Jurgen Fripp | CSIRO - Academia.edu (original) (raw)
Papers by Jurgen Fripp
2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2008
... Original image on the left and image corrected with LEMS inhomogeneity correction algorithm .... more ... Original image on the left and image corrected with LEMS inhomogeneity correction algorithm ... segmentation of the anatomically complex paraspinal muscles from adjacent abdominal fat and viscera ... The results from the present atlas-based automated segmentation of the QL are ...
Frontiers in aging neuroscience, 2015
The basal forebrain degenerates in Alzheimer's disease (AD) and this process is believed to c... more The basal forebrain degenerates in Alzheimer's disease (AD) and this process is believed to contribute to the cognitive decline observed in AD patients. Impairment in spatial navigation is an early feature of the disease but whether basal forebrain dysfunction in AD is responsible for the impaired navigation skills of AD patients is not known. Our objective was to investigate the relationship between basal forebrain volume and performance in real space as well as computer-based navigation paradigms in an elderly cohort comprising cognitively normal controls, subjects with amnestic mild cognitive impairment and those with AD. We also tested whether basal forebrain volume could predict the participants' ability to perform allocentric- vs. egocentric-based navigation tasks. The basal forebrain volume was calculated from 1.5 T magnetic resonance imaging (MRI) scans, and navigation skills were assessed using the human analog of the Morris water maze employing allocentric, egocent...
18th International Conference on Pattern Recognition (ICPR'06), 2006
... Simon K. Warfield Departments of Radiology, Brigham and Women's Hospital, an... more ... Simon K. Warfield Departments of Radiology, Brigham and Women's Hospital, and Children's Hospital Boston, MA, USA warfield@bwh.harvard.edu ... 1999. [7] HC van Assen, MG Danilouchkine, AF Frangi, S. Or-das, JJ Westenberg, JH Reiber, and BP Lelieveldt. ...
Lecture Notes in Computer Science, 2005
This paper presents the creation of 3D statistical shape models of the knee bones and their use t... more This paper presents the creation of 3D statistical shape models of the knee bones and their use to embed information into a segmentation system for MRIs of the knee. We propose utilising the strong spatial relationship between the cartilages and the bones in the knee by embedding this information into the created models. This information can then be used to automate the initialisation of segmentation algorithms for the cartilages. The approach used to automatically generate the 3D statistical shape models of the bones is based on the point distribution model optimisation framework of Davies. Our implementation of this scheme uses a parameterized surface extraction algorithm, which is used as the basis for the optimisation scheme that automatically creates the 3D statistical shape models. The current approach is illustrated by generating 3D statistical shape models of the patella, tibia and femoral bones from a segmented database of the knee. The use of these models to embed spatial relationship information to aid in the automation of segmentation algorithms for the cartilages is then illustrated.
2007 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2007
... Simon K. Warfield 2 2 Harvard Medical School, Children's Hospital Boston, Boston... more ... Simon K. Warfield 2 2 Harvard Medical School, Children's Hospital Boston, Boston, USA StuartCrozier 3 3 School of ITEE, University of Queensland, Brisbane, Australia ABSTRACT ... Workshop on Model-Based 3D Image Analysis, Bombay, India, Jan. 1998, pp. 97–106. ...
Digital Image Computing: Techniques and Applications (DICTA'05)
Deformable models are a highly accurate and flexible approach to segmenting structures in medical... more Deformable models are a highly accurate and flexible approach to segmenting structures in medical images. The primary drawback of deformable models is that they are sensitive to initialisation, with accurate and robust results often requiring initialisation close to the true object in the image. Automatically obtaining a good initialisation is problematic for many structures in the body. The cartilages of the knee are a thin elastic material that cover the ends of the bone, absorbing shock and allowing smooth movement. The degeneration of these cartilages characterize the progression of osteoarthritis. The state of the art in the segmentation of the cartilage are 2D semi-automated algorithms. These algorithms require significant time and supervison by a clinical expert, so the development of an automatic segmentation algorithm for the cartilages is an important clinical goal. In this paper we present an approach towards this goal that allows us to automatically providing a good initialisation for deformable models of the patella cartilage, by utilising the strong spatial relationship of the cartilage to the underlying bone.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference, 2008
This study presents a novel method for the automatic segmentation of the quadratus lumborum (QL) ... more This study presents a novel method for the automatic segmentation of the quadratus lumborum (QL) muscle from axial magnetic resonance (MR) images using a hybrid scheme incorporating the use of non-rigid registration with probabilistic atlases (PAs) and geodesic active contours (GACs). The scheme was evaluated on an MR database of 7mm axial images of the lumbar spine from 20 subjects (fast bowlers and athletic controls). This scheme involved several steps, including (i) image pre-processing, (ii) generation of PAs for the QL, psoas (PS) and erector spinae+multifidus (ES+MT) muscles and (iii) segmentation, using 3D GACs initialized and constrained by the propagation of the PAs using non-rigid registration. Pre-processing of the images involved bias field correction based on local entropy minimization with a bicubic spline model and a reverse diffusion interpolation algorithm to increase the slice resolution to 0.98 x 0.98 x 1.75mm. The processed images were then registered (affine and...
