docs: practical notes made for internal use, may be useful in generalprep: scripts used in preprocessing, as referencepspm: psychophysiological (skin conductance responses) analysis in PsPM (Matlab)spm/complete: fMRI analysis in SPM (Matlab)stats: statistical analysis, figures (R / RMarkdown, mricrogl)utils: various utility script used to handle data files, events, etc. (mostly Python)
Create a virtual environment and then install packages using the following command:
pip install -r requirements.txt
To install a kernel for this environment in jupyter, run:
python -m ipykernel install --user --name EmoConEnv --display-name "Python 3 (EmoCon)"
Detailed explanation here.
PsPM toolbox version 4.2.0 is needed for physiological data analysis. SPM12 is needed for fMRI data analysis. Update revision number 7487 was used. BIDS-Matlab toolbox and ini2struct function are required by some scripts. They need to be added to the path. MATLAB R2020a was used for fMRI analysis; R2018b was used for psychophysiology.
In principle, scripts are expected to be executed from the directory they're in.
On Fedora 29, running files which were supposed to save feather files resulted in ImportError: pyarrow is not installed (even though if pyarrow was installed). Apparently this is not due to pyarrow itself and could be mitigated, according to this discussion by installing a system package libnsl:
dnf install libnsl