IBSI 2 Phase 2 Compliance: Radiomic Features

Overview

IBSI 2 Phase 2 focuses on evaluating the reproducibility of radiomic features extracted from filtered images. In this phase, specific filters (Mean, LoG, Laws, Gabor, Wavelets) are applied to a digital phantom (Lung Cancer CT), and intensity features are extracted from the resulting response maps.

This page documents Pictologics' compliance with IBSI 2 Phase 2 (Configuration B), which covers 3D volumetric processing.

How to Run the Benchmarks

1. Download the Data

The IBSI 2 reference datasets are available on the IBSI GitHub repository.

CT Phantom: Download the PAT1_CT.nii.gz and PAT1_GTV.nii.gz (or similarly named image.nii.gz / mask.nii.gz) from the ibsi_2_phase_2 (or ibsi_2_validation) folder.

Place these files in a local directory (e.g., data/ibsi2/data/ct_phantom/) to run the benchmarks.

2. Run Configurations Programmatically using `RadiomicsPipeline`

You can verify any IBSI 2 configuration programmatically using the RadiomicsPipeline.

from pictologics import RadiomicsPipeline

# Path to your downloaded phantom
image_path = "data/ibsi2/data/ct_phantom/image.nii.gz"
mask_path = "data/ibsi2/data/ct_phantom/mask.nii.gz"

pipeline = RadiomicsPipeline()

# Define common IBSI 2 Preprocessing (Config B)
preprocess_steps = [
    # 1. Resample to 1x1x1 mm using Tricubic Spline interpolation
    {"step": "resample", "params": {
        "new_spacing": (1.0, 1.0, 1.0), 
        "interpolation": "cubic", 
        "mask_interpolation": "linear", 
        "mask_threshold": 0.5
    }},
    # 2. Round intensities to nearest integer
    {"step": "round_intensities", "params": {}},
    # 3. Resegment range [-1000, 400] HU
    {"step": "resegment", "params": {"range_min": -1000, "range_max": 400}},
]

# Define a filter configuration (e.g., Test 3.B: LoG)
log_config = preprocess_steps + [
    {"step": "filter", "params": {
        "type": "log",
        "sigma_mm": 1.5,
        "truncate": 4.0
    }},
    {"step": "extract_features", "params": {"families": ["intensity"]}}
]

pipeline.add_config("ibsi2_test_3b", log_config)

# Run pipeline
results = pipeline.run(image_path, mask_path, config_names=["ibsi2_test_3b"])
print(results["ibsi2_test_3b"])

Phase 2 Results

Summary: 9/9 Tests Passed (3D Configuration). Total Features: 161/161 passed.

Test 1.B: None

Configuration: Baseline (no filter)

Feature	Code	Calc	Ref	Tol	Status
Mean	stat_mean	-46.4	-46.4	5.9	✅ PASS
Variance	stat_var	5.26e+04	5.26e+04	2.8e+03	✅ PASS
Skewness	stat_skew	-2.18	-2.18	0.09	✅ PASS
(Excess) kurtosis	stat_kurt	3.71	3.71	0.47	✅ PASS
Median	stat_median	41	41	0.7	✅ PASS
Minimum	stat_min	-997	-997	3	✅ PASS
10th percentile	stat_p10	-427	-427	29	✅ PASS
90th percentile	stat_p90	92	92	0.1	✅ PASS
Maximum	stat_max	377	377	15	✅ PASS
Interquartile range	stat_iqr	67	67	9.1	✅ PASS
Range	stat_range	1.37e+03	1.37e+03	20	✅ PASS
Mean absolute deviation	stat_mad	159	159	7	✅ PASS
Robust mean absolute deviation	stat_rmad	63.6	63.6	7.3	✅ PASS
Median absolute deviation	stat_medad	121	121	6	✅ PASS
Coefficient of variation	stat_cov	-4.94	-4.94	0.64	✅ PASS
Quartile coefficient of dispersion	stat_qcod	0.944	0.944	0.925	✅ PASS
Energy	stat_energy	1.96e+10	1.96e+10	1.9e+09	✅ PASS
Root mean square	stat_rms	234	234	7	✅ PASS

