| Literature DB >> 35170063 |
Dónal M McSweeney1,2, Edward G Henderson1,2, Marcel van Herk1,2, Jamie Weaver3, Paul A Bromiley4, Andrew Green1,2, Alan McWilliam1,2.
Abstract
BACKGROUND: Skeletal muscle segmentation is an important procedure for assessing sarcopenia, an emerging imaging biomarker of patient frailty. Data annotation remains the bottleneck for training deep learning auto-segmentation models.Entities:
Keywords: deep learning; sarcopenia; segmentation
Mesh:
Year: 2022 PMID: 35170063 PMCID: PMC9313817 DOI: 10.1002/mp.15533
Source DB: PubMed Journal: Med Phys ISSN: 0094-2405 Impact factor: 4.506
FIGURE 1Experimental workflow. Fourfold cross‐validation was performed. (a) Training sets of varying sizes were sub‐sampled from the resulting training & validation split. During training, the excluded fold was used as validation data. Images used for our observer study were kept independent and formed the test set. (b) Four pretext tasks were used for pre‐training: image classification, image segmentation, unsupervised image reconstruction, and self‐supervised jigsaws. (c) Weights from pre‐trained models were transferred to a FCN‐ResNet101 trained to segment skeletal muscle on each subset until convergence. Randomly initialized models were also trained on each subset for comparison. (d) Model predictions and observer masks were evaluated on the same test set () with expert gold‐standard delineations
FIGURE 2An example CT slice from our inter‐observer study, with multiple observer delineations in different colors
FIGURE 3Mean DSC, of CNN predictions evaluated against expert gold‐standard, as a function of training set size. Error bars represent confidence intervals. Mean observer variation (; standard error (SE)) was found by calculating mean DSC for all observer segmentations against the clinical expert's
FIGURE 4Mean RMS‐DTA (in cm), of CNN predictions evaluated against expert gold‐standard, as a function of training set size. Error bars represent confidence intervals. Note, results from the sixteen randomly initialized models at have been omitted as the mean RMS‐DTA was cm. Mean observer variation (; standard error (SE)) was found by calculating mean RMS‐DTA for all observer segmentations against the clinical expert's
Resulting p‐values from performing Dunnett's tests to identify significant differences in DSC (Top) & RMS‐DTA (Bottom) between model predictions and observer delineations (control=observer delineations). Models that outperformed observers are indicated in bold and models that were significantly worse are underlined
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| Rand. Init. |
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| 0.038 |
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| Classification |
| 0.777 |
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| Segmentation | 0.999 | 0.036 |
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| Jigsaw |
| 0.885 |
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| Reconstruction |
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| 0.746 |
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| Rand. Init. |
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| 0.999 | 1.000 | 1.000 | 0.971 | 0.833 |
| Classification |
| 0.077 | 0.999 | 0.864 | 0.785 | 0.714 | 0.482 |
| Segmentation |
| 0.395 | 0.992 | 0.826 | 0.644 | 0.550 | 0.440 |
| Jigsaw |
| 0.245 | 0.999 | 0.864 | 0.785 | 0.714 | 0.482 |
| Reconstruction |
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| 0.983 | 1.000 | 1.000 | 0.996 | 0.892 |
FIGURE 5(a) Difference in skeletal muscle density extracted from model predictions and expert gold‐standard. Defined as prediction—gold‐standard. Note that results from the 16 randomly initialized models at have been omitted as the mean difference was HU. (b) Difference in skeletal muscle area between predictions and gold‐standard, defined as above. Dotted lines indicate mean observer difference and the associated standard error ()
