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@@ -1,27 +1,3 @@
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----
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-title: "Faster than thought: Detecting sub-second activation sequences with sequential fMRI pattern analysis"
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-subtitle: "Short project title: highspeed"
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-author:
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- - Lennart Wittkuhn^[Max Planck Institute for Human Development, wittkuhn@mpib-berlin.mpg.de]
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- - Nicolas W. Schuck^[Max Planck Institute for Human Development, schuck@mpib-berlin.mpg.de]
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-date: "Last update: `r format(Sys.time(), '%d %B, %Y')`"
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-output:
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- html_document:
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- toc: true
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- self_contained: true
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- toc_float: true
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- toc_depth: 3
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- number_sections: true
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- highlight: pygments
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- theme: cosmo
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- df_print: paged
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- fig_caption: true
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-fig.align: "center"
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-header-includes:
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- - \usepackage{fontspec}
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- - \setmainfont{AgfaRotisSansSerif}
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-email: wittkuhn@mpib-berlin.mpg.de
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----
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```{r, echo=FALSE, message=FALSE, include=FALSE}
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if (!requireNamespace("pacman")) install.packages("pacman")
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@@ -34,19 +10,15 @@ if (basename(here::here()) == "highspeed"){
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}
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```
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-# MRI quality control
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+## MRI quality control
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-## Step 1: MRI quality control using [MRIQC](https://mriqc.readthedocs.io/en/stable/)
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-
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-### Overview
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+#### Overview
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> MRIQC extracts no-reference IQMs (image quality metrics) from structural (T1w and T2w) and functional MRI (magnetic resonance imaging) data.
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Please see the [official MRIQC documentation](https://mriqc.readthedocs.io/en/stable/) for details and refer to the paper listed in the References section.
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-### Code and software
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-
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-#### `mriqc` container, version 0.15.2rc1
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+#### Container: `mriqc` container, version 0.15.2rc1
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MRIQC quality control was performed using [`mriqc`](https://mriqc.readthedocs.io/en/stable/), version 0.15.2rc1
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@@ -70,6 +42,6 @@ Afterwards, one can run the `highspeed-mriqc-group-level.sh` script to acquire g
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```{bash, echo=TRUE, code=readLines(file.path(path_root, "code", "mriqc", "highspeed-mriqc-group-level.sh")), eval=FALSE}
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```
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-### References
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+#### References
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> Esteban, O., Birman, D., Schaer, M., Koyejo, O. O., Poldrack, R. A., & Gorgolewski, K. J. (2017). MRIQC: Advancing the automatic prediction of image quality in MRI from unseen sites. PLoS ONE, 12(9), e0184661. [doi: 10.1371/journal.pone.0184661](https://doi.org/10.1371/journal.pone.0184661)
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Lennart Wittkuhn