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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)
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