Data Augmentation and Transfer Learning to Improve Generalizability of an Automated Prostate Segmentation Model
Abstract
Materials and Methods
Study Population
Dataset | No. of Patients | MRI System Vendor(s)a | Field Strengthb | Median x/y Resolution (mm) | Slice Thickness or Gap (mm) | TR (ms) | TE (ms) | FOV (mm2) | No. of T2-Weighted Slices Acquired |
---|---|---|---|---|---|---|---|---|---|
Training dataset | |||||||||
Cohort 1 | 365 | Philips Healthcare (100) | 3 T (100) | 0.27 | 3 | 4434 | 120 | 140 × 140 | 26 |
Cohort 2 | 283 | Philips Healthcare (100) | 3 T (100) | 0.27 | 3 | 4434 | 120 | 140 × 140 | 26 |
Testing dataset | |||||||||
Independent cohort | 166 | Philips Healthcare (100) | 3 T (100) | 0.27 | 3 | 4434 | 120 | 140 × 140 | 26 |
External center 1 | 42 | Siemens Healthcare (90) and GE Healthcare (10) | 3 T (98) and 1.5 T (2) | 0.57 | 3 | 3460 | 137 | 200X200 | 28 |
External center 2 | 75 | Siemens Healthcare (100) | 3 T (100) | 0.56 | 3 | 3730 | 121 | NA | 28 |
External center 3 | 10 | Philips Healthcare (100) | 3 T (100) | 0.54 | 3 | 7203 | 160 | 180X180 | 26 |
External center 4 | 55 | Philips Healthcare (100) | 3 T (100) | 0.46 | 3 | 4726 | 80 | 200 × 200 | 24 |
External center 5 | 58 | GE Healthcare (100) | 3 T (100) | 0.43 | 3 | 3662 | 105 | 220 × 220 | 35 |
Note—x/y Resolution = in-plane pixel resolution of multiparametric MR images, NA = not available.
Ground Truth Segmentation
Convolutional Neural Network Architecture and Data Augmentation
Training and Fine-Tuning
Cohort or Center | Total No. of Samples | No. of Training Samples | No. of Validation Samples | No. of Testing Samples | DSC for Whole Prostate Test Set, Mean (Range) | ||
---|---|---|---|---|---|---|---|
Without Augmentation | With DST | With Fine-Tuning | |||||
Independent cohort | 166 | 66 | 17 | 83 | 91.0 (65.5–95.5) | 90.9 (65.8–95.5) | 91.2 (64.9–95.3) |
External center 1 | 42 | 17 | 4 | 21 | 84.7 (62.5–92.1) | 90.4 (77.6–93.9) | 90.9 (83.4–94.7) |
External center 2 | 75 | 30 | 8 | 37 | 89.8 (74.6–94.2) | 91.6 (84.3–94.8) | 92.0 (86.5–94.6) |
External center 3 | 10 | 4 | 1 | 5 | 76.2 (58.0–89.4) | 86.3 (81.7–91.3) | 89.6 (85.5–93.3) |
External center 4 | 55 | 22 | 6 | 27 | 89.3 (68.6–94.6) | 92.6 (77.7–95.4) | 92.9 (83.1–95.7) |
External center 5 | 58 | 23 | 6 | 29 | 86.4 (64.1–93.4) | 90.6 (87.8–93.6) | 91.4 (88.7–93.8) |
All | 406 | 162 | 42 | 202 | 88.8 (58.0–95.5) | 91.0 (65.8–95.5) | 91.5 (64.9–95.7) |
Note—DSC = Dice similarity coefficient, DST = deep stack transformation.
Results
Demographic and Clinical Data | Cohort 1 (n = 365) | Cohort 2 (n = 283) |
---|---|---|
Age (y), mean (range) | 68 (18–89) | 66 (46–81) |
Weight (kg), mean (range) | 85 (30–146) | 88 (44–139) |
Whole prostate size (cm3), mean (range) | 70 (16–265) | 44 (10–255) |
Transition zone size (cm3), mean (range) | 45 (3–222) | 20 (4–279) |
Highest PI-RADS score, no. (%) of patients | ||
1 | 80 (22) | 4 (1) |
2 | 38 (10) | 7 (2) |
3 | 96 (26) | 13 (5) |
4 | 102 (28) | 124 (44) |
5 | 49 (13) | 135 (48) |
Note—PI-RADS = Prostate Imaging Reporting and Data System.
