participant --nprocs 8 --omp-nthreads 12 -w work -vv --skip-bids-validation --anat-only --bids-filter-file bids-filters.json</code></li>
- <li>Date preprocessed: 2024-09-02 14:22:53 +0200</li>
- </ul>
- </div>
- </div>
- <div id="boilerplate" class="ps-4 pe-4 mb-2">
- <h2 class="sub-report-group mt-4">Methods</h2><p class="elem-caption"><p>We kindly ask to report results preprocessed with this tool using the following boilerplate.</p>
- <p class="alert alert-info" role="alert">
- <strong>Copyright Waiver</strong>.
- The boilerplate text was automatically generated by <em>NiReports</em> with the
- express intention that users should copy and paste this text into their manuscripts <em>unchanged</em>.
- It is released under the
- <a href="https://creativecommons.org/publicdomain/zero/1.0/" target="_blank">CC0 license</a>.
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- <div class="boiler-html p-3 m-4 bg-primary" style="--bs-bg-opacity: .04; font-family: 'Bitstream Charter', 'Georgia', Times;"><p>Results included in this manuscript come from preprocessing performed
- using <em>fMRIPrep</em> 24.1.0.dev28+gfe7c9ff8.d20240822 (<span
- class="citation" data-cites="fmriprep1">Esteban et al. (2019)</span>;
- <span class="citation" data-cites="fmriprep2">Esteban et al.
- (2018)</span>; RRID:SCR_016216), which is based on <em>Nipype</em> 1.8.6
- (<span class="citation" data-cites="nipype1">K. Gorgolewski et al.
- (2011)</span>; <span class="citation" data-cites="nipype2">K. J.
- Gorgolewski et al. (2018)</span>; RRID:SCR_002502).</p>
- <dl>
- <dt>Anatomical data preprocessing</dt>
- <dd>
- <p>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 <code>N4BiasFieldCorrection</code> <span class="citation"
- data-cites="n4">(Tustison et al. 2010)</span>, distributed with ANTs
- 2.5.1 <span class="citation" data-cites="ants">(Avants et al. 2008,
- RRID:SCR_004757)</span>, and used as T1w-reference throughout the
- workflow. The T1w-reference was then skull-stripped with a
- <em>Nipype</em> implementation of the
- <code>antsBrainExtraction.sh</code> 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 <code>fast</code> <span
- class="citation" data-cites="fsl_fast">(FSL 6.0.7.12, RRID:SCR_002823,
- Zhang, Brady, and Smith 2001)</span>. Brain surfaces were reconstructed
- using <code>recon-all</code> <span class="citation"
- data-cites="fs_reconall">(FreeSurfer 7.3.2, RRID:SCR_001847, Dale,
- Fischl, and Sereno 1999)</span>, 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 <span class="citation"
- data-cites="mindboggle">(RRID:SCR_002438, Klein et al. 2017)</span>. A
- T2-weighted image was used to improve pial surface refinement. Brain
- surfaces were reconstructed using <code>recon-all</code> <span
- class="citation" data-cites="fs_reconall">(FreeSurfer 7.3.2,
- RRID:SCR_001847, Dale, Fischl, and Sereno 1999)</span>, 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 <span class="citation"
- data-cites="mindboggle">(RRID:SCR_002438, Klein et al. 2017)</span>.
- Volume-based spatial normalization to one standard space
- (MNI152NLin2009cAsym) was performed through nonlinear registration with
- <code>antsRegistration</code> (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
- <em>TemplateFlow</em> <span class="citation"
- data-cites="templateflow">(24.2.0, Ciric et al. 2022)</span>: <em>ICBM
- 152 Nonlinear Asymmetrical template version 2009c</em> [<span
- class="citation" data-cites="mni152nlin2009casym">Fonov et al.
