58 research outputs found
Deeper Image Quality Transfer: Training Low-Memory Neural Networks for 3D Images
In this paper we address the memory demands that come with the processing of
3-dimensional, high-resolution, multi-channeled medical images in deep
learning. We exploit memory-efficient backpropagation techniques, to reduce the
memory complexity of network training from being linear in the network's depth,
to being roughly constant permitting us to elongate deep architectures
with negligible memory increase. We evaluate our methodology in the paradigm of
Image Quality Transfer, whilst noting its potential application to various
tasks that use deep learning. We study the impact of depth on accuracy and show
that deeper models have more predictive power, which may exploit larger
training sets. We obtain substantially better results than the previous
state-of-the-art model with a slight memory increase, reducing the
root-mean-squared-error by . Our code is publicly available.Comment: Accepted in: MICCAI 201
Feasibility of Data-Driven, Model-Free Quantitative MRI Protocol Design: Application to Brain and Prostate Diffusion-Relaxation Imaging
Brain; Protocol design; Quantitative MRI (qMRI)Cerebro; Diseño de protocolo; Resonancia magnética cuantitativa (qMRI)Cervell; Disseny del protocol; Ressonà ncia magnÚtica quantitativa (qMRI)Purpose: We investigate the feasibility of data-driven, model-free quantitative MRI (qMRI) protocol design on in vivo brain and prostate diffusion-relaxation imaging (DRI).
Methods: We select subsets of measurements within lengthy pilot scans, without identifying tissue parameters for which to optimise for. We use the âselect and retrieve via direct upsamplingâ (SARDU-Net) algorithm, made of a selector, identifying measurement subsets, and a predictor, estimating fully-sampled signals from the subsets. We implement both using artificial neural networks, which are trained jointly end-to-end. We deploy the algorithm on brain (32 diffusion-/T1-weightings) and prostate (16 diffusion-/T2-weightings) DRI scans acquired on three healthy volunteers on two separate 3T Philips systems each. We used SARDU-Net to identify sub-protocols of fixed size, assessing reproducibility and testing sub-protocols for their potential to inform multi-contrast analyses via the T1-weighted spherical mean diffusion tensor (T1-SMDT, brain) and hybrid multi-dimensional MRI (HM-MRI, prostate) models, for which sub-protocol selection was not optimised explicitly.
Results: In both brain and prostate, SARDU-Net identifies sub-protocols that maximise information content in a reproducible manner across training instantiations using a small number of pilot scans. The sub-protocols support T1-SMDT and HM-MRI multi-contrast modelling for which they were not optimised explicitly, providing signal quality-of-fit in the top 5% against extensive sub-protocol comparisons.
Conclusions: Identifying economical but informative qMRI protocols from subsets of rich pilot scans is feasible and potentially useful in acquisition-time-sensitive applications in which there is not a qMRI model of choice. SARDU-Net is demonstrated to be a robust algorithm for data-driven, model-free protocol design.This project was funded by the Engineering and Physical Sciences Research Council (EPSRC EP/R006032/1, M020533/1, G007748, I027084, N018702). This project has received funding under the European Unionâs Horizon 2020 research and innovation programme under grant agreement No. 634541 and 666992, and from: Rosetrees Trust (United Kingdom, funding FG); Prostate Cancer United Kingdom Targeted Call 2014 (Translational Research St.2, project reference PG14-018-TR2); Cancer Research United Kingdom grant ref. A21099; Spinal Research (United Kingdom), Wings for Life (Austria), Craig H. Neilsen Foundation (United States) for jointly funding the INSPIRED study; Wings for Life (#169111); United Kingdom Multiple Sclerosis Society (grants 892/08 and 77/2017); the Department of Healthâs National Institute for Health Research (NIHR) Biomedical Research Centres and UCLH NIHR Biomedical Research Centre; Champalimaud Centre for the Unknown, Lisbon (Portugal); European Unionâs Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 101003390. FG is currently supported by the investigator-initiated PREdICT study at the Vall dâHebron Institute of Oncology (Barcelona), funded by AstraZeneca and CRIS Cancer Foundation
Progressive Subsampling for Oversampled Data -- Application to Quantitative MRI
We present PROSUB: PROgressive SUBsampling, a deep learning based, automated
methodology that subsamples an oversampled data set (e.g. multi-channeled 3D
images) with minimal loss of information. We build upon a recent dual-network
approach that won the MICCAI MUlti-DIffusion (MUDI) quantitative MRI
measurement sampling-reconstruction challenge, but suffers from deep learning
training instability, by subsampling with a hard decision boundary. PROSUB uses
the paradigm of recursive feature elimination (RFE) and progressively
subsamples measurements during deep learning training, improving optimization
stability. PROSUB also integrates a neural architecture search (NAS) paradigm,
allowing the network architecture hyperparameters to respond to the subsampling
process. We show PROSUB outperforms the winner of the MUDI MICCAI challenge,
producing large improvements >18% MSE on the MUDI challenge sub-tasks and
qualitative improvements on downstream processes useful for clinical
applications. We also show the benefits of incorporating NAS and analyze the
effect of PROSUB's components. As our method generalizes to other problems
beyond MRI measurement selection-reconstruction, our code is
https://github.com/sbb-gh/PROSU
Disease Knowledge Transfer across Neurodegenerative Diseases
We introduce Disease Knowledge Transfer (DKT), a novel technique for
transferring biomarker information between related neurodegenerative diseases.
