– From raw data to a complete project –

A unique aspect of scilpy is its emphasis on ensuring that each script performs a single, well-defined task. This granularity leads to a very high number of scripts, but allows you to manipulate data exactly as you want. You may then organize processing steps in your favorite order. To automate processes, for a single subject or a larger database, options range from simply aligning command lines sequentially in a bash script, to using more complex workflow management systems such as nextflow, nipype, snakemake, nf-neuro and more, which allow parallel processing over various subjects for accelerated workflows. Users interested in large cohorts processing may discover Tractoflow, which includes 26 scilpy scripts.

• Using bash to loop on subjects
• Using nextflow

Here are examples of start-to-finish automated processing of a single subject:

• From raw diffusion to DTI, fODF, and tractogram