arXiv subjects

Craig Engstrom

Publications and source records attributed to Craig Engstrom.

9 recordsLinked to original sources

arXiv2026

SAMRI-3D: Adapting SAM2 for 3D MRI Segmentation with Global Volume Tokens

Foundation models such as Segment Anything Model 2 (SAM2) have transformed natural-image and video segmentation, and recent work has begun adapting them to medical imaging. These adaptations, however, are largely general-purpose models that treat MRI as one modality among many; large-scale, MRI-specific modelling and benchmarking remain limited, even though MRI's low soft-tissue contrast leaves many boundaries effectively invisible on individual slices. We present SAMRI-3D, a benchmark and method for 3D MRI segmentation with SAM2. The SAMRI-3D benchmark is the largest MRI-only evaluation to date - 10,392 volumes from 34 datasets (27 public, 7 in-house) spanning 12 anatomical domains and 10+ sequences, with explicit seen/unseen splits. Freezing the image encoder and fine-tuning only the lightweight decoder and memory modules raises mean Dice from 0.58 (zero-shot SAM2) to 0.76, surpassing recent SAM-based medical models (SAMed-2 0.69, Medical-SAM2 0.49, SAM-Med3D 0.37) with strong statistical significance. To target invisible boundaries, we introduce Global Volume Tokens (GVT): persistent memory tokens trained with a Truncated Signed Distance Field (TSDF) reconstruction objective that is discarded at inference (zero added cost). This full model, SAMRI-3D, attains the best accuracy (0.78) and lowest variance across all 34 datasets and, uniquely, shows no drop on 8 held-out datasets (0.79 unseen vs. 0.78 seen); per-sequence analysis confirms the TSDF objective helps most where per-slice contrast is weakest. We will release the benchmark, code, and models in this paper.

cs.CV↗

arXiv2025

SAMRI: Segment Any MRI

Summary: SAMRI is an MRI-specialized adaptation of the Segment Anything Model achieving superior whole-body MRI segmentation, particularly for small and clinically critical structures, through box and point prompts for rapid annotation. Purpose: Existing SAM adaptations treat MRI as a generic modality, overlooking variable tissue contrast, intensity inhomogeneity, and clinically important small structures. We propose an MRI-specialized foundation model with strong whole-body segmentation and zero-shot generalization for direct use on any MRI annotation task. Methods: SAMRI fine-tunes only the mask decoder of SAM (ViT-B/16), keeping encoders frozen to preserve pretrained representations and eliminate redundant passes-reducing training time by 94%, trainable parameters by 96%, and FLOPs by ~99% versus full-model retraining. Training used 1.1 million 2D slice-mask pairs from 30 datasets spanning 47 targets, T1/T2/FLAIR/DWI contrasts, and whole-body anatomy, with focal-Dice loss and bounding-box (with optional point) prompts. Sizes were stratified by mask area (small: <0.5%; medium: 0.5-3.5%; large: >3.5%), and significance assessed by the Wilcoxon signed-rank test. Results: SAMRI with box+point prompts achieved mean DSC 0.87 +/- 0.11 across 47 targets, outperforming MedSAM (0.74 +/- 0.24) by 17.6% (p < 0.05), with largest gains for small (+42.4%) and medium (+26.9%) structures. On six zero-shot datasets, SAMRI achieved mean DSC 0.85, outperforming baselines. Inference requires only ~4.5 GB VRAM through an interactive interface on standard hardware. Conclusion: Decoder-only fine-tuning on a large, MRI-specific corpus delivers superior whole-body segmentation with strong zero-shot generalization, particularly for small and clinically salient structures. Public code, pretrained models, and an interactive interface make SAMRI deployable for MRI segmentation research and clinical workflows.

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arXiv2023

Evidence-aware multi-modal data fusion and its application to total knee replacement prediction

Deep neural networks have been widely studied for predicting a medical condition, such as total knee replacement (TKR). It has shown that data of different modalities, such as imaging data, clinical variables and demographic information, provide complementary information and thus can improve the prediction accuracy together. However, the data sources of various modalities may not always be of high quality, and each modality may have only partial information of medical condition. Thus, predictions from different modalities can be opposite, and the final prediction may fail in the presence of such a conflict. Therefore, it is important to consider the reliability of each source data and the prediction output when making a final decision. In this paper, we propose an evidence-aware multi-modal data fusion framework based on the Dempster-Shafer theory (DST). The backbone models contain an image branch, a non-image branch and a fusion branch. For each branch, there is an evidence network that takes the extracted features as input and outputs an evidence score, which is designed to represent the reliability of the output from the current branch. The output probabilities along with the evidence scores from multiple branches are combined with the Dempster's combination rule to make a final prediction. Experimental results on the public OA initiative (OAI) dataset for the TKR prediction task show the superiority of the proposed fusion strategy on various backbone models.