2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2008
Users may download and print one copy of any publication from the public portal for the purpose... more Users may download and print one copy of any publication from the public portal for the purpose of private study or research. You may not further distribute the material or use it for any profit-making activity or commercial gain You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.
NeuroImage. Clinical, 2015
The brains of patients suffering from Alzheimer's disease (AD) have three classical pathologi... more The brains of patients suffering from Alzheimer's disease (AD) have three classical pathological hallmarks: amyloid-beta (Aβ) plaques, tau tangles, and neurodegeneration, including that of cholinergic neurons of the basal forebrain. However the relationship between Aβ burden and basal forebrain degeneration has not been extensively studied. To investigate this association, basal forebrain volumes were determined from magnetic resonance images of controls, subjects with amnestic mild cognitive impairment (aMCI) and AD patients enrolled in the longitudinal Alzheimer's Disease Neuroimaging Initiative (ADNI) and Australian Imaging, Biomarkers and Lifestyle (AIBL) studies. In the AIBL cohort, these volumes were correlated within groups to neocortical gray matter retention of Pittsburgh compound B (PiB) from positron emission tomography images as a measure of Aβ load. The basal forebrain volumes of AD and aMCI subjects were significantly reduced compared to those of control subjec...
2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2009
Pathologic processes active in early-stage knee joint osteoarthritis may also affect the integrit... more Pathologic processes active in early-stage knee joint osteoarthritis may also affect the integrity of the crescent-shaped fibrocartilagenous structures called menisci. Magnetic resonance imaging can allow the detection of these structural changes, however, large-scale clinical application remains limited by tedious and labor-intensive techniques for volumetric measurement. Towards automating these quantitative measurements, we have currently developed a scheme that allows the automatic
2012 9th IEEE International Symposium on Biomedical Imaging (ISBI), 2012
The accurate segmentation of the bone from Magnetic Resonance (MR) images of the hip is important... more The accurate segmentation of the bone from Magnetic Resonance (MR) images of the hip is important for clinical studies and drug trials into conditions like Osteoarthritis. This paper presents an automatic segmentation scheme that utilises a deformable model robust to different field of views by training shape priors from partial and full bone surfaces. The deformable model with these priors
Magnetic resonance in medicine : official journal of the Society of Magnetic Resonance in Medicine / Society of Magnetic Resonance in Medicine, Jan 30, 2015
To validate a fully automated scheme to extract biochemical information from the hip joint cartil... more To validate a fully automated scheme to extract biochemical information from the hip joint cartilages using MR T2 mapping images incorporating segmentation of co-registered three-dimensional Fast-Spin-Echo (3D-SPACE) images. Manual analyses of unilateral hip (3 Tesla) MR images of 24 asymptomatic volunteers were used to validate a 3D deformable model method for automated cartilage segmentation of SPACE scans, partitioning of the individual femoral and acetabular cartilage plates into clinically defined sub-regions and propagating these results to T2 maps to calculate region-wise T2 value statistics. Analyses were completed on a desktop computer (∼10 min per case). The mean voxel overlap between automated A and manual M segmentations of the cartilage volumes in the (clinically based) SPACE images was 73% (100×2|A∩M|/[|A|+|M|]). The automated and manual analyses demonstrated a relative difference error <10% in the median "T2 average signal" for each cartilage plate. The a...
2011 International Conference on Digital Image Computing: Techniques and Applications, 2011
The human cortex is a folded ribbon of neurons with a high inter-individual variability. It is a ... more The human cortex is a folded ribbon of neurons with a high inter-individual variability. It is a challenging structure to study especially when measuring small changes resulting from normal aging and neurodegenerative disorders such as Alzheimer's Disease (AD). Recent studies have proposed surface based approaches for statistical population comparison of cortical changes since such approaches better cope with the surfacic nature of the cortex. In this paper we present a new multi-scale EM-ICP registration that is embedded into a surfacebased approach. We compare this new registration algorithm with the shape context in the context of statistical population analysis. When comparing the cortical thickness between healthy elderly subjects to Alzheimer's disease patients, the new pipeline reduces the intra class variability while increasing the statistical power of the T-tests between both groups.