Cohort or Center | Total No. of Samples | No. of Training Samples | No. of Validation Samples | No. of Testing Samples | DSC for Transition Zone Test Set, Mean (Range) | ||
---|---|---|---|---|---|---|---|
Without Augmentation | With DST | With Fine-Tuning | |||||
Independent cohort | 166 | 66 | 17 | 83 | 88.4 (49.3–96.1) | 88.7 (52.0–95.9) | 89.4 (57.3–96.0) |
External center 1 | 42 | 17 | 4 | 21 | 82.9 (63.0–90.3) | 86.9 (69.9–93.3) | 88.5 (77.1–95.0) |
External center 2 | 75 | 30 | 8 | 37 | 84.9 (22.9–93.3) | 89.2 (83.7–94.5) | 90.7 (85.6–94.9) |
External center 3 | 10 | 4 | 1 | 5 | 65.2 (46.0–78.6) | 73.5 (66.8–83.7) | 87.4 (82.0–91.9) |
External center 4 | 55 | 22 | 6 | 27 | 84.2 (58.7–92.2) | 90.5 (75.3–95.3) | 92.0 (80.9–95.7) |
External center 5 | 58 | 23 | 6 | 29 | 81.8 (61.0–90.3) | 86.2 (68.2–93.2) | 88.1 (74.7–94.0) |
All | 406 | 162 | 42 | 202 | 85.1 (22.9–96.1) | 88.1 (52.0–95.9) | 89.7 (57.3–96.0) |
Note—DSC = Dice similarity coefficient, DST = deep stack transformation.
Metric | Without Augmentation | With Augmentation | With Fine-Tuning |
---|---|---|---|
Volume similarity | |||
Whole prostate | |||
Center 1 | 0.20 (−0.06 to 0.68) | 0.00 (−0.12 to 0.17) | 0.08 (−0.03 to 0.18) |
Center 2 | 0.07 (−0.11 to 0.49) | 0.01 (−0.17 to 0.30) | 0.03 (−0.10 to 0.24) |
Center 3 | 0.37 (0.09–0.76) | 0.04 (−0.04 to 0.14) | 0.02 (−0.05 to 0.07) |
Center 4 | 0.13 (−0.04 to 0.63) | 0.03 (−0.04 to 0.44) | 0.04 (−0.06 to 0.33) |
Center 5 | 0.18 (−0.10 to 0.70) | 0.04 (−0.15 to 0.17) | 0.01 (−0.18 to 0.12) |
Independent | 0.02 (−0.17 to 0.34) | 0.00 (−0.20 to 0.26) | −0.02 (−0.20 to 0.10) |
Transition zone | |||
Center 1 | 0.15 (−0.17 to 0.74) | 0.04 (−0.17 to 0.59) | 0.09 (−0.12 to 0.42) |
Center 2 | 0.16 (−0.22 to 1.53) | 0.06 (−0.23 to 0.25) | 0.01 (−0.24 to 0.20) |
Center 3 | 0.62 (0.38–1.04) | 0.42 (0.26–0.53) | 0.13 (0.03–0.29) |
Center 4 | 0.19 (−0.35 to 0.76) | 0.01 (−0.39 to 0.17) | −0.01 (−0.31 to 0.09) |
Center 5 | 0.15 (−0.32 to 0.73) | −0.08 (−0.58 to 0.24) | −0.01 (−0.40 to 0.23) |
Independent | 0.01 (−0.51 to 0.38) | −0.02 (−0.47 to 0.28) | −0.04 (−0.49 to 0.26) |
Hausdorff distance | |||
Whole prostate | |||
Center 1 | 7.86 (4.00–18.79) | 5.80 (3.61–13.93) | 5.43 (3.00–10.25) |
Center 2 | 6.79 (3.16–16.09) | 5.96 (2.83–14.28) | 5.37 (3.00–10.82) |
Center 3 | 10.59 (6.00–16.00) | 10.15 (4.12–18.11) | 6.01 (4.12–7.81) |
Center 4 | 6.97 (3.16–16.09) | 5.45 (3.16–9.00) | 5.47 (3.00–9.16) |
