MIAL

Musculoskeletal Image Analysis

MSc Student: Neda Changizi
PhD Student: Bahareh HajGhanbari
PhD Student: Oliver van Kaick
PhD Student: Aaron Ward
Principal Investigator: Ghassan Hamarneh
PhD Student: Hengameh Mirzaalian

We are developing tools for the analysis of medical imaging data for quantification, visualization, and understanding musculoskeletal anatomy and function and their relation to diseases.

This page lists projects with a number of collaborators:

  • Dr. Mark E. Schweitzer, Department of Diagnostic Imaging, The Ottawa Hospital (formerly at NYU School of Medicine, Hospital for Joint Diseases).
  • Dr. Darlene Reid, Department of Physical Thearpy, UBC.
  • Prof. James Wakeling, School of Kinesiology, SFU

See publications list at the bottom of this page.

3D Segmentation and Shape Analysis of Thigh Muscles (with Dr. Reid)

Patients with COPD and healthy adults underwent magnetic resonance imaging of the thighs. After segmenting the individual knee extensor and flexor muscles, the three-dimensional shape of each muscle was obtained using specialized software. Eight shape descriptors were computed both globally (for the whole muscle) and regionally (for portions of the muscle). Greater regional shape anomalies in the COPD group were found in the middle to proximal regions of all knee extensor muscles and the middle region of the semimembranosus muscle, compared to those of the control group.

Tracking Muscle fascicles in Ultrasound  (with Prof. Wakeling)

We automatically tracked fascicle orientation by first filtering the images using a multiscale ridge enhancement (a technique used to enhance tube-like structures), and then fascicle orientations quantified using either the Radon transform or wavelet analysis.

Bicipital Groove of the Proximal Humerus (with Dr. Schweitzer)

The bicipital groove is an osseous groove formed in the humeral head by the medial and lateral tuberosities.  It serves to retain the long head of the biceps brachii.  In this project, we investigate the relationship between the 3D shape of the bicipital groove and the incidence of pathology of the long biceps tendon.

Bicipital groove segmentation from CT data.


Medial-based shape representation of the bicipital groove.

Two views of a humeral head extracted from MRI, with the bicipital groove indicated.


Establishing a relationship between 3D bicipital groove surface and 2D thickness fields, for qualitative inspection.

Quantitative inspection, in physical units, of measured thicknesses in a 2D thickness fields.


Supraspinatus of the Rotator Cuff (with Dr. Schweitzer)

The supraspinatus is one of several muscles making up the rotator cuff of the shoulder.  In this study, we examine the relationship between the 3D shape of the supraspinatus and its various pathological conditions.  Diagnosis of supraspinatus pathology is currently notoriously difficult without the use of invasive athroscopic techniques.

Views seen by radiologist using supraspinatus outlining tool.

Contours drawn by radiologist, visualized in 3D, with interpolated muscle surface.

Segmented supraspinatus shown in context of the MRI from which it was extracted.

Video showing several perspectives of a torn supraspinatus.


Video showing several perspectives of a normal supraspinatus.


Video showing several perspectives of the set of expert-drawn contours from which the above surface was interpolated.


Hoffa's Fat Pad (with Dr. Schweitzer)

Hoffa's fat pad is an infrapatellar (lying underneath the knee cap) fatty structure.  In this project we investigate the 3D shape deformations of Hoffa’s fat pad, between knee flexion and extension as a possible indication of a bio-mechanical behavior (cushioning) in addition to the classical energy storage function.

Deformations of Hoffa's Fat Pad for a 2-angle flexion/extension.


Knee, Hoffa's fat, rigid and nonrigid registration, and deformation field for a multi-angle flexion/extension experiment.

 

 

 

Publications (with Dr. Reid)

Shawn Andrews, Ghassan Hamarneh, Azadeh Yazdanpanah, Bahareh HajGhanbari, and W. Darlene Reid. Probabilistic Multi-Shape Segmentation of Knee Extensor and Flexor Muscles. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), pages 633-640, 2011. 

Bahareh HajGhanbari, Ghassan Hamarneh, Neda Changizi, Aaron Ward, and W. Darlene Reid. MRI-based 3D shape analysis of thigh muscles: Patients with chronic obstructive pulmonary disease versus healthy adults. Academic Radiology, 18(2):155-166, 2011.   

