Streamlining Neuroimaging - Snakemake’s Role in Developing a Striatal Segmentation Pipeline

The striatum, a component of the basal ganglia, has been extensively investigated in human and animal models due to its links to neurodegenerative diseases. One of the overarching goals of these studies is to identify biomarkers that can facilitate early detection during the prodromal or initial manifestation stages of these diseases. Various methods of diffusion magnetic resonance (dMRI) analysis are a promising avenue in human studies. A recent innovation provides a novel method of parceling the human striatum into distinct compartments with connectivity specific for the striosomes and matrix. This method involves numerous processing steps and requires significant computational resources. Integration of a scientific workflow is recommended to simplify deployment, ensure scalability and reliability, and facilitate the addition and parameterization of processes. This can potentially improve the efficiency of future research in this domain. In this study, we introduce a pipeline capable of segmenting striosome-like and matrix-like voxels in the human striatum using dMRI images, leveraging the scientific workflow tool, Snakemake.