Connectome Mapper 3 (UNDER DEVELOPMENT)

This neuroimaging processing pipeline software is developed by the Connectomics Lab at the University Hospital of Lausanne (CHUV) for use within the SNF Sinergia Project 170873, as well as for open-source software distribution.

Warning

THIS SOFTWARE IS FOR RESEARCH PURPOSES ONLY AND SHALL NOT BE USED FOR ANY CLINICAL USE. THIS SOFTWARE HAS NOT BEEN REVIEWED OR APPROVED BY THE FOOD AND DRUG ADMINISTRATION OR EQUIVALENT AUTHORITY, AND IS FOR NON-CLINICAL, IRB-APPROVED RESEARCH USE ONLY. IN NO EVENT SHALL DATA OR IMAGES GENERATED THROUGH THE USE OF THE SOFTWARE BE USED IN THE PROVISION OF PATIENT CARE.

About

Connectome Mapper 3, part of the Connectome Mapping Toolkit (CMTK), implements full anatomical, diffusion and resting-state MRI processing pipelines, from raw Diffusion / T1 / T2 / BOLD data to multi-resolution connection matrices.

The Connectome Mapper 3 pipelines uses a combination of tools from well-known software packages, including FSL, FreeSurfer, ANTs, MRtrix3, Dipy and AFNI. These pipelines were designed to provide the best software implementation for each state of processing, and will be updated as newer and better neuroimaging software become available.

This tool allows you to easily do the following:

• Take T1 / Diffusion / resting-state MRI data from raw to multi-resolution connection matrices.
• Implement tools from different software packages.
• Achieve optimal data processing quality by using the best tools available
• Automate and parallelize processing steps, which provides a significant speed-up from typical linear, manual processing.

Reproducibility and replicatibility is achieved through the distribution of a BIDSApp, a software container image which provide a frozen environment where versions of all external softwares and libraries are fixed.

Getting started

• Installation Instruction for Users
  • The Connectome Mapper 3 BIDSApp
  • The Connectome Mapper 3 BIDSApp Manager (GUI)

User Documentation

• Graphical User Interface
  • Introduction
  • Start the Graphical User Interface
  • Load a BIDS dataset
  • Pipeline stage configuration
  • Run the BIDS App
  • Check stages outputs
• Commandline Usage
  • Introduction
  • Commandline Arguments
  • Participant Level Analysis
  • Debugging
  • Support and communication
  • Not running on a local machine? - Data transfer
• Adopting Datalad for collaboration
  • Move original BIDS dataset to server
  • Datalad setup and dataset creation on Server (accessible via ssh)
  • Processing using the Connectome Mapper BIDS App on a local workstation
  • Local collaboration with Bob for Electrical Source Imaging

About Connectome Mapper

• BSD 3-Clause License
• Changes
• Citing
• Contributing to Connectome Mapper

Funding

Work supported by the SNF Sinergia Grant 170873 (http://p3.snf.ch/Project-170873).

License information

This software is distributed under the open-source license Modified BSD. See license for more details.

All trademarks referenced herein are property of their respective holders.

Aknowledgment

If your are using the Connectome Mapper 3 in your work, please acknowledge this software and its dependencies. See Citing for more details.

Eager to contribute?

See Contributing to Connectome Mapper for more details.