Yingzhu at 23:02, 22 January 2021

2021-01-22T23:02:05Z

← Older revision		Revision as of 23:02, 22 January 2021
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			=Student Reports=
			:* 2003 SA S Moser M Kuhn "Development of intra-modality image registration methods for assessment of micro-structural bone adaptation." [[Media:Moser_Kuhn_2003_FinalReport.pdf \| Download PDF]]
			:* 2003 DA C Mattmann A Kuhn "Site-specific measurement of micro-structural bone adaptation and prediction of adapting bone architecture." [[Media:SiteSpecificChange.pdf\| Download PDF]]
			:* 2004 DA F Hofer "Finite element modeling for in vivo micro-computed tomography data: high throughput characterization of bone mechanical properties." [[Media:DA Documentation FelixHofer FinalVersion.pdf\| Download PDF]]
			:* 2005 SA D Christen "Development of a fully immersive visualization cave environment for micro-computed tomography." [[Media:Christen_SA_Final_report_2005.pdf \| Download PDF]]
			:* 2005 USRP J Owoc "Generating an average image for shape variability determination." [[Media:VtkImageAverageFilter.doc \| Download Word Document]]
			:* 2006 USRP J Owoc "Introduction of scale factor to multi-resolution registration." [[Media:2006 Markin-Flanagan Final Report.pdf \| Download PDF Report]] or [[Media:AppAffineRegistration-UserDocumentation.pdf \| Download PDF User Documentation]]
			:* 2006 DA E Schwyter "Multi-modal registration of micro-CT and MR imaging for development of 3D models of articular joints."
			::[[Media:Oct2006_EtienneSchwyterFinalReport_p1.pdf \| Download PDF (part 1 of 5)]]
			::[[Media:Oct2006_EtienneSchwyterFinalReport_p2.pdf \| Download PDF (part 2 of 5)]]
			::[[Media:Oct2006_EtienneSchwyterFinalReport_p3.pdf \| Download PDF (part 3 of 5)]]
			::[[Media:Oct2006_EtienneSchwyterFinalReport_p4.pdf \| Download PDF (part 4 of 5)]]
			::[[Media:Oct2006_EtienneSchwyterFinalReport_p5.pdf \| Download PDF (part 5 of 5)]]
			:* 2006 Ronan Sicre "Three-dimensional visualization of shape differences." [[Media:Report_Ronan_SICRE.pdf \| Download PDF]]
			:* 2007 David Christen "Local Strain Mapping for Bone Microstructure Under Load" [[Media:David Christen DA final_report.pdf \| Download PDF]]
			:* 2007 Michael Hofmann "Image Guided Failure Assessment of Whole Bones Under Multiple Loading Conditions" [[Media:Michael Hofmann DA final report.pdf \| Download PDF]]
			:* 2007 Dan Baker "The Diagnosis of Osteoporosis Using Xtreme-CT Data: The Development of a Protocol" [[Media:Report Final Dec 7th.pdf \| Download PDF]]
			:* 2007 Jim DuMont "Study of Motion Artifacts and Their Compensation in Micro-Computed Tomography" [[Media:JamesDumontThesis.doc \| Download Word Document]]
			:* 2008 Olivia Norton "Cuda - Quick Guide" [[Media:cuda-quickguide.pdf \| Download PDF]]
			::* CUDA Programming Guide [[Media:NVIDIA_CUDA_Programming_Guide_2.0.pdf \| Download PDF ]]
			:* 2008 Dan Baker "Assessment of Radius Bone Strength in Torsion with the Finite Element Method - Report and Documentation" [[Media:ResearchFinalReport-1-.pdf \| Download PDF]]
			:* 2008 Mathieu Boute "Image processing strategies to extract landmark curves from CT projection data" [[Media:FINAL_REPORT_BOUTE.pdf \| Download PDF]]


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Yingzhu: Created page with "=Imaging= ==Essential Physics of Medical Imaging== '''Ch 13 - Computed Tomography''' Media:Essentialph..."

2021-01-19T00:31:28Z

Created page with "=Imaging= ==Essential Physics of Medical Imaging== *'''Ch 13 - Computed Tomography''' *Media:Essentialph..."

