Would like to read fmriprep source code

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1

Any advice on where to begin and how to read? Is there any useful online resources?

Thanks!

2

Hi @biobot ,

Did you look here to read the code?

I guess you went here to look at the documentation of the different stages of preprocessing included within fmriprep?

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Some basic pointers:

  1. fMRIPrep is written using the Nipype workflow framework. This allows us to connect interfaces that may be Python functions, CLI tools, etc.
  2. Our structural workflows have been split out into a separate repository: GitHub - nipreps/smriprep: Structural MRI PREProcessing (sMRIPrep) workflows for NIPreps (NeuroImaging PREProcessing tools)
  3. Our fieldmap workflows have been split out into a separate repository GitHub - nipreps/sdcflows: Susceptibility Distortion Correction (SDC) workflows for EPI MR schemes
  4. We have many workflows and interfaces that are in a catch-all project intended to allow sharing across packages: GitHub - nipreps/niworkflows: Common workflows for MRI (anatomical, functional, diffusion, etc)
  5. Reporting is currently in niworkflows, but we’re moving to nireports: GitHub - nipreps/nireports: The NiPreps' Reporting and Visualization system - report templates and "reportlets"
  6. Much of the Python code uses Neuroimaging in Python — NiBabel 5.1.0 documentation and Nilearn.

We hope our documentation is a helpful guide as well. Finally, we have a contributing guide, which might help.

Please feel free to open issues for where the documentation is insufficient.

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