2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2008
... Original image on the left and image corrected with LEMS inhomogeneity correction algorithm .... more ... Original image on the left and image corrected with LEMS inhomogeneity correction algorithm ... segmentation of the anatomically complex paraspinal muscles from adjacent abdominal fat and viscera ... The results from the present atlas-based automated segmentation of the QL are ...
Frontiers in aging neuroscience, 2015
The basal forebrain degenerates in Alzheimer's disease (AD) and this process is believed to c... more The basal forebrain degenerates in Alzheimer's disease (AD) and this process is believed to contribute to the cognitive decline observed in AD patients. Impairment in spatial navigation is an early feature of the disease but whether basal forebrain dysfunction in AD is responsible for the impaired navigation skills of AD patients is not known. Our objective was to investigate the relationship between basal forebrain volume and performance in real space as well as computer-based navigation paradigms in an elderly cohort comprising cognitively normal controls, subjects with amnestic mild cognitive impairment and those with AD. We also tested whether basal forebrain volume could predict the participants' ability to perform allocentric- vs. egocentric-based navigation tasks. The basal forebrain volume was calculated from 1.5 T magnetic resonance imaging (MRI) scans, and navigation skills were assessed using the human analog of the Morris water maze employing allocentric, egocent...
18th International Conference on Pattern Recognition (ICPR'06), 2006
... Simon K. Warfield Departments of Radiology, Brigham and Women&amp;#x27;s Hospital, an... more ... Simon K. Warfield Departments of Radiology, Brigham and Women&amp;#x27;s Hospital, and Children&amp;#x27;s Hospital Boston, MA, USA warfield@bwh.harvard.edu ... 1999. [7] HC van Assen, MG Danilouchkine, AF Frangi, S. Or-das, JJ Westenberg, JH Reiber, and BP Lelieveldt. ...
Lecture Notes in Computer Science, 2005
This paper presents the creation of 3D statistical shape models of the knee bones and their use t... more This paper presents the creation of 3D statistical shape models of the knee bones and their use to embed information into a segmentation system for MRIs of the knee. We propose utilising the strong spatial relationship between the cartilages and the bones in the knee by embedding this information into the created models. This information can then be used to automate the initialisation of segmentation algorithms for the cartilages. The approach used to automatically generate the 3D statistical shape models of the bones is based on the point distribution model optimisation framework of Davies. Our implementation of this scheme uses a parameterized surface extraction algorithm, which is used as the basis for the optimisation scheme that automatically creates the 3D statistical shape models. The current approach is illustrated by generating 3D statistical shape models of the patella, tibia and femoral bones from a segmented database of the knee. The use of these models to embed spatial relationship information to aid in the automation of segmentation algorithms for the cartilages is then illustrated.
2007 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2007
... Simon K. Warfield 2 2 Harvard Medical School, Children&#x27;s Hospital Boston, Boston... more ... Simon K. Warfield 2 2 Harvard Medical School, Children&#x27;s Hospital Boston, Boston, USA StuartCrozier 3 3 School of ITEE, University of Queensland, Brisbane, Australia ABSTRACT ... Workshop on Model-Based 3D Image Analysis, Bombay, India, Jan. 1998, pp. 97–106. ...
Digital Image Computing: Techniques and Applications (DICTA'05)
Deformable models are a highly accurate and flexible approach to segmenting structures in medical... more Deformable models are a highly accurate and flexible approach to segmenting structures in medical images. The primary drawback of deformable models is that they are sensitive to initialisation, with accurate and robust results often requiring initialisation close to the true object in the image. Automatically obtaining a good initialisation is problematic for many structures in the body. The cartilages of the knee are a thin elastic material that cover the ends of the bone, absorbing shock and allowing smooth movement. The degeneration of these cartilages characterize the progression of osteoarthritis. The state of the art in the segmentation of the cartilage are 2D semi-automated algorithms. These algorithms require significant time and supervison by a clinical expert, so the development of an automatic segmentation algorithm for the cartilages is an important clinical goal. In this paper we present an approach towards this goal that allows us to automatically providing a good initialisation for deformable models of the patella cartilage, by utilising the strong spatial relationship of the cartilage to the underlying bone.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference, 2008
This study presents a novel method for the automatic segmentation of the quadratus lumborum (QL) ... more This study presents a novel method for the automatic segmentation of the quadratus lumborum (QL) muscle from axial magnetic resonance (MR) images using a hybrid scheme incorporating the use of non-rigid registration with probabilistic atlases (PAs) and geodesic active contours (GACs). The scheme was evaluated on an MR database of 7mm axial images of the lumbar spine from 20 subjects (fast bowlers and athletic controls). This scheme involved several steps, including (i) image pre-processing, (ii) generation of PAs for the QL, psoas (PS) and erector spinae+multifidus (ES+MT) muscles and (iii) segmentation, using 3D GACs initialized and constrained by the propagation of the PAs using non-rigid registration. Pre-processing of the images involved bias field correction based on local entropy minimization with a bicubic spline model and a reverse diffusion interpolation algorithm to increase the slice resolution to 0.98 x 0.98 x 1.75mm. The processed images were then registered (affine and...
