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158 results on '"Hawkes, D.J."'

6. Disease Progression Modeling in Chronic Obstructive Pulmonary Disease

Author

Young, A.L., Bragman, F.J.S., Rangelov, B., Han, M.K., Galban, C.J., Lynch, D.A., Hawkes, D.J., Ginneken, B. van, Alexander, D.C., Hurst, J.R., Young, A.L., Bragman, F.J.S., Rangelov, B., Han, M.K., Galban, C.J., Lynch, D.A., Hawkes, D.J., Ginneken, B. van, Alexander, D.C., and Hurst, J.R.

Abstract

Contains fulltext : 220761.pdf (Publisher’s version ) (Closed access), Rationale: The decades-long progression of chronic obstructive pulmonary disease (COPD) renders identifying different trajectories of disease progression challenging.Objectives: To identify subtypes of patients with COPD with distinct longitudinal progression patterns using a novel machine-learning tool called "Subtype and Stage Inference" (SuStaIn) and to evaluate the utility of SuStaIn for patient stratification in COPD.Methods: We applied SuStaIn to cross-sectional computed tomography imaging markers in 3,698 Global Initiative for Chronic Obstructive Lung Disease (GOLD) 1-4 patients and 3,479 controls from the COPDGene (COPD Genetic Epidemiology) study to identify subtypes of patients with COPD. We confirmed the identified subtypes and progression patterns using ECLIPSE (Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints) data. We assessed the utility of SuStaIn for patient stratification by comparing SuStaIn subtypes and stages at baseline with longitudinal follow-up data.Measurements and Main Results: We identified two trajectories of disease progression in COPD: a "Tissue-->Airway" subtype (n = 2,354, 70.4%), in which small airway dysfunction and emphysema precede large airway wall abnormalities, and an "Airway-->Tissue" subtype (n = 988, 29.6%), in which large airway wall abnormalities precede emphysema and small airway dysfunction. Subtypes were reproducible in ECLIPSE. Baseline stage in both subtypes correlated with future FEV1/FVC decline (r = -0.16 [P < 0.001] in the Tissue-->Airway group; r = -0.14 [P = 0.011] in the Airway-->Tissue group). SuStaIn placed 30% of smokers with normal lung function at elevated stages, suggesting imaging changes consistent with early COPD. Individuals with early changes were 2.5 times more likely to meet COPD diagnostic criteria at follow-up.Conclusions: We demonstrate two distinct patterns of disease progression in COPD using SuStaIn, likely representing different endotypes. One third of healthy sm

Published
2020

7. Measurement and analysis of brain deformation during neurosurgery

Author

Hartkens, T., Hill, D.L.G., Castellano-Smith, A.D., Hawkes, D.J., Maurer, C.R., Martin, Jr. A.J., Hall, W.A., Liu, H., and Truwit, C.L.

Subjects
Brain damage, Magnetic resonance imaging, Business, Electronics, Electronics and electrical industries, Health care industry
Abstract

Recent studies have shown that the surface of the brain is deformed by up to 20 mm after the skull is opened during neurosurgery, which could lead to substantial error in commercial image-guided surgery systems. We quantitatively analyze the intraoperative brain deformation of 24 subjects to investigate whether simple rules can describe or predict the deformation. Interventional magnetic resonance images acquired at the start and end of the procedure are registered nonrigidly to obtain deformation values throughout the brain. Deformation patterns are investigated quantitatively with respect to the location and magnitude of deformation, and to the distribution and principal direction of the displacements. We also measure the volume change of the lateral ventricles by manual segmentation. Our study indicates that brain shift occurs predominantly in the hemisphere ipsi-lateral to the craniotomy, and that there is more brain deformation during resection procedures than during biopsy or functional procedures. However, the brain deformation patterns are extremely complex in this group of subjects. This paper quantitatively demonstrates that brain deformation occurs not only at the surface, but also in deeper brain structure, and that the principal direction of displacement does not always correspond with the direction of gravity. Therefore, simple computational algorithms that utilize limited intraoperative information (e.g., brain surface shift) will not always accurately predict brain deformation at the lesion. Index Terms--Interventional MRI, intraoperative brain deformation, nonrigid image registration.

Published
2003

9. Measures of folding applied to the development of the human fetal brain

Author

Batchelor, Ph.G., Smith, A.D. Castellano, Hill, D.L.G., Hawkes, D.J., Cox, T.C.S., and Dean, A.F.