Bahareh HajGhanbari, Ghassan Hamarneh, Neda Changizi, Aaron Ward, and W. Darlene Reid. 3D shape analysis of thigh muscles: people with Chronic Obstructive Pulmonary Disease versus healthy older adults. In Canadian Physiotherapy Association Congress, pages 1, 2011. 

Bahareh HajGhanbari, Ghassan Hamarneh, Neda Changizi, Aaron Ward, and W. Darlene Reid. MRI-based Three dimensional shape analysis of thigh muscles: people with Chronic Obstructive Pulmonary Disease versus healthy older adults. In Heart+Lung Health Fest, pages 1, 2011.  

 Hengameh Mirzaalian, Ghassan Hamarneh, Bahareh HajGhanbari, and W. Darlene Reid. 3D Shape Analysis of the Knee Extensor and Flexor Muscles in Patients with COPD using Mesh Projection-based Features. In Medical Image Computing and Computer-Assisted Intervention Workshop on Mesh Processing in Medical Image Analysis (MICCAI MeshMed), pages ?-?, 2011.  [poster].

Publications (with Prof. Wakeling)

Manku Rana, Ghassan Hamarneh, and James M. Wakeling. Automated tracking of muscle fascicle orientation in B-mode ultrasound imagesJournal of Biomechanics, 42(13):2068-2073, 2009.  

Manku Rana, Ghassan Hamarneh, and James M. Wakeling. In- vivo determination of 3D muscle architecture of the human triceps muscle using free hand ultrasound. In Society of Integrative and Comparative Biology (SICB), 2010. 

 

Publications (with Dr. Schweitzer)

Oliver Van Kaick, Ghassan Hamarneh, Aaron Ward, Mark Schweitzer, and Richard Zhang. Learning Fourier Descriptors for Computer-Aided Diagnosis of the Supraspinatus. Academic Radiology, 17(8):1040-1049, 2010.  

Aaron Ward, Ghassan Hamarneh, and Mark Schweitzer. 3D Bicipital Groove Shape Analysis and Relationship to Tendopathy. Journal of Digital Imaging, 21(2):219-234, 2008.   

Aaron Ward, Ghassan Hamarneh, Reem Ashry, and Mark Schweitzer. 3D Shape Analysis of the Supraspinatus Muscle: A Clinical Study of the Relationship between Shape and Pathology. Academic Radiology, 14(10):1229-1241, 2007.   

Aaron Ward, Ghassan Hamarneh, and Mark Schweitzer. Anatomical Shape Analysis: Exploring the Relationship between Shape and Pathology. In CIHR National Research Poster Competition, Canadian Student Health Research Forum (CSHRF), Winnipeg, June 6-7, 2007. 

Kevin Stevenson, Mark Schweitzer, and Ghassan Hamarneh. Multi-angle deformation analysis of Hoffa's fat pad. In SPIE Medical Imaging, volume 6143-29, pages 1-9, 2006.  

Aaron Ward, Ghassan Hamarneh, Reem Ashry, and Mark Schweitzer. 3D Shape Analysis of the Supraspinatus Muscle. In Medical Image Computing and Computer-Assisted Intervention Joint Diseases Workshop (MICCAI JD), pages 96-103, 2006. 

Aaron Ward, Ghassan Hamarneh, and Mark Schweitzer. 3D Shape Description of the Bicipital Groove: Correlation to Pathology. InMedical Image Computing and Computer-Assisted Intervention Joint Diseases Workshop (MICCAI JD), pages 80-87, 2006. 

Aaron Ward, Mark Schweitzer, and Ghassan Hamarneh. 3D shape description of the bicipital groove of the proximal humerus. In SPIE Medical Imaging, volume 6143-27, pages 1-9, 2006.  

Aaron Ward, Mark Schweitzer, and Ghassan Hamarneh. Computational and Visualization Techniques for Understanding the Shape Variations of the Bicipital Groove of the Proximal Humerus. In Annual meeting of the Society for Computer Applications in Radiology (SCAR), pages 47-49, 2006. 

Ghassan Hamarneh, Vincent Chu, Marcelo Bordalo-Rodrigues, and Mark Schweitzer. Deformation analysis of Hoffa's fat pad from CT images of knee flexion and extension. In SPIE Medical Imaging, volume 5746, pages 527-534, 2005.   

Aaron Ward, Mark Schweitzer, and Ghassan Hamarneh. Shape Description of the Bicipital Groove of the Proximal Humerus. In 1st Annual Medical Technology Research Showcase, Vancouver, BC, 2005.  

 

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