SynthSeg Workflow#

Standalone FreeSurfer SynthSeg brain segmentation workflow.

thesis.workflows.synthseg#

SynthSeg brain segmentation workflow.

thesis.workflows.synthseg.workflow#

SynthSeg brain segmentation workflow.

Builds a standalone Nipype workflow that runs FreeSurfer’s mri_synthseg on a T1-weighted image. The workflow can be executed on its own or embedded inside a larger meta-workflow via Nipype’s nested-workflow mechanism.

thesis.workflows.synthseg.workflow.resolve_t1_for_synthseg(config, context)[source]#

Resolve the T1 image path for the SynthSeg workflow.

Kept as a thin shim so the composite tract_synthseg meta-workflow and external preflight checks can still resolve the path without instantiating a PatientFile.

Parameters:
Return type:

Path

thesis.workflows.synthseg.workflow.build_workflow(*, t1, seg_dir, config, context)[source]#

Build a Nipype workflow that segments a T1w image with SynthSeg.

The workflow contains a single node (synthseg) wrapping mri_synthseg. Outputs land in {output_dir}/segmentation/synthseg/{patient_id}_synthseg.nii.gz.

Parameters:

  • t1 (Path | None) – Resolved T1-weighted image path (declared via @requires).

  • seg_dir (Path) – Resolved segmentation output directory.

  • config (PipelineConfig) – PipelineConfig (may include an optional synthseg section).

  • context (ProcessingContext) – ProcessingContext carrying patient_id.

Return type:

Workflow

Returns:

Nipype Workflow ready to run or embed in a meta-workflow.