2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2008
Users may download and print one copy of any publication from the public portal for the purpose... more Users may download and print one copy of any publication from the public portal for the purpose of private study or research. You may not further distribute the material or use it for any profit-making activity or commercial gain You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.
NeuroImage. Clinical, 2015
The brains of patients suffering from Alzheimer's disease (AD) have three classical pathologi... more The brains of patients suffering from Alzheimer's disease (AD) have three classical pathological hallmarks: amyloid-beta (Aβ) plaques, tau tangles, and neurodegeneration, including that of cholinergic neurons of the basal forebrain. However the relationship between Aβ burden and basal forebrain degeneration has not been extensively studied. To investigate this association, basal forebrain volumes were determined from magnetic resonance images of controls, subjects with amnestic mild cognitive impairment (aMCI) and AD patients enrolled in the longitudinal Alzheimer's Disease Neuroimaging Initiative (ADNI) and Australian Imaging, Biomarkers and Lifestyle (AIBL) studies. In the AIBL cohort, these volumes were correlated within groups to neocortical gray matter retention of Pittsburgh compound B (PiB) from positron emission tomography images as a measure of Aβ load. The basal forebrain volumes of AD and aMCI subjects were significantly reduced compared to those of control subjec...
2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2009
Pathologic processes active in early-stage knee joint osteoarthritis may also affect the integrit... more Pathologic processes active in early-stage knee joint osteoarthritis may also affect the integrity of the crescent-shaped fibrocartilagenous structures called menisci. Magnetic resonance imaging can allow the detection of these structural changes, however, large-scale clinical application remains limited by tedious and labor-intensive techniques for volumetric measurement. Towards automating these quantitative measurements, we have currently developed a scheme that allows the automatic
2012 9th IEEE International Symposium on Biomedical Imaging (ISBI), 2012
The accurate segmentation of the bone from Magnetic Resonance (MR) images of the hip is important... more The accurate segmentation of the bone from Magnetic Resonance (MR) images of the hip is important for clinical studies and drug trials into conditions like Osteoarthritis. This paper presents an automatic segmentation scheme that utilises a deformable model robust to different field of views by training shape priors from partial and full bone surfaces. The deformable model with these priors
Magnetic resonance in medicine : official journal of the Society of Magnetic Resonance in Medicine / Society of Magnetic Resonance in Medicine, Jan 30, 2015
To validate a fully automated scheme to extract biochemical information from the hip joint cartil... more To validate a fully automated scheme to extract biochemical information from the hip joint cartilages using MR T2 mapping images incorporating segmentation of co-registered three-dimensional Fast-Spin-Echo (3D-SPACE) images. Manual analyses of unilateral hip (3 Tesla) MR images of 24 asymptomatic volunteers were used to validate a 3D deformable model method for automated cartilage segmentation of SPACE scans, partitioning of the individual femoral and acetabular cartilage plates into clinically defined sub-regions and propagating these results to T2 maps to calculate region-wise T2 value statistics. Analyses were completed on a desktop computer (∼10 min per case). The mean voxel overlap between automated A and manual M segmentations of the cartilage volumes in the (clinically based) SPACE images was 73% (100×2|A∩M|/[|A|+|M|]). The automated and manual analyses demonstrated a relative difference error <10% in the median "T2 average signal" for each cartilage plate. The a...
2011 International Conference on Digital Image Computing: Techniques and Applications, 2011
The human cortex is a folded ribbon of neurons with a high inter-individual variability. It is a ... more The human cortex is a folded ribbon of neurons with a high inter-individual variability. It is a challenging structure to study especially when measuring small changes resulting from normal aging and neurodegenerative disorders such as Alzheimer's Disease (AD). Recent studies have proposed surface based approaches for statistical population comparison of cortical changes since such approaches better cope with the surfacic nature of the cortex. In this paper we present a new multi-scale EM-ICP registration that is embedded into a surfacebased approach. We compare this new registration algorithm with the shape context in the context of statistical population analysis. When comparing the cortical thickness between healthy elderly subjects to Alzheimer's disease patients, the new pipeline reduces the intra class variability while increasing the statistical power of the T-tests between both groups.