Workflows

OncoPrep’s processing logic is organized as Nipype workflows. Each workflow factory returns a Workflow instance with inputnode and outputnode for composable integration.

Orchestration

Anatomical preprocessing

Tumor segmentation

init_anat_seg_wf

Create tumor segmentation workflow for integration with anatomical preprocessing.

nnInteractive segmentation

init_nninteractive_seg_wf

Create an nnInteractive tumor segmentation workflow.

Segmentation fusion

init_fusion_wf	Initialize segmentation fusion workflow.
init_anat_seg_fuse_wf	Initialize anatomical segmentation fusion workflow.

Radiomics

init_anat_radiomics_wf	Create a radiomics feature extraction workflow.
init_multimodal_radiomics_wf	Create a multi-modal radiomics extraction workflow.

VASARI feature extraction

init_vasari_wf

Create a VASARI feature extraction and radiology report workflow.

Quality control (MRIQC) — temporarily disabled

Warning

MRIQC integration is temporarily disabled in this release. The --run-qc CLI flag is accepted but ignored. This module will be re-enabled in a future version.

Legacy metrics (deprecated)

init_qa_metrics_wf	Compute quality assurance metrics for preprocessing.
init_snr_metrics_wf	Compute signal-to-noise ratio metrics.
init_coverage_metrics_wf	Compute brain coverage and field-of-view metrics.
init_tissue_stats_wf	Compute detailed tissue-specific statistics.
init_registration_quality_wf	Assess quality of template registration.

Warning

The workflows in oncoprep.workflows.metrics are deprecated. MRIQC integration is temporarily disabled and will be re-enabled in a future version.

Derivatives output

BraTS-specific outputs

Surface processing (planned)

Note

Surface processing workflows are not yet implemented. The interfaces below are scaffolded for future FreeSurfer + GIFTI/CIFTI-2 integration.

init_gifti_surfaces_wf	Prepare GIFTI surfaces from FreeSurfer subjects directory.
init_gifti_morphometrics_wf	Prepare GIFTI shape files from FreeSurfer morphometrics.
init_surface_datasink_wf	Save GIFTI surfaces and morphometrics to BIDS derivatives.

Reports

init_report_wf

Generate comprehensive preprocessing report.

BIDS conversion