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Contributing to Connectome Mapper

Authors: Sebastien Tourbier
Adrien Birbaumer
Version: Revision: 2
Copyright: Copyright (C) 2017-2019, Brain Communication Pathways Sinergia Consortium, Switzerland. This software is distributed under the open-source license Modified BSD.

Philosophy

The development philosophy for this new version of the Connectome Mapper is to:

I. Keep the code of the processing as much as possible outside of the actual main Connectome Mapper code, through the use and extension of existing Nipype interfaces and an external library (dubbed cmtklib).

  1. Separation between the code of the graphical interface and the actual main Connectomer Mapper code, achieved through inheritance of the actual main stages and pipelines.
  2. Enhance portability by freezing the computing environment with all software dependencies installed, through the adoption of the BIDS App framework relying on light software container technologies.
  3. Enhance interoperability by working with datasets structured following the Brain Imaging Data Structure structured dataset.

Further development, typically additions of other tools and configuration options should go in this direction.

Enhancements

Possible enhancements are probably to be included in the following list:

  1. Adding of a configuration option to an existing stage
  2. Adding a new interface to cmtklib
  3. Adding of a new stage
  4. Adding of a new pipeline

The adding of newer configuration options to existing stages should be self- understandable. If the addition is large enough to be considered a "sub-module" of an existing stage, see the Diffusion stage example.

Adding a new stage implies the addition of the stage folder to the cmp/stages and cmp/bidsappmanager/stages directory and according modification of the parent pipeline along with insertion of a new image in cmp/bidsappmanager/stages. Copy-paste of existing stage (such as segmentation stage) is recommended.

Adding a new pipeline implies the creation of a new pipeline script and folder in the cmp/pipelines and cmp/bidsappmanager/pipelines directories Again copy-pasting an existing pipeline is the better idea here. Modification of cmp/project.py and cmp/bidsappmanager/project.py file is also needed.

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