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arXiv2022

Automated anomaly-aware 3D segmentation of bones and cartilages in knee MR images from the Osteoarthritis Initiative

In medical image analysis, automated segmentation of multi-component anatomical structures, which often have a spectrum of potential anomalies and pathologies, is a challenging task. In this work, we develop a multi-step approach using U-Net-based neural networks to initially detect anomalies (bone marrow lesions, bone cysts) in the distal femur, proximal tibia and patella from 3D magnetic resonance (MR) images of the knee in individuals with varying grades of osteoarthritis. Subsequently, the extracted data are used for downstream tasks involving semantic segmentation of individual bone and cartilage volumes as well as bone anomalies. For anomaly detection, the U-Net-based models were developed to reconstruct the bone profiles of the femur and tibia in images via inpainting so anomalous bone regions could be replaced with close to normal appearances. The reconstruction error was used to detect bone anomalies. A second anomaly-aware network, which was compared to anomaly-na\"ive segmentation networks, was used to provide a final automated segmentation of the femoral, tibial and patellar bones and cartilages from the knee MR images containing a spectrum of bone anomalies. The anomaly-aware segmentation approach provided up to 58% reduction in Hausdorff distances for bone segmentations compared to the results from the anomaly-na\"ive segmentation networks. In addition, the anomaly-aware networks were able to detect bone lesions in the MR images with greater sensitivity and specificity (area under the receiver operating characteristic curve [AUC] up to 0.896) compared to the anomaly-na\"ive segmentation networks (AUC up to 0.874).

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arXiv2022

Structure Guided Manifolds for Discovery of Disease Characteristics

In medical image analysis, the subtle visual characteristics of many diseases are challenging to discern, particularly due to the lack of paired data. For example, in mild Alzheimer's Disease (AD), brain tissue atrophy can be difficult to observe from pure imaging data, especially without paired AD and Cognitively Normal ( CN ) data for comparison. This work presents Disease Discovery GAN ( DiDiGAN), a weakly-supervised style-based framework for discovering and visualising subtle disease features. DiDiGAN learns a disease manifold of AD and CN visual characteristics, and the style codes sampled from this manifold are imposed onto an anatomical structural "blueprint" to synthesise paired AD and CN magnetic resonance images (MRIs). To suppress non-disease-related variations between the generated AD and CN pairs, DiDiGAN leverages a structural constraint with cycle consistency and anti-aliasing to enforce anatomical correspondence. When tested on the Alzheimer's Disease Neuroimaging Initiative ( ADNI) dataset, DiDiGAN showed key AD characteristics (reduced hippocampal volume, ventricular enlargement, and atrophy of cortical structures) through synthesising paired AD and CN scans. The qualitative results were backed up by automated brain volume analysis, where systematic pair-wise reductions in brain tissue structures were also measured

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arXiv2022

Transformer Compressed Sensing via Global Image Tokens

Convolutional neural networks (CNN) have demonstrated outstanding Compressed Sensing (CS) performance compared to traditional, hand-crafted methods. However, they are broadly limited in terms of generalisability, inductive bias and difficulty to model long distance relationships. Transformer neural networks (TNN) overcome such issues by implementing an attention mechanism designed to capture dependencies between inputs. However, high-resolution tasks typically require vision Transformers (ViT) to decompose an image into patch-based tokens, limiting inputs to inherently local contexts. We propose a novel image decomposition that naturally embeds images into low-resolution inputs. These Kaleidoscope tokens (KD) provide a mechanism for global attention, at the same computational cost as a patch-based approach. To showcase this development, we replace CNN components in a well-known CS-MRI neural network with TNN blocks and demonstrate the improvements afforded by KD. We also propose an ensemble of image tokens, which enhance overall image quality and reduces model size. Supplementary material is available: https://github.com/uqmarlonbran/TCS.git

cs.CV↗

arXiv2021

Automated volumetric and statistical shape assessment of cam-type morphology of the femoral head-neck region from 3D magnetic resonance images