DKT infers robust multimodal biomarker trajectories in rare neurodegenerative
diseases even when only limited, unimodal data is available, by transferring
information from larger multimodal datasets from common neurodegenerative
diseases. DKT is a joint-disease generative model of biomarker progressions,
which exploits biomarker relationships that are shared across diseases. Our
proposed method allows, for the first time, the estimation of plausible,
multimodal biomarker trajectories in Posterior Cortical Atrophy (PCA), a rare
neurodegenerative disease where only unimodal MRI data is available. For this
we train DKT on a combined dataset containing subjects with two distinct
diseases and sizes of data available: 1) a larger, multimodal typical AD (tAD)
dataset from the TADPOLE Challenge, and 2) a smaller unimodal Posterior
Cortical Atrophy (PCA) dataset from the Dementia Research Centre (DRC), for
which only a limited number of Magnetic Resonance Imaging (MRI) scans are
available. Although validation is challenging due to lack of data in PCA, we
validate DKT on synthetic data and two patient datasets (TADPOLE and PCA
cohorts), showing it can estimate the ground truth parameters in the simulation
and predict unseen biomarkers on the two patient datasets. While we
demonstrated DKT on Alzheimer's variants, we note DKT is generalisable to other
forms of related neurodegenerative diseases. Source code for DKT is available
online: https://github.com/mrazvan22/dkt.Comment: accepted at MICCAI 2019, 13 pages, 5 figures, 2 table
Degenerative adversarial neuroimage nets for brain scan simulations: Application in ageing and dementia
© 2021 The Author(s). Published by Elsevier B.V. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY), https://creativecommons.org/licenses/by/4.0/Accurate and realistic simulation of high-dimensional medical images has become an important research area relevant to many AI-enabled healthcare applications. However, current state-of-the-art approaches lack the ability to produce satisfactory high-resolution and accurate subject-specific images. In this work, we present a deep learning framework, namely 4D-Degenerative Adversarial NeuroImage Net (4D-DANI-Net), to generate high-resolution, longitudinal MRI scans that mimic subject-specific neurodegeneration in ageing and dementia. 4D-DANI-Net is a modular framework based on adversarial training and a set of novel spatiotemporal, biologically-informed constraints. To ensure efficient training and overcome memory limitations affecting such high-dimensional problems, we rely on three key technological advances: i) a new 3D training consistency mechanism called Profile Weight Functions (PWFs), ii) a 3D super-resolution module and iii) a transfer learning strategy to fine-tune the system for a given individual. To evaluate our approach, we trained the framework on 9852 T1-weighted MRI scans from 876 participants in the Alzheimer's Disease Neuroimaging Initiative dataset and held out a separate test set of 1283 MRI scans from 170 participants for quantitative and qualitative assessment of the personalised time series of synthetic images. We performed three evaluations: i) image quality assessment; ii) quantifying the accuracy of regional brain volumes over and above benchmark models; and iii) quantifying visual perception of the synthetic images by medical experts. Overall, both quantitative and qualitative results show that 4D-DANI-Net produces realistic, low-artefact, personalised time series of synthetic T1 MRI that outperforms benchmark models.Peer reviewe
Learning Morphological Feature Perturbations for Calibrated Semi-Supervised Segmentation
We propose MisMatch, a novel consistency-driven semi-supervised segmentation
framework which produces predictions that are invariant to learnt feature
perturbations. MisMatch consists of an encoder and a two-head decoders. One
decoder learns positive attention to the foreground regions of interest (RoI)
on unlabelled images thereby generating dilated features. The other decoder
learns negative attention to the foreground on the same unlabelled images
thereby generating eroded features. We then apply a consistency regularisation
on the paired predictions. MisMatch outperforms state-of-the-art
semi-supervised methods on a CT-based pulmonary vessel segmentation task and a
MRI-based brain tumour segmentation task. In addition, we show that the
effectiveness of MisMatch comes from better model calibration than its
supervised learning counterpart
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