Atlas-to-Patient Workflow#

Warp cohort atlas maps into patient space using pre-computed template-to-patient ANTs transforms. Driven entirely by transforms.jobs[] — each job specifies input files, direction, interpolation, and an output subdirectory.

thesis.workflows.atlas_to_patient.workflow#

Atlas-to-patient-space transform workflow.

Transforms cohort-level atlas maps (mean, std, probability, etc.) into individual patient space using the template-to-patient transforms defined under transforms.template_to_patient.

The images to transform are specified explicitly via transforms.jobs in configuration. The workflow delegates the actual transform execution to the generic thesis.workflows.transforms.workflow module.

Register as thesis run -w atlas_to_patient -p <patient_id> -c <config>.

thesis.workflows.atlas_to_patient.workflow.build_workflow(*, config, context)[source]#

Build the atlas-to-patient-space transform workflow.

Delegates to the generic transform workflow after validating that the required transforms are configured. Raises ValueError when no jobs are configured.

Parameters:
Return type:

Workflow

thesis.workflows.atlas_to_patient.workflow.verify_requirements(config, context)[source]#

Preflight checks: antsApplyTransforms on PATH and template_to_patient transforms configured (plus everything from the base transform verifier).

Parameters:
Return type:

List[str]