- (2009)</span>, RRID:SCR_008796; TemplateFlow ID:
- MNI152NLin2009cAsym].</p>
- </dd>
- </dl>
- <p>Many internal operations of <em>fMRIPrep</em> use <em>Nilearn</em>
- 0.10.4 <span class="citation" data-cites="nilearn">(Abraham et al. 2014,
- RRID:SCR_001362)</span>, mostly within the functional processing
- workflow. For more details of the pipeline, see <a
- href="https://fmriprep.readthedocs.io/en/latest/workflows.html"
- title="FMRIPrep's documentation">the section corresponding to
- workflows in <em>fMRIPrep</em>’s documentation</a>.</p>
- <h3 id="copyright-waiver">Copyright Waiver</h3>
- <p>The above boilerplate text was automatically generated by fMRIPrep
- with the express intention that users should copy and paste this text
- into their manuscripts <em>unchanged</em>. It is released under the <a
- href="https://creativecommons.org/publicdomain/zero/1.0/">CC0</a>
- license.</p>
- <h3 class="unnumbered" id="references">References</h3>
- <div id="refs" class="references csl-bib-body hanging-indent"
- data-entry-spacing="0" role="list">
- <div id="ref-nilearn" class="csl-entry" role="listitem">
- Abraham, Alexandre, Fabian Pedregosa, Michael Eickenberg, Philippe
- Gervais, Andreas Mueller, Jean Kossaifi, Alexandre Gramfort, Bertrand
- Thirion, and Gael Varoquaux. 2014. <span>“Machine Learning for
- Neuroimaging with Scikit-Learn.”</span> <em>Frontiers in
- Neuroinformatics</em> 8. <a
- href="https://doi.org/10.3389/fninf.2014.00014">https://doi.org/10.3389/fninf.2014.00014</a>.
- </div>
- <div id="ref-ants" class="csl-entry" role="listitem">
- Avants, B. B., C. L. Epstein, M. Grossman, and J. C. Gee. 2008.
- <span>“Symmetric Diffeomorphic Image Registration with
- Cross-Correlation: Evaluating Automated Labeling of Elderly and
- Neurodegenerative Brain.”</span> <em>Medical Image Analysis</em> 12 (1):
- 26–41. <a
- href="https://doi.org/10.1016/j.media.2007.06.004">https://doi.org/10.1016/j.media.2007.06.004</a>.
- </div>
- <div id="ref-templateflow" class="csl-entry" role="listitem">
- Ciric, R., William H. Thompson, R. Lorenz, M. Goncalves, E. MacNicol, C.
- J. Markiewicz, Y. O. Halchenko, et al. 2022.
- <span>“<span>TemplateFlow</span>: <span>FAIR</span>-Sharing of
- Multi-Scale, Multi-Species Brain Models.”</span> <em>Nature Methods</em>
- 19: 1568–71. <a
- href="https://doi.org/10.1038/s41592-022-01681-2">https://doi.org/10.1038/s41592-022-01681-2</a>.
- </div>
- <div id="ref-fs_reconall" class="csl-entry" role="listitem">
- Dale, Anders M., Bruce Fischl, and Martin I. Sereno. 1999.
- <span>“Cortical Surface-Based Analysis: I. Segmentation and Surface
- Reconstruction.”</span> <em>NeuroImage</em> 9 (2): 179–94. <a
- href="https://doi.org/10.1006/nimg.1998.0395">https://doi.org/10.1006/nimg.1998.0395</a>.
- </div>
- <div id="ref-fmriprep2" class="csl-entry" role="listitem">
- Esteban, Oscar, Ross Blair, Christopher J. Markiewicz, Shoshana L.
- Berleant, Craig Moodie, Feilong Ma, Ayse Ilkay Isik, et al. 2018.
- <span>“fMRIPrep 24.1.0.dev28+gfe7c9ff8.d20240822.”</span>
- <em>Software</em>. <a
- href="https://doi.org/10.5281/zenodo.852659">https://doi.org/10.5281/zenodo.852659</a>.
- </div>
- <div id="ref-fmriprep1" class="csl-entry" role="listitem">
- Esteban, Oscar, Christopher Markiewicz, Ross W Blair, Craig Moodie, Ayse
- Ilkay Isik, Asier Erramuzpe Aliaga, James Kent, et al. 2019.
- <span>“<span class="nocase">fMRIPrep</span>: A Robust Preprocessing
- Pipeline for Functional <span>MRI</span>.”</span> <em>Nature
- Methods</em> 16: 111–16. <a
- href="https://doi.org/10.1038/s41592-018-0235-4">https://doi.org/10.1038/s41592-018-0235-4</a>.
- </div>
- <div id="ref-mni152nlin2009casym" class="csl-entry" role="listitem">
- Fonov, VS, AC Evans, RC McKinstry, CR Almli, and DL Collins. 2009.
- <span>“Unbiased Nonlinear Average Age-Appropriate Brain Templates from
- Birth to Adulthood.”</span> <em>NeuroImage</em> 47, Supplement 1: S102.
- <a
- href="https://doi.org/10.1016/S1053-8119(09)70884-5">https://doi.org/10.1016/S1053-8119(09)70884-5</a>.
