highspeed-bids/code/docs/highspeed-bids-docs.Rmd

---
title: "Faster than thought: Detecting sub-second activation sequences with sequential fMRI pattern analysis"
subtitle: "Short project title: highspeed"
author:
  - Lennart Wittkuhn^[Max Planck Institute for Human Development, wittkuhn@mpib-berlin.mpg.de]
  - Nicolas W. Schuck^[Max Planck Institute for Human Development, schuck@mpib-berlin.mpg.de]
date: "Last update: `r format(Sys.time(), '%d %B, %Y')`"
output:
 html_document:
    toc: true
    self_contained: true
    toc_float: true
    toc_depth: 3
    number_sections: true
    highlight: pygments
    theme: cosmo
    df_print: paged
    fig_caption: true
fig.align: "center"
header-includes:
  - \usepackage{fontspec}
  - \setmainfont{AgfaRotisSansSerif}
email: wittkuhn@mpib-berlin.mpg.de
---

```{r, libraries, echo=FALSE, message=FALSE, include=FALSE}
if (!requireNamespace("pacman")) install.packages("pacman")
packages_cran <- c("here")
pacman::p_load(char = packages_cran)
if (basename(here::here()) == "highspeed"){
  path_root = here::here("highspeed-bids")
} else {
  path_root = here::here()
}
```

# BIDS conversion

## Heudiconv

### Heuristic file

```{python, echo=TRUE, code=readLines(file.path(path_root, "code", "heudiconv", "highspeed-heudiconv-heuristic.py")), eval=FALSE, python.reticulate=FALSE}
```

### Anonymizer file

```{python, echo=TRUE, code=readLines(file.path(path_root, "code", "heudiconv", "highspeed-heudiconv-anonymizer.py")), eval=FALSE, python.reticulate=FALSE}
```

### Cluster file

```{bash, echo=TRUE, code=readLines(file.path(path_root, "code", "heudiconv", "highspeed-heudiconv-cluster.sh")), eval=FALSE}
```