add initial documentation for code

code/docs/highspeed-bids-docs.Rmd

@@ -0,0 +1,54 @@
+---
+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}
+```