Connectome Mapper 3

Latest released version: v3.0.4

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. Source code is hosted on GitHub.

GitHub release (latest by date including pre-releases) GitHub Release Date Zenodo Digital Object Identifier Joss Paper Digital Object Identifier PyPI Docker Image Version (latest by date) Docker Pulls Continuous Integration Status Code Coverage Documentation Status Code Quality Review Status All-contributors

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

_images/flowchart_bidsapp.png

Connectome Mapper 3 is an open-source Python3 image processing pipeline software, with a Graphical User Interface (GUI), that implements full anatomical, diffusion and resting-state MRI processing pipelines, from raw T1 / Diffusion / BOLD data to multi-resolution connection matrices based on a new version of the Lausanne parcellation atlas, aka Lausanne2018.

Connectome Mapper 3 pipelines use a combination of tools from well-known software packages, including FSL, FreeSurfer, ANTs, MRtrix3, Dipy and AFNI, empowered by the Nipype dataflow library. These pipelines are designed to provide the best software implementation for each state of processing at the time of conception, and can be easily updated as newer and better neuroimaging software become available.

To enhance reproducibility and replicatibility, the processing pipelines with all dependencies are encapsulated in a Docker image container, which handles datasets organized following the BIDS standard and is distributed as a BIDS App @ Docker Hub. For execution on high-performance computing cluster, a Singularity image is also made freely available @ Sylabs Cloud.

To enhanced accessibility and reduce the risk of misconfiguration, Connectome Mapper 3 comes with an interactive GUI, aka cmpbidsappmanager, which supports the user in all the steps involved in the configuration of the pipelines, the configuration and execution of the BIDS App, and the control of the output quality. In addition, to facilitate the use by users not familiar with Docker and Singularity containers, Connectome Mapper 3 provides two Python commandline wrappers (connectomemapper3_docker and connectomemapper3_singularity) that will generate and run the appropriate command.

Since v3.0.3, CMP3 provides a new pipeline py:class:EEGPipeline dedicated to EEG modality with a collection of interfaces based on MNE, MNE-Connectivity, and PyCartool. Please check this notebook for a demonstration using the public VEPCON dataset.

Carbon footprint estimation of BIDS App run 🌍🌳✨

In support to the Organisation for Human Brain Mapping (OHBM) Sustainability and Environmental Action (OHBM-SEA) group, CMP3 enables you since v3.0.3 to be more aware about the adverse impact of your processing on the environment!

With the new --track_carbon_footprint option of the connectomemapper3_docker and connectomemapper3_singularity BIDS App python wrappers, and the new "Track carbon footprint" option of the BIDS Interface Window of cmpbidsappmanager, you can estimate the carbon footprint incurred by the execution of the BIDS App. Estimations are conducted using codecarbon to estimate the amount of carbon dioxide (CO2) produced to execute the code by the computing resources and save the results in <bids_dir>/code/emissions.csv.

Then, to visualize, interpret and track the evolution of the emitted CO2 emissions, you can use the visualization tool of codecarbon aka carbonboard that takes as input the csv created:

$ carbonboard --filepath="<bids_dir>/code/emissions.csv" --port=xxxx

Please check https://ohbm-environment.org to learn more about OHBM-SEA!

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. See Citing for more details.

Help/Questions

If you run into any problems or have any questions, you can post to the CMTK-users group. Code bugs can be reported by creating a “New Issue” on the source code repository.

Eager to contribute?

Connectome Mapper 3 is open-source and all kind of contributions (bug reporting, documentation, code,…) are welcome! See Contributing to Connectome Mapper for more details.

Contents

Funding

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