Test 2.B: Mean

Configuration: 3D, support=5

Feature	Code	Calc	Ref	Tol	Status
Mean	stat_mean	-49.9	-49.9	5.7	✅ PASS
Variance	stat_var	4.44e+04	4.44e+04	2.3e+03	✅ PASS
Skewness	stat_skew	-2.13	-2.13	0.09	✅ PASS
(Excess) kurtosis	stat_kurt	3.59	3.59	0.46	✅ PASS
Median	stat_median	37.3	37.3	0.6	✅ PASS
Minimum	stat_min	-906	-906	5	✅ PASS
10th percentile	stat_p10	-389	-389	25	✅ PASS
90th percentile	stat_p90	77.2	77.2	0.1	✅ PASS
Maximum	stat_max	316	316	7	✅ PASS
Interquartile range	stat_iqr	92.6	92.6	13.5	✅ PASS
Range	stat_range	1.22e+03	1.22e+03	10	✅ PASS
Mean absolute deviation	stat_mad	149	149	6	✅ PASS
Robust mean absolute deviation	stat_rmad	68.1	68.1	6.9	✅ PASS
Median absolute deviation	stat_medad	114	114	5	✅ PASS
Coefficient of variation	stat_cov	-4.22	-4.22	0.47	✅ PASS
Quartile coefficient of dispersion	stat_qcod	2.97	2.97	0.58	✅ PASS
Energy	stat_energy	1.68e+10	1.68e+10	1.6e+09	✅ PASS
Root mean square	stat_rms	217	217	7	✅ PASS

Test 3.B: LoG

Configuration: σ=1.5mm, truncate=4σ

Feature	Code	Calc	Ref	Tol	Status
Mean	stat_mean	-2.92	-2.94	0.2	✅ PASS
Variance	stat_var	720	720	33	✅ PASS
Skewness	stat_skew	0.428	0.428	0.009	✅ PASS
(Excess) kurtosis	stat_kurt	6.13	6.13	0.27	✅ PASS
Median	stat_median	-0.927	-0.919	0.024	✅ PASS
Minimum	stat_min	-173	-173	5	✅ PASS
10th percentile	stat_p10	-32.1	-32.2	0.5	✅ PASS
90th percentile	stat_p90	17.5	17.4	1.9	✅ PASS
Maximum	stat_max	204	204	1	✅ PASS
Interquartile range	stat_iqr	11.4	11.4	0.3	✅ PASS
Range	stat_range	377	377	5	✅ PASS
Mean absolute deviation	stat_mad	15.5	15.5	0.4	✅ PASS
Robust mean absolute deviation	stat_rmad	6.36	6.37	0.19	✅ PASS
Median absolute deviation	stat_medad	15.3	15.3	0.4	✅ PASS
Coefficient of variation	stat_cov	-9.18	-9.12	1.63	✅ PASS
Quartile coefficient of dispersion	stat_qcod	-2.34	-2.34	0.07	✅ PASS
Energy	stat_energy	2.61e+08	2.61e+08	1.9e+07	✅ PASS
Root mean square	stat_rms	27	27	0.6	✅ PASS

Test 4.B: Laws

Configuration: L5E5E5, rot-inv max, energy δ=7

Feature	Code	Calc	Ref	Tol	Status
Mean	stat_mean	142	142	3	✅ PASS
Variance	stat_var	1.11e+04	1.11e+04	300	✅ PASS
Skewness	stat_skew	0.645	0.645	0.028	✅ PASS
(Excess) kurtosis	stat_kurt	-0.711	-0.711	0.044	✅ PASS
Median	stat_median	113	113	4	✅ PASS
Minimum	stat_min	28.5	28.5	0.1	✅ PASS
10th percentile	stat_p10	35.6	35.6	0.1	✅ PASS
90th percentile	stat_p90	293	293	4	✅ PASS
Maximum	stat_max	525	525	1	✅ PASS
Interquartile range	stat_iqr	188	188	4	✅ PASS
Range	stat_range	496	496	1	✅ PASS
Mean absolute deviation	stat_mad	92.4	92.4	1.4	✅ PASS
Robust mean absolute deviation	stat_rmad	75.9	75.9	1.4	✅ PASS
Median absolute deviation	stat_medad	90.8	90.8	1.6	✅ PASS
Coefficient of variation	stat_cov	0.743	0.743	0.005	✅ PASS
Quartile coefficient of dispersion	stat_qcod	0.699	0.699	0.003	✅ PASS
Energy	stat_energy	1.12e+10	1.12e+10	7e+08	✅ PASS
Root mean square	stat_rms	177	177	3	✅ PASS