Subjects
Fetal brain -- Medical examination, Diagnostic imaging -- Research, Brain -- Abnormalities, Business, Electronics, Electronics and electrical industries, Health care industry
Abstract

Previous work has suggested the existence of differences between the cerebral cortex of normal individuals, and those of patients with diseases such as epilepsy and schizophrenia. These shape abnormalities may be of developmental origin. Improved shape measures could provide useful tools for neuroscience research and patient diagnosis. We consider the theoretically desirable properties of measures of brain shape. We have implemented seven measures, three from the neuroscience literature, and four new to this field. Three of the measures are zero-order and four are second-order with respect to the surface. We validate the measures using simple geometrical shapes, and a collection of magnetic resonance scans of ten histologically normal ex vivo fetal brains with gestational ages from 19-42 weeks. We then apply the measures to MR scans from two histologically abnormal ex vivo brains. We demonstrate that our implementation of the measures is sensitive to anatomical variability rather than to the discreteness of the image data. All the measures were sensitive to changes in shape during fetal development. Several of the measures could distinguish between the normal and abnormal fetal brains. We propose a multivariate approach to studying the shape of the cerebral cortex, in which both zero-order and second-order measures are used to quantify folding. Index Terms--Brain folding, cortical shape, curvature, development, fetal.

Published
2002

12. Nonrigid Registration Using Free-Form Deformations: Application to Breast MR Images

Author

Rueckert, D., Sonoda, L.I., Hayes, C., Hill, D.L.G., Leach, M.O., and Hawkes, D.J.

Subjects
Diagnostic imaging -- Methods, Medical imaging equipment -- Design and construction, Mammography -- Methods, Magnetic resonance imaging -- Methods, Business, Electronics, Electronics and electrical industries, Health care industry
Abstract

In this paper we present a new approach for the nonrigid registration of contrast-enhanced breast MRI. A hierarchical transformation model of the motion of the breast has been developed. The global motion of the breast is modeled by an affine transformation while the local breast motion is described by a free-form deformation (FFD) based on B-splines. Normalized mutual information is used as a voxel-based similarity measure which is insensitive to intensity changes as a result of the contrast enhancement. Registration is achieved by minimizing a cost function, which represents a combination of the cost associated with the smoothness of the transformation and the cost associated with the image similarity. The algorithm has been applied to the fully automated registration of three-dimensional (3-D) breast MRI in volunteers and patients. In particular, we have compared the results of the proposed nonrigid registration algorithm to those obtained using rigid and affine registration techniques. The results clearly indicate that the nonrigid registration algorithm is much better able to recover the motion and deformation of the breast than rigid or affine registration algorithms.

Published
1999

17. 3D volume reconstruction from serial breast specimen radiographs for mapping between histology and 3D whole specimen imaging

Author

Mertzanidou, T., Hipwell, J.H., Reis, S., Hawkes, D.J., Ehteshami Bejnordi, B., Dalmis, M.U., Vreemann, S., Platel, B., Laak, J.A.W.M. van der, Karssemeijer, N., Hermsen, M., Bult, P., and Mann, R.M.

Subjects
Women's cancers Radboud Institute for Molecular Life Sciences [Radboudumc 17], Women's cancers Radboud Institute for Health Sciences [Radboudumc 17]
Abstract