Femoroacetabular impingement (FAI) cam morphology is routinely assessed using two-dimensional alpha angles which do not provide specific data on cam size characteristics. The purpose of this study is to implement a novel, automated three-dimensional (3D) pipeline, CamMorph, for segmentation and measurement of cam volume, surface area and height from magnetic resonance (MR) images in patients with FAI. The CamMorph pipeline involves two processes: i) proximal femur segmentation using an approach integrating 3D U-net with focused shape modelling (FSM); ii) use of patient-specific anatomical information from 3D FSM to simulate healthy femoral bone models and pathological region constraints to identify cam bone mass. Agreement between manual and automated segmentation of the proximal femur was evaluated with the Dice similarity index (DSI) and surface distance measures. Independent t-tests or Mann-Whitney U rank tests were used to compare the femoral head volume, cam volume, surface area and height data between female and male patients with FAI. There was a mean DSI value of 0.964 between manual and automated segmentation of proximal femur volume. Compared to female FAI patients, male patients had a significantly larger mean femoral head volume (66.12cm3 v 46.02cm3, p<0.001). Compared to female FAI patients, male patients had a significantly larger mean cam volume (1136.87mm3 v 337.86mm3, p<0.001), surface area (657.36mm2 v 306.93mm2 , p<0.001), maximum-height (3.89mm v 2.23mm, p<0.001) and average-height (1.94mm v 1.00mm, p<0.001). Automated analyses of 3D MR images from patients with FAI using the CamMorph pipeline showed that, in comparison with female patients, male patients had significantly greater cam volume, surface area and height.

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arXiv2020

Manipulating Medical Image Translation with Manifold Disentanglement

Medical image translation (e.g. CT to MR) is a challenging task as it requires I) faithful translation of domain-invariant features (e.g. shape information of anatomical structures) and II) realistic synthesis of target-domain features (e.g. tissue appearance in MR). In this work, we propose Manifold Disentanglement Generative Adversarial Network (MDGAN), a novel image translation framework that explicitly models these two types of features. It employs a fully convolutional generator to model domain-invariant features, and it uses style codes to separately model target-domain features as a manifold. This design aims to explicitly disentangle domain-invariant features and domain-specific features while gaining individual control of both. The image translation process is formulated as a stylisation task, where the input is "stylised" (translated) into diverse target-domain images based on style codes sampled from the learnt manifold. We test MDGAN for multi-modal medical image translation, where we create two domain-specific manifold clusters on the manifold to translate segmentation maps into pseudo-CT and pseudo-MR images, respectively. We show that by traversing a path across the MR manifold cluster, the target output can be manipulated while still retaining the shape information from the input.

cs.CV↗

arXiv2020

Generalisable 3D Fabric Architecture for Streamlined Universal Multi-Dataset Medical Image Segmentation

Data scarcity is common in deep learning models for medical image segmentation. Previous works proposed multi-dataset learning, either simultaneously or via transfer learning to expand training sets. However, medical image datasets have diverse-sized images and features, and developing a model simultaneously for multiple datasets is challenging. This work proposes Fabric Image Representation Encoding Network (FIRENet), a universal architecture for simultaneous multi-dataset segmentation and transfer learning involving arbitrary numbers of dataset(s). To handle different-sized image and feature, a 3D fabric module is used to encapsulate many multi-scale sub-architectures. An optimal combination of these sub-architectures can be implicitly learnt to best suit the target dataset(s). For diverse-scale feature extraction, a 3D extension of atrous spatial pyramid pooling (ASPP3D) is used in each fabric node for a fine-grained coverage of rich-scale image features. In the first experiment, FIRENet performed 3D universal bone segmentation of multiple musculoskeletal datasets of the human knee, shoulder and hip joints and exhibited excellent simultaneous multi-dataset segmentation performance. When tested for transfer learning, FIRENet further exhibited excellent single dataset performance (when pre-training on a prostate dataset), as well as significantly improved universal bone segmentation performance. The following experiment involves the simultaneous segmentation of the 10 Medical Segmentation Decathlon (MSD) challenge datasets. FIRENet demonstrated good multi-dataset segmentation results and inter-dataset adaptability of highly diverse image sizes. In both experiments, FIRENet's streamlined multi-dataset learning with one unified network that requires no hyper-parameter tuning.

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