Test 5.B: Gabor

Configuration: σ=5mm, λ=2mm, γ=1.5, rot-inv avg

Feature	Code	Calc	Ref	Tol	Status
Mean	stat_mean	40.2	40.2	0.2	✅ PASS
Variance	stat_var	231	231	2	✅ PASS
Skewness	stat_skew	1.57	1.57	0.03	✅ PASS
(Excess) kurtosis	stat_kurt	4.34	4.34	0.2	✅ PASS
Median	stat_median	37.2	37.2	0.1	✅ PASS
Minimum	stat_min	9.53	9.53	0.11	✅ PASS
10th percentile	stat_p10	24.6	24.6	0.1	✅ PASS
90th percentile	stat_p90	59.3	59.3	0.3	✅ PASS
Maximum	stat_max	175	175	3	✅ PASS
Interquartile range	stat_iqr	17.4	17.4	0.1	✅ PASS
Range	stat_range	165	165	3	✅ PASS
Mean absolute deviation	stat_mad	11.3	11.3	0.1	✅ PASS
Robust mean absolute deviation	stat_rmad	7.31	7.31	0.06	✅ PASS
Median absolute deviation	stat_medad	11	11	0.1	✅ PASS
Coefficient of variation	stat_cov	0.377	0.377	0.004	✅ PASS
Quartile coefficient of dispersion	stat_qcod	0.226	0.226	0.002	✅ PASS
Energy	stat_energy	6.62e+08	6.62e+08	9e+06	✅ PASS
Root mean square	stat_rms	43	43	0.2	✅ PASS

Test 6.B: Daubechies 3

Configuration: LLH level 1, rot-inv avg

Feature	Code	Calc	Ref	Tol	Status
Mean	stat_mean	-0.182	-0.182	0.024	✅ PASS
Variance	stat_var	250	250	9	✅ PASS
Skewness	stat_skew	0.157	0.157	0.018	✅ PASS
(Excess) kurtosis	stat_kurt	8.98	8.98	0.35	✅ PASS
Median	stat_median	0.0576	0.0575	0.0046	✅ PASS
Minimum	stat_min	-148	-148	1	✅ PASS
10th percentile	stat_p10	-13.8	-13.8	0.5	✅ PASS
90th percentile	stat_p90	12.1	12.1	0.4	✅ PASS
Maximum	stat_max	155	155	1	✅ PASS
Interquartile range	stat_iqr	9.35	9.35	0.15	✅ PASS
Range	stat_range	303	303	2	✅ PASS
Mean absolute deviation	stat_mad	9.26	9.26	0.22	✅ PASS
Robust mean absolute deviation	stat_rmad	4.21	4.21	0.09	✅ PASS
Median absolute deviation	stat_medad	9.25	9.25	0.22	✅ PASS
Coefficient of variation	stat_cov	-86.9	-86.9	32.6	✅ PASS
Quartile coefficient of dispersion	stat_qcod	-162	-162	27	✅ PASS
Energy	stat_energy	8.96e+07	8.96e+07	5.3e+06	✅ PASS
Root mean square	stat_rms	15.8	15.8	0.3	✅ PASS

