**averaged_matrix.m**
Creates averaged brain images for 3 laterality groups for each contrast.
**average_matrix_mirror.m**
Creates averages mirror images for 3 laterality groups for each contrast.
**batch_FLIRT_Lisa_b.sh**
Initial processing of fMRI images to be suitable for LI toolbox.
**compute_GAM_LI.rmd**
Uses complex GAM method to compute the LI for Word Generation and Pyramids and Palm trees from .eps files.
**LI_boot_DB.m**
Used with LI_DB to do compute LI using standard toolbox method
**LI_DB.m**
Used with LI_boot_DB.m to compute LI using standard toolbox method - based on LI.m but has some minor changes.
**LIhistos_create.rmd**
Creates figs 2-4 from a sample LI toolbox output.
**Magick_image_manipulation.zip**
Used to assemble larger brain figures from the png outputs of MRIcroGL.
**Make_diff_ni.m**
Makes mirror image .nii files that are used in brain image plots.
**Mirror.m**
Does computations for mirror LI. Based on LI.m and uses the same data.
**Mirror_boot.m**
Main computation function for mirror.m
**Process_LI_mirror_ftcd.rmd**
Creates a big data file (bigdf.csv) which combines LIs from all the different methods, ROIs and tasks in long format. Also computed correlation heatmap.
**Python_3gp_LR_avgs.py**
Used with MRIcroGL to make png files showing L and R brain for group averaged files, with red/blue showing activation/deactivation.
**Python_3gp_mirror_avgs.py**
Used with MRIcroGL to make png averaged files showing hemisphere where green indicates L lateralisation and yellow indicates R lateralisation.