- </div>
- <div id="ref-nipype1" class="csl-entry" role="listitem">
- Gorgolewski, K., C. D. Burns, C. Madison, D. Clark, Y. O. Halchenko, M.
- L. Waskom, and S. Ghosh. 2011. <span>“Nipype: A Flexible, Lightweight
- and Extensible Neuroimaging Data Processing Framework in Python.”</span>
- <em>Frontiers in Neuroinformatics</em> 5: 13. <a
- href="https://doi.org/10.3389/fninf.2011.00013">https://doi.org/10.3389/fninf.2011.00013</a>.
- </div>
- <div id="ref-nipype2" class="csl-entry" role="listitem">
- Gorgolewski, Krzysztof J., Oscar Esteban, Christopher J. Markiewicz,
- Erik Ziegler, David Gage Ellis, Michael Philipp Notter, Dorota Jarecka,
- et al. 2018. <span>“Nipype.”</span> <em>Software</em>. <a
- href="https://doi.org/10.5281/zenodo.596855">https://doi.org/10.5281/zenodo.596855</a>.
- </div>
- <div id="ref-mindboggle" class="csl-entry" role="listitem">
- Klein, Arno, Satrajit S. Ghosh, Forrest S. Bao, Joachim Giard, Yrjö
- Häme, Eliezer Stavsky, Noah Lee, et al. 2017. <span>“Mindboggling
- Morphometry of Human Brains.”</span> <em>PLOS Computational Biology</em>
- 13 (2): e1005350. <a
- href="https://doi.org/10.1371/journal.pcbi.1005350">https://doi.org/10.1371/journal.pcbi.1005350</a>.
- </div>
- <div id="ref-n4" class="csl-entry" role="listitem">
- Tustison, N. J., B. B. Avants, P. A. Cook, Y. Zheng, A. Egan, P. A.
- Yushkevich, and J. C. Gee. 2010. <span>“N4ITK: Improved N3 Bias
- Correction.”</span> <em>IEEE Transactions on Medical Imaging</em> 29
- (6): 1310–20. <a
- href="https://doi.org/10.1109/TMI.2010.2046908">https://doi.org/10.1109/TMI.2010.2046908</a>.
- </div>
- <div id="ref-fsl_fast" class="csl-entry" role="listitem">
- Zhang, Y., M. Brady, and S. Smith. 2001. <span>“Segmentation of Brain
- <span>MR</span> Images Through a Hidden Markov Random Field Model and
- the Expectation-Maximization Algorithm.”</span> <em>IEEE Transactions on
- Medical Imaging</em> 20 (1): 45–57. <a
- href="https://doi.org/10.1109/42.906424">https://doi.org/10.1109/42.906424</a>.
- </div>
- </div></div>
- </div>
- <div class="tab-pane fade " id="md-tab-pane" role="tabpanel" aria-labelledby="md-tab" tabindex="0">
- <div class="boiler-md p-3 m-4 bg-primary" style="--bs-bg-opacity: .04;"><pre>
- Results included in this manuscript come from preprocessing
- performed using *fMRIPrep* 24.1.0.dev28+gfe7c9ff8.d20240822
- (@fmriprep1; @fmriprep2; RRID:SCR_016216),
- which is based on *Nipype* 1.8.6
- (@nipype1; @nipype2; RRID:SCR_002502).
- 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 `N4BiasFieldCorrection` [@n4], distributed with ANTs 2.5.1
- [@ants, RRID:SCR_004757], and used as T1w-reference throughout the workflow.
- The T1w-reference was then skull-stripped with a *Nipype* implementation of
- the `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 `fast` [FSL 6.0.7.12, RRID:SCR_002823, @fsl_fast].
- Brain surfaces were reconstructed using `recon-all` [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 [RRID:SCR_002438, @mindboggle].
- A T2-weighted image was used to improve pial surface refinement.
- Brain surfaces were reconstructed using `recon-all` [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 [RRID:SCR_002438, @mindboggle].
- Volume-based spatial normalization to one standard space (MNI152NLin2009cAsym) was performed through
- nonlinear registration with `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 *TemplateFlow* [24.2.0, @templateflow]:
- *ICBM 152 Nonlinear Asymmetrical template version 2009c* [@mni152nlin2009casym, RRID:SCR_008796; TemplateFlow ID: MNI152NLin2009cAsym].
- Many internal operations of *fMRIPrep* use
- *Nilearn* 0.10.4 [@nilearn, RRID:SCR_001362],
- mostly within the functional processing workflow.
