Connectome Mapper 3: a software pipeline for multi-scale connectome mapping of multimodal MR data

Connectome Mapper (CMP) is an open-source software pipeline with a Graphical User Interface (GUI) written in Python. It was historically designed to help researchers in all the organization and processing of raw structural MRI (sMRI) and diffusion MRI (dMRI) data to obtain a hierarchical multi-scale brain parcellation (Cammoun 2012) and its corresponding structural connectomes (Daducci 2012). While the first two versions were designed with ease-of-use, modularity, configurability, re-executability and transparency in mind, they have shown to be limited in terms of interoperability, reusability, portability, and reproducibility. Following recent advances in the standardization of neuroimaging data organization (Gorgolewski 2016) and processing (Gorgolewski 2017), we present the third version of CMP (CMP3). It has massively evolved in terms of the underlying code, the processing tools and the scope of functionality provided, being extended to the processing of resting-state fMRI (rfMRI) data.