Reproducible Analysis (reproa) is the main pipeline system for ReproStat written primarily in OCTAVE/MATLAB.
- MATLAB or OCTAVE - when using the OCTAVE container, it is strongly advised to pull it from the reprostat collection
- SPM - when using under OCTAVE, you need to recompile the mex-files
You can download reproa either using git clone or downloading the archive of the latest release or the developmental branch.
You only need to add the top-level directory, which contains reproaSetup, to the MATLAB/OCTAVE path. Calling reproaSetup, typically the first command of the user script will take care of the rest, including the user-specific configuration. You will also need to provide some extra argument if, for example, you want to access the extensions. For more info type help reproaSetup.
reproa is highly modular and the processing steps can be easily rearranged and combined. The list of use cases is not exhaustive and includes only the pre-specified workflows used for testing. Feel free to recombine them also taking advantage of the growing list of reproa extensions.
- Retrieval of supported datasets, including MoAEpilot (demo dataset for SPM manual, chapter 30), OpenNEURO (datasets #114 and #2737 already included, and more can be added to the dataset specification), MPI-LEMON
- Preprocessing anatomical images using DARTEL
- Task-based fMRI, as descibed in SPM manual, chapter 30.
- Extended analysis of multi-run task-based fMRI using dual-echo fieldmaps, slicetiming, and DARTEL-based normalisation
- Workflow connection: Analysis of a data already preprocessed using reproa
Reproa follows as core+extension model. The extensions can be loaded upon calling reproaSetup. Type help reproaSetup for details.
Current list of extensions
- fconn - functional connectivity
- freesurfer - integrating FreeSurfer
- fsl - integrating FSL and other related tools, such as ICA-AROMA
You can read about the supported use-cases of each extension in their README.md.