highspeed-fmriprep/code/docs/highspeed-fmriprep-docs.Rmd

```{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-fmriprep")
} else {
  path_root = here::here()
}
```

## MRI pre-processing:Running fMRIPrep

### Overview

We used [fMRIPrep](https://fmriprep.org/en/stable/), version 1.2.2, to pre-process the BIDS-converted MRI data.

According to the [fMRIPrep documentation](https://fmriprep.org/en/stable/) ...

> fMRIPrep is a functional magnetic resonance imaging (fMRI) data preprocessing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting. It performs basic processing steps (coregistration, normalization, unwarping, noise component extraction, segmentation, skullstripping etc.) providing outputs that can be easily submitted to a variety of group level analyses, including task-based or resting-state fMRI, graph theory measures, surface or volume-based statistics, etc.

Please see the [fMRIPrep documentation](https://fmriprep.org/en/stable/) for details and refer to the paper listed in the References section.

#### Data availability

The data is freely available from https://github.com/lnnrtwttkhn/highspeed-fmriprep and https://gin.g-node.org/lnnrtwttkhn/highspeed-fmriprep.

#### License

The dataset is licensed under Creative Commons Attribution-ShareAlike 4.0.
Please see https://creativecommons.org/licenses/by-sa/4.0/ for details.

### Software: `fmriprep` container, version 1.2.2

We first generated a Singularity container based on the fMRIPrep docker image:

``` bash
singularity pull docker://poldracklab/fmriprep:1.2.2
```

### Run fMRIPrep on HPC

We then ran fMRIPrep on the high-performance cluster (HPC) of the Max Planck Institute for Human Development, Berlin, Germany using the code in `highspeed-fmriprep-cluster.sh`:

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

### References

> Esteban, O., Markiewicz, C. J., Blair, R. W., Moodie, C. A., Isik, A. I., Erramuzpe, A., Kent, J. D., Goncalves, M., DuPre, E., Snyder, M., and et al. (2019). fMRIPrep 1.2.2. [doi:10.5281/zenodo.852659](dx.doi.org/10.5281/zenodo.852659)

> Esteban, O., Markiewicz, C. J., Blair, R. W., Moodie, C. A., Isik, A. I., Erramuzpe, A., Kent, J. D., Goncalves, M., DuPre, E., Snyder, M., and et al. (2018). fMRIPrep: A robust preprocessing pipeline for functional MRI. Nature Methods, 16(1):111–116. [doi:10.1038/s41592-018-0235-4](http://dx.doi.org/10.1038/s41592-018-0235-4)

> Esteban, O., Ciric, R., Finc, K., Blair, R. W., Markiewicz, C. J., Moodie, C. A., Kent, J. D., Goncalves, M., DuPre, E., Gomez, D. E. P., and et al. (2020). Analysis of task-based functional mri data preprocessed with fmriprep. Nature Protocols. [doi:10.1038/s41596-020-0327-3](http://dx.doi.org/10.1038/s41596-020-0327-3)