Florian Thamm

Building Brains: Subvolume Recombination for Data Augmentation in Large Vessel Occlusion Detection

Ischemic strokes are often caused by large vessel occlusions (LVOs), which can be visualized and diagnosed with Computed Tomography Angiography scans. As time is brain, a fast, accurate and automated diagnosis of these scans is desirable. Human readers compare the left and right hemispheres in their assessment of strokes. A large training data set is required for a standard deep learning-based model to learn this strategy from data. As labeled medical data in this field is rare, other approaches need to be developed. To both include the prior knowledge of side comparison and increase the amount of training data, we propose an augmentation method that generates artificial training samples by recombining vessel tree segmentations of the hemispheres or hemisphere subregions from different patients. The subregions cover vessels commonly affected by LVOs, namely the internal carotid artery (ICA) and middle cerebral artery (MCA). In line with the augmentation scheme, we use a 3D-DenseNet fed with task-specific input, fostering a side-by-side comparison between the hemispheres. Furthermore, we propose an extension of that architecture to process the individual hemisphere subregions. All configurations predict the presence of an LVO, its side, and the affected subregion. We show the effect of recombination as an augmentation strategy in a 5-fold cross validated ablation study. We enhanced the AUC for patient-wise classification regarding the presence of an LVO of all investigated architectures. For one variant, the proposed method improved the AUC from 0.73 without augmentation to 0.89. The best configuration detects LVOs with an AUC of 0.91, LVOs in the ICA with an AUC of 0.96, and in the MCA with 0.91 while accurately predicting the affected side.

https://arxiv.org/pdf/2205.02848.pdf 

Can you tell which one is fake?

No? Don’t worry*, radiologists neither can 😉 Check out our most recent work “SyNCCT” published at MICCAI to see how we synthesized CT images from angiography scans.

SyNCCT: Synthetic Non-contrast Images of the Brain from Single-Energy Computed Tomography Angiography

By injecting contrast agent during a CT acquisition, the vascular system can be enhanced. This acquisition type is known as CT Angiography (CTA). However, due to typically lower dose levels of CTA scans compared to non-contrast CT acquisitions (NCCT) and the employed reconstruction designed specifically for vessel reconstruction, soft tissue contrast in the brain parenchyma is usually subpar. Hence, an NCCT scan is preferred for the visualization of such tissue. We propose SyNCCT, an approach which synthesizes NCCT images from the CTA domain by removing enhanced vessel structures and improving soft tissue contrast. Contrary to virtual non-contrast (VNC) images based on dual energy scans, which target the physically accurate removal of iodine rather than generating a realistic NCCT with improved gray/white matter separation, our approach only requires a conventional single-energy acquisition. By design, our method integrates prior domain knowledge and employs residual learning as well as a discriminator to achieve perceptual realism. In our data set of patients with ischemic stroke, the absolute differences in automatic ASPECT scoring, which rates early signs of an occlusion in the anterior circulation on a scale from 0 (most severe) to 10 (no signs), was 0.78 ± 0.75 (median of 1) when comparing our SyNCCT to the real NCCT images. Qualitatively, realistic appearance of the images was confirmed by means of a Turing test with a radiologist, who classified 64% of 64 (32 real, 32 generated) images correctly. Two other physicians classified 65% correctly, on average.

https://www.springerprofessional.de/syncct-synthetic-non-contrast-images-of-the-brain-from-single-en/19692102

*And by the way, the left one was fake 😉

VirtualDSA++: Automated Segmentation, Vessel Labeling, Occlusion Detection and Graph Search on CT-Angiography Data

Computed Tomography Angiography (CTA) is one of the most commonly used modalities in the diagnosis of cerebrovascular diseases like ischemic strokes. Usually, the anatomy of interest in ischemic stroke cases is the Circle of Willis and its peripherals, the cerebral arteries, as these vessels are the most prominent candidates for occlusions. The diagnosis of occlusions in these vessels remains challenging, not only because of the large amount of surrounding vessels but also due to the large number of anatomical variants. We propose a fully automated image processing and visualization pipeline, which provides a full segmentation and modelling of the cerebral arterial tree for CTA data. The model itself enables the interactive masking of unimportant vessel structures e.g. veins like the Sinus Sagittalis, and the interactive planning of shortest paths meant to be used to prepare further treatments like a mechanical thrombectomy. Additionally, the algorithm automatically labels the cerebral arteries (Middle Cerebral Artery left and right, Anterior Cerebral Artery, Posterior Cerebral Artery left and right) and detects occlusions or interruptions in these vessels. The proposed pipeline does not require a prior non-contrast CT scan and achieves a comparable segmentation appearance as in a Digital Subtraction Angiography (DSA).

https://diglib.eg.org/bitstream/handle/10.2312/vcbm20201181/151-155.pdf 

A 1minute Teaser 😉

Video: https://www.youtube.com/embed/m1KaOnsYTqQ?enablejsapi=1&autoplay=0&cc_load_policy=0&cc_lang_pref=&iv_load_policy=1&loop=0&modestbranding=1&rel=0&fs=1&playsinline=0&autohide=2&theme=dark&color=red&controls=1&

And here is more Material

Watch the playlist with 3 videos on youtube https://youtu.be/b_IshmarO7E?list=PLJgm15h1F7z5pvrb6qHB9Z0QHbcALefQj

Video: https://www.youtube.com/embed/b_IshmarO7E?enablejsapi=1&listType=playlist&list=PLJgm15h1F7z5pvrb6qHB9Z0QHbcALefQj&autoplay=0&cc_load_policy=0&cc_lang_pref=&iv_load_policy=1&loop=0&modestbranding=1&rel=0&fs=1&playsinline=0&autohide=2&theme=dark&color=red&controls=1&