Note

This page is a reference documentation. It only explains the function signature, and not how to use it. Please refer to the user guide for the big picture.

brainprep.interfaces.synb0disco.synthb0

brainprep.interfaces.synb0disco.synthb0(t1_file, dwi_file, workspace_dir, output_dir, entities, mask_file=None)

Apply Synb0-DISCO.

The Synb0-DISCO tool aims to enable susceptibility distortion correction with historical and/or limited datasets that do not include specific sequences for distortion correction (i.e. reverse phase-encoded scans). In short, the tool synthesizes an “undistorted” b=0 image that matches the geometry of structural T1w images and also matches the contrast from diffusion images. This synthesized ‘undistorted’ image can then be used in standard pipelines (i.e. TOPUP).

Parameters:

t1_fileFile

Path to the input T1w image file.

dwi_fileFile

Path to the input diffusion weighted image file of one subject.

workspace_dir: Directory

Working directory with the workspace of the current processing.

output_dirDirectory

Directory where the generated images will be saved.

entitiesdict

A dictionary of parsed BIDS entities including modality.

mask_file: File | None

Binary brain mask image file. If this parameter is not set, the mask is computed using bet. Default None.

Returns:

commandslist[list[str]]

Synb0-DISCO preprocessing command-lines.

outputstuple[File]

• b0_file : File - synthesized b=0 image as input to topup.

• sidecar_file : File - associated JSON sidecar with reverse phase encoding and an effective echo spacing of 0 (infinite bandwidth).