Evaluating nnU-Net for Type B Aortic Dissection

segmentation on CTA images

Yicun Li1, Chengzhi Gui1, Xin Li1, Tongyun Chen2, Xiquan Song2,
Qingliang Chen2*, Xingwei An1*
1. Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
2. Tianjin Chest Hospital, Tianjin, China

November 11, 2023

1. BACKGROUND

Aortic Dissection
Aortic Dissection (AD) is a condition
characterized by a tear in the tunica intima of the
aorta [3], leading to the entry of blood into the
vessel wall and the separation of the aortic
lumen into True Lumen (TL) and False Lumen
(FL).
Stanford Classification
Clinically, AD is classified into Type A aortic
dissection (TAAD) involving the ascending
aorta, and Type B aortic dissection (TBAD)
involving the descending aorta or aortic arch,
Figure 1: Aortic dissection and Stanford classification according to the Stanford classification [6].

[3]Thubrikar M J, Agali P, Robicsek F. Wall stress as a possible mechanism for the development of transverse intimal tears in aortic dissections[J]. Journal of medical
engineering & technology, 1999, 23(4): 127-134.
2 103-113.
[6]LeMaire S A, Russell L. Epidemiology of thoracic aortic dissection[J]. Nature reviews cardiology, 2011, 8(2):
1. BACKGROUND
nnU-Net: "no new"U-Net
nnU-Net [15] is a U-Net-based framework for medical
image segmentation. It focuses on non-structural
factors, including preprocessing, training parameters,
inference, and post-processing, while automatically
configuring these settings. nnU-Net has outperformed
most existing methods on 23 public datasets in
international biomedical segmentation challenges.

Li’s work [16] has demonstrated that nnU-Net

effectively segments healthy human aorta near the heart,
fulfilling the preoperative requirements in a clinical
setting.
Figure 2: nnU-Net [15]

[15]Isensee F, Jaeger P F, Kohl S A A, et al. nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation[J]. Nature methods, 2021,
18(2): 203-211.
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[16]Li F, Sun L, Lam K Y, et al. Segmentation of human aorta using 3D nnU-net-oriented deep learning[J]. Review of Scientific Instruments, 2022, 93(11).
2. DATASETS
ImageTBAD dataset [17]
The dataset consisted of CTA images from 100
patients with TBAD, 68 were annotated with
three substructures: TL, FL, and FLT(false lumen
thrombus), while 32 cases without FLT were
labeled with two substructures: TL and FL.
Figure 3: ImageTBAD dataset [17]

AVT dataset [18]

(a multicenter dataset segmented Whole aorta)
Only three case were TBAD: R1, R2, and R8.
The original whole aorta Ground Truth (GT) was
adjusted to maintain consistency with the
ImageTBAD dataset.
Figure 4: Adjusted R1, R2, R8 in AVT dataset

[17]Yao Z, Xie W, Zhang J, et al. ImageTBAD: A 3D computed tomography angiography image dataset for automatic segmentation of type-B aortic dissection[J].
Frontiers in Physiology, 2021, 12: 732711.
[18]Radl L, Jin Y, Pepe A, et al. AVT: Multicenter aortic vessel tree CTA dataset collection with ground truth 4
segmentation masks[J]. Data in brief, 2022, 40: 107801.
3. METHOD
1.Preprocessing
The nnU-Net employs various preprocessing techniques, including cropping, resampling, and
normalization, based on the median shape, distribution of spacings, and intensity distribution of CTA
data.
2.Network
The network architecture and training
hyperparameters of nnU-Net are adaptively
generated based on the size and voxel spacing of
the data, as well as the available GPU memory.
In this study, we selected the 3D full
resolution U-Net , which is a 6-layer U-
shaped architecture.
3.The loss function Figure 5: nnU-Net Network Architecture

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4. IMPLEMENTATION
Five-fold Cross-validation No post-processing

Removing all but the largest

component decreased the dice score for
TL.
Some severe cases where the TL diameter
was too small to be segmented in certain
slices, leading to the TL being split into
upper and lower parts. In such cases,
removing all but the largest component
would result in the loss of a significant
number of correctly segmented voxels.

