The pre-built Singularity container can be downloaded at https://zenodo.org/records/15376547.
Paper in Neuroinformatics: https://link.springer.com/article/10.1007/s12021-026-09769-2.
Usuage:
singularity run --bind [INPUT_DIR]:/input,[OUTPUT_DIR]:/output [PATH_TO_HARFI_SIF_FILE] [R] [DISCRETE] [TR] [N] [FMRI_IMAGE_NAME] [BRAIN_MASK_NAME] [REFERENCE_IMAGE_NAME] [OUTPUT_NAME]
The parameters are:
R: radius of integration (voxels)
DISCRETE: discrete steps in integration
TR: repetition Time (in seconds)
N: number of volumes to remove from beginning
Users need to provide FMRI_IMAGE_NAME, BRAIN_MASK_NAME, and REFERENCE_IMAGE_NAME in the INPUT_DIR. The output files, OUTPUT_NAME.mat (MATLAB data storing all parameters and results), OUTPUT_NAME.nii.gz (correlation maps), and OUTPUT_NAME_SH_even4.nii.gz (FODs), will be saved to the OUTPUT_DIR.