Configuration

autods-pet reads parameters from an INI file. Generate a template with autods-pet create-config or copy one of the example configs from the configs/ folder (standard.ini, quick.ini, full.ini, advanced.ini, brain.ini). The file is parsed by autods_pet.config.load_config().

[paths] Section

Parameter	Default	Description
basepath	(required)	Root directory containing one subfolder per patient.
patient_list	(empty)	Path to a text file listing patient IDs (one per line, # for comments).
metadata_csv	(empty)	Path to a CSV with PET metadata (radiopharmaceutical tags, patient weight). When patients have incomplete metadata, an auto-generated template is written to output_dir/metadata.csv.
output_dir	(empty)	Root directory for all outputs. Per-patient results are written to output_dir/{patient_id}_results/ with subfolders images/, segmentations/, metadata/, DeauvilleScores/, and SUV/. Batch summaries (batch_results_DS.csv, batch_results_SUV.csv) are written directly to output_dir/.

[lumbar_vb] Section

Lumbar vertebral body bone marrow ROI.

Parameter	Default	Description
labels	29, 28, 27	TotalSegmentator label IDs for L3, L4, L5. Add 31, 30 for L1, L2.
erosion_mm	3.0	Physical erosion radius in mm.
stats	p95	Statistics to compute.

[aorta_mbp] Section

Mediastinal blood pool reference ROI.

Parameter	Default	Description
vertebra_labels	36, 37, 38, 39, 40	T4–T8 labels for slice-gating slab.
slab_axis	2	SimpleITK axis for slice-gating (0=x, 1=y, 2=z).
heart_exclusion_mode	dilate_intersection	dilate_intersection or distance.
heart_dilation_mm	6.0	Heart buffer dilation (mode: dilate_intersection).
heart_distance_mm	12.0	Heart distance threshold (mode: distance).
aorta_erosion_mm	4.0	Intraluminal erosion radius.
stats	median	Statistics to compute.

[liver] Section

Liver reference ROI.

Parameter	Default	Description
erosion_mm	10.0	Physical erosion radius in mm.
max_hole_volume_mm3	none	Fill only holes below this volume (mm3). Default none fills all holes.
stats	median	Statistics to compute.

[long_bones] Section

Femoral and humeral diaphysis ROIs.

Parameter	Default	Description
diaphysis_keep_pct	60	Central percentage of the bone axis to keep.
stats	p95	Statistics to compute.

Per-bone erosion is set via sub-sections [long_bones.femur_L], [long_bones.femur_R], [long_bones.humerus_L], [long_bones.humerus_R], each with an erosion_mm key.

[brain] Section

Brain cortical grey matter ROI (for Brain-to-Liver Ratio).

Parameter	Default	Description
label	90	TotalSegmentator label ID for brain.
grey_matter_only	true	If true, extract cortical grey matter shell (original minus eroded). If false, use the full brain mask.
cortical_thickness_mm	5.0	Erosion radius in mm for the shell extraction (only when grey_matter_only is true).
stats	median	Statistics to compute.

[output] Section

Controls mask saving during ROI extraction.

Parameter	Default	Description
save_raw_masks	false	Save individual raw TotalSegmentator label masks as NIfTI in {seg_dir}/raw/.
save_refined_masks	true	Save refined ROI masks (after erosion, slabbing, etc.) as NIfTI in {seg_dir}/refined/.
subtract_lesions_from_marrow	false	Subtract target lesion masks (FL, PM, EM, custom) from marrow ROIs (Lumbar VB, Long bones) before computing statistics. See the note below.

Note

Lesion subtraction and input consistency

When subtract_lesions_from_marrow is enabled, the accuracy of the corrected marrow uptake depends entirely on the completeness and consistency of the input lesion masks. If lesion segmentation criteria vary across patients (e.g. only the hottest lesion is segmented in some patients while multiple lesions are segmented in others), the subtraction will be applied unevenly, potentially introducing a systematic bias. To ensure valid cohort-level comparisons, users should apply uniform lesion segmentation criteria across all patients.

[deauville] Section

Deauville Score scoring parameters.

Parameter	Default	Description
liver_multiplier	2.0	Multiplier applied to the liver reference for the DS 4 / DS 5 cutoff (DS 5 = target uptake > liver_multiplier × liver). The default of 2.0 follows the Lugano 2014 consensus; set to 3.0 for protocols using a 3× liver threshold.

[totalsegmentator] Section

TotalSegmentator runtime options.

Parameter	Default	Description
license	(empty)	TotalSegmentator license key (set automatically via totalseg_set_license).
fast	false	Use TotalSegmentator fast mode (lower accuracy, faster). Note: the vertebrae_body task always runs in high-res regardless of this setting. Output is a single multilabel file (TotSeg_multilabel.nii.gz); no individual per-label files are created.

[dicom] Section

Parameter	Default	Description
size_threshold_kb	100	Minimum file size (KB) to consider as DICOM.

Target ROIs

Opt-in sections for user-provided manual lesion masks. Both NIfTI/NRRD and DICOM SEG inputs are supported and the discovery is recursive: the mask file may live anywhere under the patient input directory, including nested study/series sub-folders exported by DICOM viewers.

Each section may set:

• mask_filename – one stem (or comma-separated list of stems) for .nii.gz / .nii / .nrrd files. Searched recursively under input_dir. Existing NIfTI workflows keep working unchanged – the only difference from previous releases is that the search now descends into sub-folders as well as the patient root and segmentations/.

• segment_label – one DICOM SEG SegmentLabel (or comma list, case-insensitive). The SEG file is identified by matching its ReferencedSeriesSequence to the patient’s PET SeriesInstanceUID (read from PET_metadata.json); no filename or location is required. A single multi-segment SEG file may supply several target sections at once. Only consulted for .dcm files.

Set either, both, or neither. When both formats resolve the same target for the same patient, DICOM SEG wins and a note is logged. A target with neither key set is treated as disabled.

A configured target whose mask cannot be found anywhere produces a loud warning naming the patient, the patterns searched for, and the locations checked – it never silently disappears from the output.

Sections:

• [focal_lesion] – Focal lesion (FL)

• [paramedullary] – Paramedullary disease (PM)

• [extramedullary] – Extramedullary disease (EM)

• [targets.<name>] – Custom targets

Use autods-pet validate-config <config> --patients <id1,id2> to preview which masks would be discovered for each patient before launching a full extract / score run, or pass --explain-masks to extract / score / run to print the discovery report alongside the actual computation.

Available Statistics

Name	Description
mean	Arithmetic mean of voxel values in the mask.
median	Voxelwise median.
min	Minimum value.
max	Maximum value.
p<N>	N-th percentile (e.g. p90, p95, p99).