- For more details of the pipeline, see [the section corresponding
- to workflows in *fMRIPrep*'s documentation](https://fmriprep.readthedocs.io/en/latest/workflows.html "FMRIPrep's documentation").
- ### 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 *unchanged*.
- It is released under the [CC0](https://creativecommons.org/publicdomain/zero/1.0/) license.
- ### References
- </pre></div>
- </div>
- <div class="tab-pane fade " id="tex-tab-pane" role="tabpanel" aria-labelledby="tex-tab" tabindex="0">
- <div class="boiler-tex p-3 m-4 bg-primary" style="--bs-bg-opacity: .04;"><pre>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}</pre>
- <h3>Bibliography</h3>
- <pre>@article{fmriprep1,
- author = {Esteban, Oscar and Markiewicz, Christopher and Blair, Ross W and Moodie, Craig and Isik, Ayse Ilkay and Erramuzpe Aliaga, Asier and Kent, James and Goncalves, Mathias and DuPre, Elizabeth and Snyder, Madeleine and Oya, Hiroyuki and Ghosh, Satrajit and Wright, Jessey and Durnez, Joke and Poldrack, Russell and Gorgolewski, Krzysztof Jacek},
- title = {{fMRIPrep}: a robust preprocessing pipeline for functional {MRI}},
- volume = {16},
- pages = {111--116},
- year = {2019},
- doi = {10.1038/s41592-018-0235-4},
- journal = {Nature Methods}
- }
- @article{fmriprep2,
- author = {Esteban, Oscar and Blair, Ross and Markiewicz, Christopher J. and Berleant, Shoshana L. and Moodie, Craig and Ma, Feilong and Isik, Ayse Ilkay and Erramuzpe, Asier and Kent, James D. andGoncalves, Mathias and DuPre, Elizabeth and Sitek, Kevin R. and Gomez, Daniel E. P. and Lurie, Daniel J. and Ye, Zhifang and Poldrack, Russell A. and Gorgolewski, Krzysztof J.},
- title = {fMRIPrep <version>},
- year = 2018,
- doi = {10.5281/zenodo.852659},
- publisher = {Zenodo},
- journal = {Software}
- }
- @article{templateflow,
- author = {Ciric, R. and Thompson, William H. and Lorenz, R. and Goncalves, M. and MacNicol, E. and Markiewicz, C. J. and Halchenko, Y. O. and Ghosh, S. S. and Gorgolewski, K. J. and Poldrack, R. A. and Esteban, O.},
- title = {{TemplateFlow}: {FAIR}-sharing of multi-scale, multi-species brain models},
- volume = {19},
- pages = {1568--1571},
- year = {2022},
- doi = {10.1038/s41592-022-01681-2},
- journal = {Nature Methods}
- }
- @article{nipype1,
- author = {Gorgolewski, K. and Burns, C. D. and Madison, C. and Clark, D. and Halchenko, Y. O. and Waskom, M. L. and Ghosh, S.},
- doi = {10.3389/fninf.2011.00013},
- journal = {Frontiers in Neuroinformatics},
- pages = 13,
- shorttitle = {Nipype},
- title = {Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in Python},
- volume = 5,
- year = 2011
- }
- @article{nipype2,
- author = {Gorgolewski, Krzysztof J. and Esteban, Oscar and Markiewicz, Christopher J. and Ziegler, Erik and Ellis, David Gage and Notter, Michael Philipp and Jarecka, Dorota and Johnson, Hans and Burns, Christopher and Manhães-Savio, Alexandre and Hamalainen, Carlo and Yvernault, Benjamin and Salo, Taylor and Jordan, Kesshi and Goncalves, Mathias and Waskom, Michael and Clark, Daniel and Wong, Jason and Loney, Fred and Modat, Marc and Dewey, Blake E and Madison, Cindee and Visconti di Oleggio Castello, Matteo and Clark, Michael G. and Dayan, Michael and Clark, Dav and Keshavan, Anisha and Pinsard, Basile and Gramfort, Alexandre and Berleant, Shoshana and Nielson, Dylan M. and Bougacha, Salma and Varoquaux, Gael and Cipollini, Ben and Markello, Ross and Rokem, Ariel and Moloney, Brendan and Halchenko, Yaroslav O. and Wassermann , Demian and Hanke, Michael and Horea, Christian and Kaczmarzyk, Jakub and Gilles de Hollander and DuPre, Elizabeth and Gillman, Ashley and Mordom, David and Buchanan, Colin and Tungaraza, Rosalia and Pauli, Wolfgang M. and Iqbal, Shariq and Sikka, Sharad and Mancini, Matteo and Schwartz, Yannick and Malone, Ian B. and Dubois, Mathieu and Frohlich, Caroline and Welch, David and