SDCFlows

SDCFlows (Susceptibility Distortion Correction workFlows) is a Python library of NiPype-based workflows to preprocess B0 mapping data, estimate the corresponding fieldmap and finally correct for susceptibility distortions. Susceptibility-derived distortions are typically displayed by images acquired with EPI (echo-planar imaging) MR schemes.

The library is designed to provide an easily accessible, state-of-the-art interface that is robust to differences in scan acquisition protocols and that requires minimal user input.

This open-source neuroimaging data processing tool is being developed as a part of the MRI image analysis and reproducibility platform offered by NiPreps.

Contents

• Installation
  • External Dependencies
• Examples
  • Susceptibility Distortions in a nutshell
    • Data: a brain
    • The effects of this physical phenomenon
• Methods and implementation
  • Fieldmap estimation: theory and methods
    • Direct B0 mapping sequences
    • Phase-difference B0 estimation
    • PEPOLAR techniques
    • Fieldmap-less approaches
    • Other (unsupported) approaches
    • Estimation tooling
  • Unwarping the distorted data
  • Discovering fieldmaps in a BIDS dataset
    • Explicit specification with B0FieldIdentifier
    • Implicit specification with IntendedFor
    • Fieldmap-less by registration to a T1-weighted image
  • References
• Standalone command line usage
  • Positional Arguments
  • Named Arguments
  • Options related to BIDS
  • Options to handle performance
  • Instrumental options
• Library API (application program interface)
  • sdcflows.cli package
    • Submodules
  • sdcflows.config module
    • Configuration sections
    • Usage
    • Logging
    • Other responsibilities
    • dumps()
    • environment
    • execution
    • file_path
    • from_dict()
    • get()
    • load()
    • loggers
    • nipype
    • restore_env()
    • to_filename()
    • workflow
  • sdcflows.data package
    • load()
    • load.readable()
    • load.as_path()
    • load.cached()
    • Loader
  • sdcflows.fieldmaps module
    • EstimatorType
    • FieldmapEstimation
    • FieldmapFile
    • MetadataError
    • clear_registry()
    • get_identifier()
  • sdcflows.interfaces package
    • Submodules
  • sdcflows.transform module
    • B0FieldTransform
    • disp_to_fmap()
    • fmap_to_disp()
    • grid_bspline_weights()
    • unwarp_parallel()
    • worker()
  • sdcflows.utils package
    • Submodules
  • sdcflows.viz package
    • Submodules
  • sdcflows.workflows package
    • Subpackages
    • Submodules
• What’s new?
  • 2.10.0 (July 04, 2024)
    • CHANGES
  • 2.9.0 (June 13, 2024)
  • 2.8.1 (January 22, 2024)
  • 2.8.0 (January 10, 2024)
  • 2.7.0 (December 18, 2023)
  • 2.6.0 (November 10, 2023)
  • 2.5.2 (November 09, 2023)
  • 2.5.1 (June 08, 2023)
  • 2.5.0 (June 01, 2023)
  • 2.4.3 (April 24, 2023)
  • 2.4.2 (April 20, 2023)
  • 2.4.1 (March 20, 2023)
  • 2.4.0 (March 10, 2023)
  • 2.3.0 (March 01, 2023)
  • 2.2.2 (January 04, 2023)
  • 2.2.1 (December 12, 2022)
  • 2.2.0 (December 09, 2022)
  • 2.1.1 (August 29, 2022)
  • 2.1.0 (May 26, 2022)
  • 2.0.13 (April 08, 2022)
  • 2.0.12 (February 08, 2022)
  • 2.0.11 (January 22, 2022)
  • 2.0.10 (December 13, 2021)
  • 2.0.9 (November 16, 2021)
  • 2.0.8 (October 15, 2021)
  • 2.0.7 (September 30, 2021)
  • 2.0.6 (September 1, 2021)
  • 2.0.5 (August 24, 2021)
  • 2.0.4 (May 18, 2021)
  • 2.0.3 (May 14, 2021)
  • 2.0.2 (May 11, 2021)
  • 2.0.1 (March 05, 2021)
  • 2.0.0 (January 25, 2021)
  • 1.3.x series
    • 1.3.5 (February 14, 2024)
    • 1.3.4 (July 07, 2023)
    • 1.3.3 (September 4, 2020)
    • 1.3.2 (August 14, 2020)
    • 1.3.1 (May 22, 2020)
    • 1.3.0 (May 4, 2020)
  • Pre-1.3.x releases
    • 1.2.2 (April 16, 2020)
    • 1.2.1 (April 01, 2020)
    • 1.2.0 (February 15, 2020)
    • 1.1.0 (February 3, 2020)
    • 1.0.6 (April 15, 2020)
    • 1.0.5 (February 14, 2020)
    • 1.0.4 (January 27, 2020)
    • 1.0.3 (December 18, 2019)
    • 1.0.2 (December 18, 2019)
    • 1.0.1 (December 04, 2019)
    • 1.0.0 (November 25, 2019)
    • 0.1.4 (November 22, 2019)
    • 0.1.3 (October 15, 2019)
    • 0.1.2 (October 10, 2019)
    • 0.1.1 (July 23, 2019)
    • 0.1.0 (July 22, 2019)