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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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+
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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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+packages_cran <- c("here")
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+pacman::p_load(char = packages_cran)
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+if (basename(here::here()) == "highspeed"){
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+ path_root = here::here("highspeed-mriqc")
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+} else {
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+ path_root = here::here()
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+}
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+```
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+
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+# MRI quality control
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+
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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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+
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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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+
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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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+
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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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+
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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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+
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+``` bash
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+singularity pull docker://poldracklab/mriqc:0.15.2rc1
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+```
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+
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+#### MRIQC subject-level reports: `highspeed-mriqc-subject-level.sh`
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+
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+First, MRIQC has to run on the individual subject-, (if available, session-), modality- and run- level.
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+This is achieved by running the `highspeed-mriqc-subject-level.sh` shell-script.
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+The script is parallelizing all subjects, sessions, modalities and runs on the cluster.
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+
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+```{bash, echo=TRUE, code=readLines(file.path(path_root, "code", "mriqc", "highspeed-mriqc-subject-level.sh")), eval=FALSE}
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+```
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+
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+#### MRIQC group-level reports: `highspeed-mriqc-group-level.sh`
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+
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+Afterwards, one can run the `highspeed-mriqc-group-level.sh` script to acquire group statistics of the quality metrics.
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+
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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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+
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+### References
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+
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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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