Center 5 | 7.28 (3.16–15.81) | 6.03 (3.32–9.43) | 5.64 (4.00–10.49) |
Independent | 5.40 (3.00–20.25) | 5.39 (2.45–10.95) | 5.35 (2.83–11.79) |
Transition zone | |||
Center 1 | 6.80 (3.16–14.04) | 5.19 (3.00–12.00) | 4.71 (3.00–11.00) |
Center 2 | 7.37 (3.61–24.45) | 6.09 (3.16–17.55) | 6.06 (3.16–13.19) |
Center 3 | 11.53 (7.28–16.28) | 9.59 (5.83–12.00) | 4.81 (3.32–6.08) |
Center 4 | 8.56 (3.16–25.50) | 5.58 (3.16–11.04) | 4.86 (3.00–11.87) |
Center 5 | 8.18 (4.00–18.44) | 6.70 (3.16–14.00) | 6.04 (3.16–12.00) |
Independent | 5.12 (2.24–12.21) | 5.00 (2.00–12.04) | 4.85 (2.24–12.21) |
Mean surface distance | |||
Whole prostate | |||
Center 1 | 1.69 (0.77–3.97) | 1.02 (0.73–2.55) | 0.94 (0.58–1.82) |
Center 2 | 1.25 (0.63–4.31) | 0.97 (0.50–2.19) | 0.90 (0.50–1.68) |
Center 3 | 2.49 (1.09–4.61) | 1.49 (0.87–2.42) | 1.05 (0.69–1.33) |
Center 4 | 1.36 (0.53–3.79) | 0.86 (0.56–2.67) | 0.82 (0.58–1.97) |
Center 5 | 1.50 (0.64–5.26) | 1.02 (0.63–1.46) | 0.92 (0.52–1.46) |
Independent | 0.95 (0.45–3.37) | 0.96 (0.44–3.35) | 0.92 (0.47–3.46) |
Transition zone | |||
Center 1 | 1.49 (0.68–4.66) | 1.07 (0.59–3.72) | 0.92 (0.54–2.82) |
Center 2 | 1.54 (0.68–7.93) | 1.07 (0.59–2.51) | 0.91 (0.55–1.72) |
Center 3 | 2.92 (1.91–5.08) | 2.18 (1.45–2.62) | 0.97 (0.66–1.41) |
Center 4 | 1.66 (0.69–5.23) | 0.91 (0.51–1.94) | 0.73 (0.53–1.27) |
Center 5 | 1.66 (0.83–4.76) | 1.22 (0.69–2.54) | 1.03 (0.63–1.85) |
Independent | 0.94 (0.40–3.34) | 0.91 (0.42–3.21) | 0.85 (0.42–2.72) |
Standard surface distance | |||
Whole prostate | |||
Center 1 | 1.73 (0.77–4.64) | 1.04 (0.68–2.58) | 0.97 (0.68–1.72) |
Center 2 | 1.29 (0.69–4.11) | 1.01 (0.59–2.38) | 0.94 (0.61–1.69) |
Center 3 | 2.35 (1.08–3.96) | 1.58 (0.85–2.97) | 1.11 (0.72–1.50) |
Center 4 | 1.46 (0.58–4.62) | 0.90 (0.64–1.95) | 0.91 (0.63–1.54) |
Center 5 | 1.44 (0.67–4.98) | 1.05 (0.68–1.67) | 0.96 (0.67–1.76) |
Independent | 0.99 (0.58–3.19) | 0.97 (0.56–2.02) | 0.93 (0.57–1.96) |
Transition zone | |||
Center 1 | 1.48 (0.67–3.50) | 0.97 (0.64–2.79) | 0.90 (0.57–2.88) |
Center 2 | 1.47 (0.70–5.90) | 1.1 (0.64–3.40) | 1.02 (0.62–1.96) |
Center 3 | 2.70 (1.53–4.42) | 2.13 (1.19–2.48) | 0.94 (0.64–1.42) |
Center 4 | 1.72 (0.67–5.65) | 0.97 (0.59–3.05) | 0.78 (0.59–1.28) |
Center 5 | 1.56 (0.81–4.60) | 1.20 (0.65–2.60) | 1.06 (0.64–2.22) |
Independent | 0.96 (0.54–2.41) | 0.93 (0.54–2.41) | 0.89 (0.55–2.52) |
Discussion
Conclusion
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