Forbes, Jessica and Kent, James and Watanabe, Aimi and Cumba, Chad and Huntenburg, Julia M. and Kastman, Erik and Nichols, B. Nolan and Eshaghi, Arman and Ginsburg, Daniel and Schaefer, Alexander and Acland, Benjamin and Giavasis, Steven and Kleesiek, Jens and Erickson, Drew and Küttner, René and Haselgrove, Christian and Correa, Carlos and Ghayoor, Ali and Liem, Franz and Millman, Jarrod and Haehn, Daniel and Lai, Jeff and Zhou, Dale and Blair, Ross and Glatard, Tristan and Renfro, Mandy and Liu, Siqi and Kahn, Ari E. and Pérez-García, Fernando and Triplett, William and Lampe, Leonie and Stadler, Jörg and Kong, Xiang-Zhen and Hallquist, Michael and Chetverikov, Andrey and Salvatore, John and Park, Anne and Poldrack, Russell and Craddock, R. Cameron and Inati, Souheil and Hinds, Oliver and Cooper, Gavin and Perkins, L. Nathan and Marina, Ana and Mattfeld, Aaron and Noel, Maxime and Lukas Snoek and Matsubara, K and Cheung, Brian and Rothmei, Simon and Urchs, Sebastian and Durnez, Joke and Mertz, Fred and Geisler, Daniel and Floren, Andrew and Gerhard, Stephan and Sharp, Paul and Molina-Romero, Miguel and Weinstein, Alejandro and Broderick, William and Saase, Victor and Andberg, Sami Kristian and Harms, Robbert and Schlamp, Kai and Arias, Jaime and Papadopoulos Orfanos, Dimitri and Tarbert, Claire and Tambini, Arielle and De La Vega, Alejandro and Nickson, Thomas and Brett, Matthew and Falkiewicz, Marcel and Podranski, Kornelius and Linkersdörfer, Janosch and Flandin, Guillaume and Ort, Eduard and Shachnev, Dmitry and McNamee, Daniel and Davison, Andrew and Varada, Jan and Schwabacher, Isaac and Pellman, John and Perez-Guevara, Martin and Khanuja, Ranjeet and Pannetier, Nicolas and McDermottroe, Conor and Ghosh, Satrajit},
- title = {Nipype},
- year = 2018,
- doi = {10.5281/zenodo.596855},
- publisher = {Zenodo},
- journal = {Software}
- }
- @article{n4,
- author = {Tustison, N. J. and Avants, B. B. and Cook, P. A. and Zheng, Y. and Egan, A. and Yushkevich, P. A. and Gee, J. C.},
- doi = {10.1109/TMI.2010.2046908},
- issn = {0278-0062},
- journal = {IEEE Transactions on Medical Imaging},
- number = 6,
- pages = {1310-1320},
- shorttitle = {N4ITK},
- title = {N4ITK: Improved N3 Bias Correction},
- volume = 29,
- year = 2010
- }
- @article{fs_reconall,
- author = {Dale, Anders M. and Fischl, Bruce and Sereno, Martin I.},
- doi = {10.1006/nimg.1998.0395},
- issn = {1053-8119},
- journal = {NeuroImage},
- number = 2,
- pages = {179-194},
- shorttitle = {Cortical Surface-Based Analysis},
- title = {Cortical Surface-Based Analysis: I. Segmentation and Surface Reconstruction},
- url = {https://www.sciencedirect.com/science/article/pii/S1053811998903950},
- volume = 9,
- year = 1999
- }
- @article{mindboggle,
- author = {Klein, Arno and Ghosh, Satrajit S. and Bao, Forrest S. and Giard, Joachim and Häme, Yrjö and Stavsky, Eliezer and Lee, Noah and Rossa, Brian and Reuter, Martin and Neto, Elias Chaibub and Keshavan, Anisha},
- doi = {10.1371/journal.pcbi.1005350},
- issn = {1553-7358},
- journal = {PLOS Computational Biology},
- number = 2,
- pages = {e1005350},
- title = {Mindboggling morphometry of human brains},
- url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005350},
- volume = 13,
- year = 2017
- }
- @article{mni152lin,
- title = {A {Probabilistic} {Atlas} of the {Human} {Brain}: {Theory} and {Rationale} for {Its} {Development}: {The} {International} {Consortium} for {Brain} {Mapping} ({ICBM})},
- author = {Mazziotta, John C. and Toga, Arthur W. and Evans, Alan and Fox, Peter and Lancaster, Jack},
- volume = {2},
- issn = {1053-8119},
- shorttitle = {A {Probabilistic} {Atlas} of the {Human} {Brain}},
- doi = {10.1006/nimg.1995.1012},
- number = {2, Part A},
- journal = {NeuroImage},
- year = {1995},
- pages = {89--101}
- }
- @article{mni152nlin2009casym,
