add mriqc docs and move mriqc script to /code/mriqc

.gitattributes

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 * annex.backend=MD5E
 **/.git* annex.largefiles=nothing
 CHANGELOG.md annex.largefiles=nothing
-README.md annex.largefiles=nothing
+README.md annex.largefiles=nothing
+highspeed-mriqc.Rproj annex.largefiles=nothing

.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

code/docs/highspeed-mriqc-docs.Rmd

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+---
+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, 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-mriqc")
+} else {
+  path_root = here::here()
+}
+```
+
+# MRI quality control
+
+## Step 1: MRI quality control using [MRIQC](https://mriqc.readthedocs.io/en/stable/)
+
+### Overview
+
+> MRIQC extracts no-reference IQMs (image quality metrics) from structural (T1w and T2w) and functional MRI (magnetic resonance imaging) data.
+
+Please see the [official MRIQC documentation](https://mriqc.readthedocs.io/en/stable/) for details and refer to the paper listed in the References section.
+
+### Code and software
+
+#### `mriqc` container, version 0.15.2rc1
+
+MRIQC quality control was performed using [`mriqc`](https://mriqc.readthedocs.io/en/stable/), version 0.15.2rc1
+
+``` bash
+singularity pull docker://poldracklab/mriqc:0.15.2rc1
+```
+
+#### MRIQC subject-level reports: `highspeed-mriqc-subject-level.sh`
+
+First, MRIQC has to run on the individual subject-, (if available, session-), modality- and run- level.
+This is achieved by running the `highspeed-mriqc-subject-level.sh` shell-script.
+The script is parallelizing all subjects, sessions, modalities and runs on the cluster.
+
+```{bash, echo=TRUE, code=readLines(file.path(path_root, "code", "mriqc", "highspeed-mriqc-subject-level.sh")), eval=FALSE}
+```
+
+#### MRIQC group-level reports: `highspeed-mriqc-group-level.sh`
+
+Afterwards, one can run the `highspeed-mriqc-group-level.sh` script to acquire group statistics of the quality metrics.
+
+```{bash, echo=TRUE, code=readLines(file.path(path_root, "code", "mriqc", "highspeed-mriqc-group-level.sh")), eval=FALSE}
+```
+
+### References
+
+> 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)

code/highspeed-mriqc-group-level.sh

@@ -3,7 +3,7 @@
 # SCRIPT INFORMATION:
 # ==============================================================================
 # SCRIPT: CREATE GROUP-LEVEL MRIQC REPORTS FOR A BIDS-STRUCTURED DATASET
-# NOTE: ONLY RUN AFTER ALL PARTICIPANT-LEVEL REPORTS ARE FINISHED!
+# ONLY RUN AFTER ALL PARTICIPANT-LEVEL REPORTS ARE FINISHED!
 # PROJECT: HIGHSPEED
 # WRITTEN BY LENNART WITTKUHN, 2018 - 2020
 # CONTACT: WITTKUHN AT MPIB HYPHEN BERLIN DOT MPG DOT DE

highspeed-mriqc.Rproj

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