Test 7.B: Daubechies 3

Configuration: HHH level 2, rot-inv avg

Feature	Code	Calc	Ref	Tol	Status
Mean	stat_mean	-0.0406	-0.0406	0.0051	✅ PASS
Variance	stat_var	422	422	11	✅ PASS
Skewness	stat_skew	-0.0112	-0.0112	0.0027	✅ PASS
(Excess) kurtosis	stat_kurt	5.45	5.45	0.09	✅ PASS
Median	stat_median	-0.0164	-0.0164	0.0013	✅ PASS
Minimum	stat_min	-203	-203	3	✅ PASS
10th percentile	stat_p10	-20.6	-20.6	0.4	✅ PASS
90th percentile	stat_p90	20.4	20.4	0.4	✅ PASS
Maximum	stat_max	201	201	4	✅ PASS
Interquartile range	stat_iqr	16.3	16.3	0.2	✅ PASS
Range	stat_range	404	404	7	✅ PASS
Mean absolute deviation	stat_mad	13.4	13.4	0.2	✅ PASS
Robust mean absolute deviation	stat_rmad	7.2	7.2	0.1	✅ PASS
Median absolute deviation	stat_medad	13.4	13.4	0.2	✅ PASS
Coefficient of variation	stat_cov	-506	-506	149	✅ PASS
Quartile coefficient of dispersion	stat_qcod	-684	-684	130	✅ PASS
Energy	stat_energy	1.51e+08	1.51e+08	7e+06	✅ PASS
Root mean square	stat_rms	20.6	20.6	0.3	✅ PASS

Test 8.B: Simoncelli

Configuration: B map level 1

Feature	Code	Calc	Ref	Tol	Status
Mean	stat_mean	0.32	0.32	0.059	✅ PASS
Variance	stat_var	1.81e+03	1.81e+03	70	✅ PASS
Skewness	stat_skew	-0.0719	-0.0719	0.0163	✅ PASS
(Excess) kurtosis	stat_kurt	7.64	7.64	0.33	✅ PASS
Median	stat_median	-0.00194	-0.00947	0.0107	✅ PASS
Minimum	stat_min	-411	-411	5	✅ PASS
10th percentile	stat_p10	-36.6	-36.5	1.3	✅ PASS
90th percentile	stat_p90	38.1	38.1	1.3	✅ PASS
Maximum	stat_max	374	374	3	✅ PASS
Interquartile range	stat_iqr	25.5	25.5	0.4	✅ PASS
Range	stat_range	785	785	6	✅ PASS
Mean absolute deviation	stat_mad	25.3	25.3	0.6	✅ PASS
Robust mean absolute deviation	stat_rmad	11.7	11.7	0.3	✅ PASS
Median absolute deviation	stat_medad	25.3	25.3	0.6	✅ PASS
Coefficient of variation	stat_cov	133	134	27	✅ PASS
Energy	stat_energy	6.48e+08	6.48e+08	3.9e+07	✅ PASS
Root mean square	stat_rms	42.5	42.5	0.9	✅ PASS

Test 9.B: Simoncelli

Configuration: B map level 2

Feature	Code	Calc	Ref	Tol	Status
Mean	stat_mean	2.68	2.68	0.22	✅ PASS
Variance	stat_var	5.49e+03	5.49e+03	220	✅ PASS
Skewness	stat_skew	-0.0858	-0.0858	0.0107	✅ PASS
(Excess) kurtosis	stat_kurt	5.58	5.58	0.18	✅ PASS
Median	stat_median	0.233	0.233	0.046	✅ PASS
Minimum	stat_min	-605	-605	2	✅ PASS
10th percentile	stat_p10	-65.9	-65.9	2.2	✅ PASS
90th percentile	stat_p90	82.9	82.8	1.8	✅ PASS
Maximum	stat_max	471	471	13	✅ PASS
Interquartile range	stat_iqr	41.4	41	1	✅ PASS
Range	stat_range	1.08e+03	1.08e+03	20	✅ PASS
Mean absolute deviation	stat_mad	45.1	45.1	1.1	✅ PASS
Robust mean absolute deviation	stat_rmad	21	21	0.5	✅ PASS
Median absolute deviation	stat_medad	45	45	1.1	✅ PASS
Coefficient of variation	stat_cov	27.7	27.7	20.4	✅ PASS
Quartile coefficient of dispersion	stat_qcod	47.4	47.4	20.7	✅ PASS
Energy	stat_energy	1.97e+09	1.97e+09	1.4e+08	✅ PASS
Root mean square	stat_rms	74.1	74.1	1.6	✅ PASS

Known Deviations

2D Configuration (Config A) Not Implemented

The following tests check filter performance in 2D mode (Config A). These are skipped because Pictologics is purely a 3D radiomics library.

Tests 1.A - 9.A: 2D versions of the above tests.