- title = {Unbiased nonlinear average age-appropriate brain templates from birth to adulthood},
- author = {Fonov, VS and Evans, AC and McKinstry, RC and Almli, CR and Collins, DL},
- doi = {10.1016/S1053-8119(09)70884-5},
- journal = {NeuroImage},
- pages = {S102},
- volume = {47, Supplement 1},
- year = 2009
- }
- @article{mni152nlin6asym,
- author = {Evans, AC and Janke, AL and Collins, DL and Baillet, S},
- title = {Brain templates and atlases},
- doi = {10.1016/j.neuroimage.2012.01.024},
- journal = {NeuroImage},
- volume = {62},
- number = {2},
- pages = {911--922},
- year = 2012
- }
- @article{ants,
- author = {Avants, B.B. and Epstein, C.L. and Grossman, M. and Gee, J.C.},
- doi = {10.1016/j.media.2007.06.004},
- issn = {1361-8415},
- journal = {Medical Image Analysis},
- number = 1,
- pages = {26-41},
- shorttitle = {Symmetric diffeomorphic image registration with cross-correlation},
- title = {Symmetric diffeomorphic image registration with cross-correlation: Evaluating automated labeling of elderly and neurodegenerative brain},
- url = {https://www.sciencedirect.com/science/article/pii/S1361841507000606},
- volume = 12,
- year = 2008
- }
- @article{fsl_fast,
- author = {Zhang, Y. and Brady, M. and Smith, S.},
- doi = {10.1109/42.906424},
- issn = {0278-0062},
- journal = {IEEE Transactions on Medical Imaging},
- number = 1,
- pages = {45-57},
- title = {Segmentation of brain {MR} images through a hidden Markov random field model and the expectation-maximization algorithm},
- volume = 20,
- year = 2001
- }
- @article{fieldmapless1,
- author = {Wang, Sijia and Peterson, Daniel J. and Gatenby, J. C. and Li, Wenbin and Grabowski, Thomas J. and Madhyastha, Tara M.},
- doi = {10.3389/fninf.2017.00017},
- issn = {1662-5196},
- journal = {Frontiers in Neuroinformatics},
- language = {English},
- title = {Evaluation of Field Map and Nonlinear Registration Methods for Correction of Susceptibility Artifacts in Diffusion {MRI}},
- url = {https://www.frontiersin.org/articles/10.3389/fninf.2017.00017/full},
- volume = 11,
- year = 2017
- }
- @phdthesis{fieldmapless2,
- address = {Berlin},
- author = {Huntenburg, Julia M.},
- language = {eng},
- school = {Freie Universität},
- title = {Evaluating nonlinear coregistration of {BOLD} {EPI} and T1w images},
- type = {Master's Thesis},
- url = {https://hdl.handle.net/11858/00-001M-0000-002B-1CB5-A},
- year = 2014
- }
- @article{fieldmapless3,
- author = {Treiber, Jeffrey Mark and White, Nathan S. and Steed, Tyler Christian and Bartsch, Hauke and Holland, Dominic and Farid, Nikdokht and McDonald, Carrie R. and Carter, Bob S. and Dale, Anders Martin and Chen, Clark C.},
- doi = {10.1371/journal.pone.0152472},
- issn = {1932-6203},
- journal = {PLOS ONE},
- number = 3,
- pages = {e0152472},
- title = {Characterization and Correction of Geometric Distortions in 814 Diffusion Weighted Images},
- url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0152472},
- volume = 11,
- year = 2016
- }
- @article{flirt,
- title = {A global optimisation method for robust affine registration of brain images},
- volume = {5},
- issn = {1361-8415},
- url = {https://www.sciencedirect.com/science/article/pii/S1361841501000366},
- doi = {10.1016/S1361-8415(01)00036-6},
- number = {2},
- urldate = {2018-07-27},
- journal = {Medical Image Analysis},
- author = {Jenkinson, Mark and Smith, Stephen},
- year = {2001},
- keywords = {Affine transformation, flirt, fsl, Global optimisation, Multi-resolution search, Multimodal registration, Robustness},
- pages = {143--156}
- }
- @article{mcflirt,
- author = {Jenkinson, Mark and Bannister, Peter and Brady, Michael and Smith, Stephen},
- doi = {10.1006/nimg.2002.1132},
- issn = {1053-8119},
- journal = {NeuroImage},
- number = 2,
- pages = {825-841},
- title = {Improved Optimization for the Robust and Accurate Linear Registration and Motion Correction of Brain Images},
