connectomemapper 3.0.1

Connectome Mapper 3: A Flexible and Open-Source Pipeline Software for Multiscale Multimodal Human Connectome Mapping

Connectome Mapper 3

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.

Description

Connectome Mapper 3 is an open-source Python3 image processing pipeline software, with a Graphical User Interface, that implements full anatomical, diffusion and resting-state MRI processing pipelines, from raw Diffusion / T1 / T2 / 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, orchestrated by the Nipype dataflow library. These pipelines were designed to provide the best software implementation for each state of processing at the time conceptualization, and can be 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.

How to install the python wrappers and the GUI?

You need to have first either Docker or Singularity engine and miniconda installed. We refer to the dedicated documentation page for more instruction details.

Then, download the appropriate environment.yml / environment_macosx.yml and create a conda environment py37cmp-gui with the following command:

$ conda create env -f /path/to/environment[_macosx].yml

Once the environment is created, activate it and install Connectome Mapper 3 with PyPI as follows:

$ conda activate py37cmp-gui
(py37cmp-gui)$ pip install connectomemapper

You are ready to use Connectome Mapper 3!

Resources

• Documentation: https://connectome-mapper-3.readthedocs.io
• Mailing list: https://groups.google.com/forum/#!forum/cmtk-users
• Source: https://github.com/connectomicslab/connectomemapper3
• Bug reports: https://github.com/connectomicslab/connectomemapper3/issues

Usage

Having the py37cmp-gui conda environment previously installed activated, the BIDS App can easily be run using connectomemapper3_docker, the python wrapper for Docker, as follows:

    (py37cmp-gui)$ connectomemapper3_docker -h

    usage: connectomemapper3_docker [-h]
          [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
          [--session_label SESSION_LABEL [SESSION_LABEL ...]]
          [--anat_pipeline_config ANAT_PIPELINE_CONFIG]
          [--dwi_pipeline_config DWI_PIPELINE_CONFIG]
          [--func_pipeline_config FUNC_PIPELINE_CONFIG]
          [--number_of_threads NUMBER_OF_THREADS]
          [--number_of_participants_processed_in_parallel NUMBER_OF_PARTICIPANTS_PROCESSED_IN_PARALLEL]
          [--mrtrix_random_seed MRTRIX_RANDOM_SEED]
          [--ants_random_seed ANTS_RANDOM_SEED]
          [--ants_number_of_threads ANTS_NUMBER_OF_THREADS]
          [--fs_license FS_LICENSE] [--coverage] [--notrack] [-v]
          bids_dir output_dir {participant,group}

    Entrypoint script of the BIDS-App Connectome Mapper version v3.0.1 via Docker

    positional arguments:
      bids_dir              The directory with the input dataset formatted
                            according to the BIDS standard.
      output_dir            The directory where the output files should be stored.
                            If you are running group level analysis this folder
                            should be prepopulated with the results of the
                            participant level analysis.
      {participant,group}   Level of the analysis that will be performed. Multiple
                            participant level analyses can be run independently
                            (in parallel) using the same output_dir.

    optional arguments:
      -h, --help            show this help message and exit
      --participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
                            The label(s) of the participant(s) that should be
                            analyzed. The label corresponds to
                            sub-<participant_label> from the BIDS spec (so it does
                            not include "sub-"). If this parameter is not provided
                            all subjects should be analyzed. Multiple participants
                            can be specified with a space separated list.
      --session_label SESSION_LABEL [SESSION_LABEL ...]
                            The label(s) of the session that should be analyzed.
                            The label corresponds to ses-<session_label> from the
                            BIDS spec (so it does not include "ses-"). If this
                            parameter is not provided all sessions should be
                            analyzed. Multiple sessions can be specified with a
                            space separated list.
      --anat_pipeline_config ANAT_PIPELINE_CONFIG
                            Configuration .txt file for processing stages of the
                            anatomical MRI processing pipeline
      --dwi_pipeline_config DWI_PIPELINE_CONFIG
                            Configuration .txt file for processing stages of the
                            diffusion MRI processing pipeline
      --func_pipeline_config FUNC_PIPELINE_CONFIG
                            Configuration .txt file for processing stages of the
                            fMRI processing pipeline
      --number_of_threads NUMBER_OF_THREADS
                            The number of OpenMP threads used for multi-threading
                            by Freesurfer (Set to [Number of available CPUs -1] by default).
      --number_of_participants_processed_in_parallel NUMBER_OF_PARTICIPANTS_PROCESSED_IN_PARALLEL
                            The number of subjects to be processed in parallel
                            (One by default).
      --mrtrix_random_seed MRTRIX_RANDOM_SEED
                            Fix MRtrix3 random number generator seed to the
                            specified value
      --ants_random_seed ANTS_RANDOM_SEED
                            Fix ANTS random number generator seed to the specified
                            value
      --ants_number_of_threads ANTS_NUMBER_OF_THREADS
                            Fix number of threads in ANTs. If not specified ANTs
                            will use the same number as the number of OpenMP
                            threads (see `----number_of_threads` option flag)
      --fs_license FS_LICENSE
                            Freesurfer license.txt
      --coverage            Run connectomemapper3 with coverage
      --notrack             Do not send event to Google analytics to report BIDS
                            App execution, which is enabled by default.
      -v, --version         show program's version number and exit

Contributors ✨

Thanks goes to these wonderful people (emoji key):

Sébastien Tourbier 💻 🎨 🚇 ⚠️ 💡 🤔 🧑‍🏫 📆 👀 ✅ 📢	joanrue 🐛 💻 ⚠️ 🤔	Katharina Glomb 🐛 💻 ⚠️ 🤔	anilbey 💻 ⚠️ 🤔 📖	jwirsich 🐛 💻 🤔	kuba-fidel 💻 📖 🤔	Stefan 💻 ✅ 🤔
Mikkel Schöttner ✅ 💻 🤔	yasseraleman 💻 🤔	agriffa 💻 🤔	Emeline Mullier 💻	Patric Hagmann 🤔 🔍

Thanks also goes to all these wonderful people that contributed to Connectome Mapper 1 and 2:

• Collaborators from Signal Processing Laboratory (LTS5), EPFL, Lausanne:

  • Jean-Philippe Thiran
  • Leila Cammoun
  • Adrien Birbaumer (abirba)
  • Alessandro Daducci (daducci)
  • Stephan Gerhard (unidesigner)
  • Christophe Chênes (Cwis)
  • Oscar Esteban (oesteban)
  • David Romascano (davidrs06)
  • Alia Lemkaddem (allem)
  • Xavier Gigandet

• Collaborators from Children's Hospital, Boston:

  • Ellen Grant
  • Daniel Ginsburg (danginsburg)
  • Rudolph Pienaar (rudolphpienaar)
  • Nicolas Rannou (NicolasRannou)

This project follows the all-contributors specification. Contributions of any kind welcome!

Funding

Work supported by the Sinergia SNFNS-170873 Grant.

License

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.

Copyright (C) 2009-2022, Hospital Center and University of Lausanne (UNIL-CHUV), Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland & Contributors.