Resulting p‐values from performing Dunnett's tests to identify significant differences in SMD (Top) & SMA (Bottom) between model predictions and expert delineations (control=expert delineations). Models that extracted significantly less accurate muscle characteristics are underlined
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| Rand. Init. |
| 0.306 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| Classification | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| Segmentation | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| Jigsaw | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| Reconstruction | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
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Rand. Init. | 0.641 | 0.655 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| Classification | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| Segmentation | 0.999 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| Jigsaw | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| Reconstruction | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
| Jigsaw | Classification | Rand. Init. | Segmentation | Reconstruction | |
|---|---|---|---|---|---|
| Jigsaw | 1.0 | 0.2694 | **** | **** | **** |
| Classification | 0.2694 | 1.0 | **** | **** | **** |
| Rand. Init. | **** | **** | 1.0 | **** | **** |
| Segmentation | **** | **** | **** | 1.0 | **** |
| Reconstruction | **** | **** | **** | **** | 1.0 |
| Jigsaw | Classification | Rand. Init. | Segmentation | Reconstruction | |
|---|---|---|---|---|---|
| Jigsaw | 1.0 | 0.5638 | ***** | **** | **** |
| Classification | 0.5638 | 1.0 | **** | **** | **** |
| Rand. Init. | **** | **** | 1.0 | **** | 0.9588 |
| Segmentation | **** | **** | **** | 1.0 | **** |
| Reconstruction | **** | **** | 0.9588 | **** | 1.0 |
| Jigsaw | Classification | Rand. Init. | Segmentation | Reconstruction | |
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| Jigsaw | 1.0 | 0.4806 | *** | 0.9723 | *** |
| Classification | 0.4806 | 1.0 | *** | 0.4553 | *** |
| Rand. Init. | *** | *** | 1.0 | *** | *** |
| Segmentation | 0.9723 | 0.4553 | *** | 1.0 | *** |
| Reconstruction | *** | *** | *** | *** | 1.0 |
| Jigsaw | Classification | Rand. Init. | Segmentation | Reconstruction | |
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| Jigsaw | 1.0 | 0.7182 | *** | 0.1848 | *** |
| Classification | 0.7182 | 1.0 | *** | 0.3653 | *** |
| Rand. Init. | *** | *** | 1.0 | *** | *** |
| Segmentation | 0.1848 | 0.3653 | *** | 1.0 | *** |
| Reconstruction | *** | *** | *** | *** | 1.0 |
| Jigsaw | Classification | Rand. Init. | Segmentation | Reconstruction | |
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| Jigsaw | 1.0 | 0.5641 | **** | 0.9997 | **** |
| Classification | 0.5641 | 1.0 | **** | 0.5645 | **** |
| Rand. Init. | **** | **** | 1.0 | **** | 0.1332 |
| Segmentation | 0.9997 | 0.5645 | **** | 1.0 | **** |
| Reconstruction | **** | **** | 0.1332 | **** | 1.0 |
| Jigsaw | Classification | Rand. Init. | Segmentation | Reconstruction | |
|---|---|---|---|---|---|
| Jigsaw | 1.0 | 0.7497 | 0.0521 | 0.1863 | **** |
| Classification | 0.7497 | 1.0 | 0.0184 | 0.3398 | **** |
| Rand. Init. | 0.0521 | 0.0184 | 1.0 | **** | 0.0100 |
| Segmentation | 0.1863 | 0.3398 | **** | 1.0 | **** |
| Reconstruction | **** | **** | 0.0100 | **** | 1.0 |
| Jigsaw | Classification | Rand. Init. | Segmentation | Reconstruction | |
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| Jigsaw | 1.0 | 0.7402 | 0.0191 | 0.4232 | **** |
| Classification | 0.7402 | 1.0 | 0.0392 | 0.2392 | **** |
| Rand. Init. | 0.0191 | 0.0392 | 1.0 | 0.0012 | 0.0958 |
| Segmentation | 0.4232 | 0.2392 | **** | 1.0 | **** |
| Reconstruction | **** | **** | 0.0958 | **** | 1.0 |
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| Jigsaw | **** | **** | **** | **** | 0.0234 | 0.0805 |
| Classification | **** | **** | **** | **** | 0.0111 | 0.2547 |
| Rand. Init. | **** | **** | **** | **** | **** | 0.2187 |
| Segmentation | **** | **** | **** | **** | **** | 0.1606 |
| Reconstruction | **** | **** | **** | **** | **** | 0.0312 |