- url = {https://www.sciencedirect.com/science/article/pii/S1053811902911328},
- volume = 17,
- year = 2002
- }
- @article{bbr,
- author = {Greve, Douglas N and Fischl, Bruce},
- doi = {10.1016/j.neuroimage.2009.06.060},
- issn = {1095-9572},
- journal = {NeuroImage},
- number = 1,
- pages = {63-72},
- title = {Accurate and robust brain image alignment using boundary-based registration},
- volume = 48,
- year = 2009
- }
- @article{power_fd_dvars,
- author = {Power, Jonathan D. and Mitra, Anish and Laumann, Timothy O. and Snyder, Abraham Z. and Schlaggar, Bradley L. and Petersen, Steven E.},
- doi = {10.1016/j.neuroimage.2013.08.048},
- issn = {1053-8119},
- journal = {NeuroImage},
- number = {Supplement C},
- pages = {320-341},
- title = {Methods to detect, characterize, and remove motion artifact in resting state fMRI},
- url = {https://www.sciencedirect.com/science/article/pii/S1053811913009117},
- volume = 84,
- year = 2014
- }
- @article{confounds_satterthwaite_2013,
- author = {Satterthwaite, Theodore D. and Elliott, Mark A. and Gerraty, Raphael T. and Ruparel, Kosha and Loughead, James and Calkins, Monica E. and Eickhoff, Simon B. and Hakonarson, Hakon and Gur, Ruben C. and Gur, Raquel E. and Wolf, Daniel H.},
- doi = {10.1016/j.neuroimage.2012.08.052},
- issn = {10538119},
- journal = {NeuroImage},
- number = 1,
- pages = {240--256},
- title = {{An improved framework for confound regression and filtering for control of motion artifact in the preprocessing of resting-state functional connectivity data}},
- url = {https://www.sciencedirect.com/science/article/pii/S1053811912008609},
- volume = 64,
- year = 2013
- }
- @article{nilearn,
- author = {Abraham, Alexandre and Pedregosa, Fabian and Eickenberg, Michael and Gervais, Philippe and Mueller, Andreas and Kossaifi, Jean and Gramfort, Alexandre and Thirion, Bertrand and Varoquaux, Gael},
- doi = {10.3389/fninf.2014.00014},
- issn = {1662-5196},
- journal = {Frontiers in Neuroinformatics},
- language = {English},
- title = {Machine learning for neuroimaging with scikit-learn},
- url = {https://www.frontiersin.org/articles/10.3389/fninf.2014.00014/full},
- volume = 8,
- year = 2014
- }
- @article{lanczos,
- author = {Lanczos, C.},
- doi = {10.1137/0701007},
- issn = {0887-459X},
- journal = {Journal of the Society for Industrial and Applied Mathematics Series B Numerical Analysis},
- number = 1,
- pages = {76-85},
- title = {Evaluation of Noisy Data},
- url = {https://epubs.siam.org/doi/10.1137/0701007},
- volume = 1,
- year = 1964
- }
- @article{compcor,
- author = {Behzadi, Yashar and Restom, Khaled and Liau, Joy and Liu, Thomas T.},
- doi = {10.1016/j.neuroimage.2007.04.042},
- issn = {1053-8119},
- journal = {NeuroImage},
- number = 1,
- pages = {90-101},
- title = {A component based noise correction method ({CompCor}) for {BOLD} and perfusion based fMRI},
- url = {https://www.sciencedirect.com/science/article/pii/S1053811907003837},
- volume = 37,
- year = 2007
- }
- @article{hcppipelines,
- author = {Glasser, Matthew F. and Sotiropoulos, Stamatios N. and Wilson, J. Anthony and Coalson, Timothy S. and Fischl, Bruce and Andersson, Jesper L. and Xu, Junqian and Jbabdi, Saad and Webster, Matthew and Polimeni, Jonathan R. and Van Essen, David C. and Jenkinson, Mark},
- doi = {10.1016/j.neuroimage.2013.04.127},
- issn = {1053-8119},
- journal = {NeuroImage},
- pages = {105-124},
- series = {Mapping the Connectome},
- title = {The minimal preprocessing pipelines for the Human Connectome Project},
- url = {https://www.sciencedirect.com/science/article/pii/S1053811913005053},
- volume = 80,
- year = 2013
- }
- @article{fs_template,
- author = {Reuter, Martin and Rosas, Herminia Diana and Fischl, Bruce},
- doi = {10.1016/j.neuroimage.2010.07.020},
- journal = {NeuroImage},
- number = 4,
- pages = {1181-1196},
- title = {Highly accurate inverse consistent registration: A robust approach},