Figure 6: Loss curves during training

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5. RESULTS
Evaluation Metrics
Dice score: Hausdorff distance:

Table 1: Comparisons of TBAD segmentation results

TL FL FLT Aorta
Method Dice HD Dice HD Dice HD Dice HD
Best 0.86 288.4 0.78 597.5 978.6 0.91 300.2
0.29
baseline[17] (±0.08) (±426) (±0.21) (±1117.3) (±2887.3) (±0.04) (±273.6)
0.94 37.9 0.90 47.3 0.42 153.3 0.94 43.2
nnU-Net
(±0.05) (±45.6) (±0.14) (±56.1) (±0.30) (±95.7) (±0.05) (±48.7)
The term "Best baseline" refers to the highest score among all baseline methods mentioned in the ImageTBAD dataset
paper. The Dice scores for FLT are only calculated for images where GT includes FLT (The mean FLT dice of the 100
images was 0.52, and excluding the 32 images with no FLT that had a dice count of 1, the mean FLT dice of the
remaining 68 images was 0.29, and the standard deviation could not be acquired).
[17]Yao Z, Xie W, Zhang J, et al. ImageTBAD: A 3D computed tomography angiography image dataset for automatic segmentation of type-B aortic dissection[J].
Frontiers in Physiology, 2021, 12: 732711.
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5. RESULTS

Figure 8: Correlation analysis between

Dice of FLT and FLT volume of Ground Truth.
In Figure 4, we observe a Strong Correlation
between FLT volume and Dice of FLT. This indicates
that as the FLT volume increases, the Dice of FLT
Figure 7: Visual comparisons of TBAD segmentation results.
(Green labels: TL; yellow labels: FL; brown labels: FLT. Blue boxes indicate
tends to be higher.
successful segmentation, yellow circles indicate poor segmentation, and red
circles indicate erroneous segmentation.)
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6. EXTERNAL VALIDATION

Table 3: External Validation

Results
TL FL FLT Aorta
Case Dice HD Dice HD Dice HD Dice HD
R1 0.80 30.0 0.85 26.1 \ \ 0.95 14.0
R2 0.94 13.5 0.91 32.2 0.86 54.2 0.92 13.5
R8 0.97 7.2 0.98 3.8 \ \ 0.97 7.2
Mean 0.90 16.9 0.91 20.7 0.86 54.2 0.95 11.6

Figure 9: Visual external validation results.

(Green labels: TL; yellow labels: FL; brown labels: FLT. Yellow circles indicate
poor segmentation, and red circles indicate erroneous segmentation.)

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7. DISCUSSION
 Conclusions
In this study, we employed nnU-Net for the segmentation of Type B Aortic Dissection on the ImageTBAD dataset. The
segmentation results obtained using nnU-Net outperformed the baseline methods mentioned in the original paper.
Furthermore, we applied the nnU-Net model trained on the ImageTBAD dataset to segment TBAD cases in the AVT
dataset. nnU-Net successfully accomplishes the task of TBAD segmentation and exhibits good generalization
capabilities.
 Improvement
The suboptimal segmentation of FLT can be attributed to the difficulty in segmenting small-volume FLT, which may be
related to the downsampling along the z-axis in nnU-Net. The inclusion of residual skip-connections in the nnU-Net
network might improve this outcome.

 Prospect
Currently, the majority of segmentation studies for AD utilize their own private datasets, We look forward to the release
of more openly accessible AD datasets, as this would significantly accelerate the progress of segmentation techniques in
the field.

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Thanks For Your Listening!
Yicun Li, Tianjin University
liyicun@tju.edu.cn

November 11, 2023

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