Contains fulltext : 170535.pdf (Publisher’s version ) (Open Access) PURPOSE: In breast imaging, radiological in vivo images, such as x-ray mammography and magnetic resonance imaging (MRI), are used for tumor detection, diagnosis, and size determination. After excision, the specimen is typically sliced into slabs and a small subset is sampled. Histopathological imaging of the stained samples is used as the gold standard for characterization of the tumor microenvironment. A 3D volume reconstruction of the whole specimen from the 2D slabs could facilitate bridging the gap between histology and in vivo radiological imaging. This task is challenging, however, due to the large deformation that the breast tissue undergoes after surgery and the significant undersampling of the specimen obtained in histology. In this work, we present a method to reconstruct a coherent 3D volume from 2D digital radiographs of the specimen slabs. METHODS: To reconstruct a 3D breast specimen volume, we propose the use of multiple target neighboring slices, when deforming each 2D slab radiograph in the volume, rather than performing pairwise registrations. The algorithm combines neighborhood slice information with free-form deformations, which enables a flexible, nonlinear deformation to be computed subject to the constraint that a coherent 3D volume is obtained. The neighborhood information provides adequate constraints, without the need for any additional regularization terms. RESULTS: The volume reconstruction algorithm is validated on clinical mastectomy samples using a quantitative assessment of the volume reconstruction smoothness and a comparison with a whole specimen 3D image acquired for validation before slicing. Additionally, a target registration error of 5 mm (comparable to the specimen slab thickness of 4 mm) was obtained for five cases. The error was computed using manual annotations from four observers as gold standard, with interobserver variability of 3.4 mm. Finally, we illustrate how the reconstructed volumes can be used to map histology images to a 3D specimen image of the whole sample (either MRI or CT). CONCLUSIONS: Qualitative and quantitative assessment has illustrated the benefit of using our proposed methodology to reconstruct a coherent specimen volume from serial slab radiographs. To our knowledge, this is the first method that has been applied to clinical breast cases, with the goal of reconstructing a whole specimen sample. The algorithm can be used as part of the pipeline of mapping histology images to ex vivo and ultimately in vivo radiological images of the breast.

Published
2017

26. The effect of motion correction on pharmacokinetic parameter estimation in dynamic-contrast-enhanced MRI.

Author

Melbourne, A., Hipwell, J., Modat, M., Mertzanidou, T., Huisman, H.J., Ourselin, S., Hawkes, D.J., Melbourne, A., Hipwell, J., Modat, M., Mertzanidou, T., Huisman, H.J., Ourselin, S., and Hawkes, D.J.

Abstract

Contains fulltext : 96425.pdf (Publisher’s version ) (Open Access), A dynamic-contrast-enhanced magnetic resonance imaging (DCE-MRI) dataset consists of many imaging frames, often acquired both before and after contrast injection. Due to the length of time spent acquiring images, patient motion is likely and image re-alignment or registration is required before further analysis such as pharmacokinetic model fitting. Non-rigid image registration procedures may be used to correct motion artefacts; however, a careful choice of registration strategy is required to reduce misregistration artefacts associated with enhancing features. This work investigates the effect of registration on the results of model-fitting algorithms for 52 DCE-MR mammography cases for 14 patients. Results are divided into two sections: a comparison of registration strategies in which a DCE-MRI-specific algorithm is preferred in 50% of cases, followed by an investigation of parameter changes with known applied deformations, inspecting the effect of magnitude and timing of motion artefacts. Increased motion magnitude correlates with increased model-fit residual and is seen to have a strong influence on the visibility of strongly enhancing features. Motion artefacts in images close to the contrast agent arrival have a disproportionate effect on discrepancies in parameter estimation. The choice of algorithm, magnitude of motion and timing of the motion are each shown to influence estimated pharmacokinetic parameters even when motion magnitude is small.

Published
2011

48. Comparison and evaluation of retrospective intermodality brain image registration techniques

Author

West, J., Fitzpatrick, J.M., Wang, M.Y., Dawant, B.M., Maurer Jr., C.R., Kessler, R.M., Maciunas, R.J., Barillot, C., Lemoine, D., Collignon, A., Maes, F., Suetens, P., Vandermeulen, D., van den Elsen, P.A., Napel, S., Sumanaweera, T.S., Harkness, B., Hemler, P.F., Hill, D.L.G., Hawkes, D.J., Studholme, C., Maintz, J.B.A., Viergever, M.A., Malandain, G., Pennac, X., Noz, Marilyn E., Maguire Jr., Gerald Q., Pollack, M., Pelizzari, C.A., Robb, R.A., Hanson, D., Woods, R.P., West, J., Fitzpatrick, J.M., Wang, M.Y., Dawant, B.M., Maurer Jr., C.R., Kessler, R.M., Maciunas, R.J., Barillot, C., Lemoine, D., Collignon, A., Maes, F., Suetens, P., Vandermeulen, D., van den Elsen, P.A., Napel, S., Sumanaweera, T.S., Harkness, B., Hemler, P.F., Hill, D.L.G., Hawkes, D.J., Studholme, C., Maintz, J.B.A., Viergever, M.A., Malandain, G., Pennac, X., Noz, Marilyn E., Maguire Jr., Gerald Q., Pollack, M., Pelizzari, C.A., Robb, R.A., Hanson, D., and Woods, R.P.

Abstract

QC 20111110

Published
1997
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