- volume = 53,
- year = 2010
- }
- @article{afni,
- author = {Cox, Robert W. and Hyde, James S.},
- doi = {10.1002/(SICI)1099-1492(199706/08)10:4/5<171::AID-NBM453>3.0.CO;2-L},
- journal = {NMR in Biomedicine},
- number = {4-5},
- pages = {171-178},
- title = {Software tools for analysis and visualization of fMRI data},
- volume = 10,
- year = 1997
- }
- @article{posse_t2s,
- author = {Posse, Stefan and Wiese, Stefan and Gembris, Daniel and Mathiak, Klaus and Kessler, Christoph and Grosse-Ruyken, Maria-Liisa and Elghahwagi, Barbara and Richards, Todd and Dager, Stephen R. and Kiselev, Valerij G.},
- doi = {10.1002/(SICI)1522-2594(199907)42:1<87::AID-MRM13>3.0.CO;2-O},
- journal = {Magnetic Resonance in Medicine},
- number = 1,
- pages = {87-97},
- title = {Enhancement of {BOLD}-contrast sensitivity by single-shot multi-echo functional {MR} imaging},
- volume = 42,
- year = 1999
- }
- @article{topup,
- author = {Jesper L.R. Andersson and Stefan Skare and John Ashburner},
- title = {How to correct susceptibility distortions in spin-echo echo-planar images: application to diffusion tensor imaging},
- journal = {NeuroImage},
- volume = 20,
- number = 2,
- pages = {870-888},
- year = 2003,
- issn = {1053-8119},
- doi = {10.1016/S1053-8119(03)00336-7},
- url = {https://www.sciencedirect.com/science/article/pii/S1053811903003367}
- }
- @article{patriat_improved_2017,
- title = {An improved model of motion-related signal changes in {fMRI}},
- volume = {144, Part A},
- issn = {1053-8119},
- url = {https://www.sciencedirect.com/science/article/pii/S1053811916304360},
- doi = {10.1016/j.neuroimage.2016.08.051},
- abstract = {Head motion is a significant source of noise in the estimation of functional connectivity from resting-state functional MRI (rs-fMRI). Current strategies to reduce this noise include image realignment, censoring time points corrupted by motion, and including motion realignment parameters and their derivatives as additional nuisance regressors in the general linear model. However, this nuisance regression approach assumes that the motion-induced signal changes are linearly related to the estimated realignment parameters, which is not always the case. In this study we develop an improved model of motion-related signal changes, where nuisance regressors are formed by first rotating and translating a single brain volume according to the estimated motion, re-registering the data, and then performing a principal components analysis (PCA) on the resultant time series of both moved and re-registered data. We show that these “Motion Simulated (MotSim)” regressors account for significantly greater fraction of variance, result in higher temporal signal-to-noise, and lead to functional connectivity estimates that are less affected by motion compared to the most common current approach of using the realignment parameters and their derivatives as nuisance regressors. This improvement should lead to more accurate estimates of functional connectivity, particularly in populations where motion is prevalent, such as patients and young children.},
- urldate = {2017-01-18},
- journal = {NeuroImage},
- author = {Patriat, Rémi and Reynolds, Richard C. and Birn, Rasmus M.},
- month = jan,
- year = {2017},
- keywords = {Motion, Correction, Methods, Rs-fMRI},
- pages = {74--82},
- }
- </pre>
- </div>
- </div>
- </div>
- <div id="errors" class="ps-4 pe-4 mb-2">
- <h2 class="sub-report-group mt-4">Errors</h2> <p class="alert alert-success" role="alert">No errors to report!</p>
- </div>
- </div>
- <script type="text/javascript">
- function toggle(id) {
- var element = document.getElementById(id);
- if(element.style.display == 'block')
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- else
- element.style.display = 'block';
- }
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