Connectome Mapper 3¶
Latest released version: v3.0.0-RC4
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.
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.
Connectome Mapper 3 implements full anatomical, diffusion and
resting-state MRI processing pipelines, from raw Diffusion / T1 /
T2 / BOLD data to multi-resolution connection matrices.
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 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:
Handle T1 / Diffusion / resting-state MRI data, organized following the Brain Imaging Data Structure (BIDS) standard, 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.
Portability, reproducibility and replicatibility are achieved through the distribution of a BIDSApp, a software container image which (1) takes datasets organized following the Brain Imaging Data Structure (BIDS) standard, and which (2) provides a frozen computing environment where versions of all external softwares and libraries are fixed.
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.
If your are using the Connectome Mapper 3 in your work, please acknowledge this software. See Citing for more details.
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.
- Connectome Mapper 3 and the BIDS standard
- Commandline Usage
- Graphical User Interface
- Outputs of Connectome Mapper 3
- Packages and modules
- cmp package
- Pipelines and stages modules
- GUI modules
- cmtklib package
- cmp package
- Adopting Datalad for collaboration
- Running on a cluster (HPC)