New page

=Imaging=
==Essential Physics of Medical Imaging==
*[[Media:Essentialphysicsofmedicalimagingch13computedtomography.pdf|'''Ch 13 - Computed Tomography''']]
*[[Media:Essentialphysicsofmedicalimagingch14nuclearmagneticresonance.pdf|'''Ch 14 - Nuclear Magnetic Resonance''']]
*[[Media:Essentialphysicsofmedicalimagingch15magneticresonanceimaging.pdf|'''Ch 15 - Magnetic Resonance Imaging''']]

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=Bone=
==Books on Bone==
*[[Media:Bonemechanicshandbook.pdf|'''Bone Mechanics Handbook''']]
*[[Media:Thephysicalmeasurementofbone.pdf|'''The Physical Measurement of Bone''']]
*[[Media:Boneresearchprotocols.pdf|'''Bone Research Protocols''']]

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==Bone Morphometry and Densitometry==
===Suggested readings===
*[[Media:2010-bouxsein-guidelines-for-assessment-of-bone-microstructure-in-rodents-using-micro-computed-tomography.pdf|Guidelines for Assessment of Bone Microstructure in Rodents Using Micro-Computed Tomography]]
*[[Media:2007-koller-calibration-of-micro-ct-data-for-quantifying-bone-mineral.pdf|Calibration of Micro-CT Data for Quantifying Bone Mineral and Biomaterial Density and Microarchitecture]]
*[[Media:1997-hildebrand-model-independent-3d-thickness-measurement.pdf|A New Method for the Model-independent Assessment of Thickness in Three-dimensional Images]]
*[[Media:1997-hildebrand-quantification-of-structure-model-index.pdf|Quantification of Bone Microarchitecture with the Structure Model Index]]
*[[Media:1993-odgaard-quantification-of-connectivity-density.pdf|Quantification of Connectivity in Cancellous Bone, with Special Emphasis on 3D Reconstructions]]
*[[Media:2008_-_Sode_-_Resolution_dependence_of_the_non-metric_trabecular_structure_indices.pdf|Resolution Dependence of the Non-metric Trabecular Structure Indices]]
*[[Media:1999-ding-accuracy-of-cancellous-bone-volume-fraction-measured-by-micro-ct-scanning.pdf|Accuracy of Cancellous Bone Volume Fraction Measured by Micro-CT Scanning]]

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===Model-Independent (Direct) Structural Measurements===
Bone structural parameters are measured on segmented (i.e., binary) data. Typically the bone is extracted from the background using a global threshold approach; other filtering steps are also commonly employed (e.g., Gaussian smoothing to suppress noise).

====Voxel Counting Method====
*'''Bone Volume (BV)''': The volume of bone, usually applied to the trabecular compartment. Measured using the voxel counting (VOX) method. Output units are mm3.

*'''Total Volume (TV)''': The volume of bone, pores, and marrow cavities, usually applied to the trabecular compartment. Measured using the voxel counting (VOX) method. Output units are mm3.

*'''Bone Volume Fraction (BV/TV)''': The ratio of bone to the total volume, usually applied to the trabecular compartment. Calculated by dividing BV by TV, as measured using the voxel counting (VOX) method. This is a dimensionless (non-metric) parameter but is often expressed as a percentage.
[[File:BVTV.JPG|800px]]

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====Maximal Spheres Method====
Refer to [[Media:1997-hildebrand-model-independent-3d-thickness-measurement.pdf|'''this article''']] for more details.

*'''Trabecular Thickness (TbTh)''': The mean thickness of the trabecular struts. Measured using the distance transform (DT) method of fitting maximal spheres inside the bone structure. The standard deviation of the TbTh distribution (TbThSD) provides an estimation of variation in this parameter. Output units are mm.

*'''Trabecular Separation (TbSp)''': The mean thickness of the marrow cavities (i.e., the edge of one trabeculae to the next). Measured using the distance transform (DT) method of fitting maximal spheres inside the marrow spaces. The standard deviation of the TbSp distribution (TbSpSD) provides an estimation of variation in this parameter. Output units are mm.

*'''Trabecular Number (TbN)''': The average number of trabeculae per unit length. Calculated as the inverse of the mean distance between the midaxes of the bone structure. The mean distances between the midaxes is determined using the distance transform (DT) method of fitting maximal spheres. The standard deviation of the TbN distribution provides an estimation of variation in this parameter. Output units are 1/mm.

*'''Cortical Thickness (CtTh)''': The mean thickness of the cortex. Measured using the distance transform (DT) method of fitting maximal spheres inside the bone structure. Pores in the cortex lead to significant underestimation of CtTh and should be "filled in" prior to measurement (i.e., the apparent CtTh). Output units are mm.

[[File:TbThSpN.JPG|800px]]

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====Marching Cubes Method====
Refer to [[Media:1987-lorensen-marching-cubes-a-high-resolution-3d-surface-construction-algorithm.pdf|'''this article''']] for more details.

*'''Bone Surface (BS)''': A measure of the bone surface area. Measured using the Marching Cubes method to triangulate (TRI) the surface. Output units are mm2.

*'''Structure Model Index (SMI)''': An estimation of the plate-rod characteristic of the bone structure. SMI is calculated from the curvature of a triangulated surface (TRI) of the structure from the equation: SMI=6{[BV(dBS/dr)]/BS2]. For an ideal plate structure SMI=0 and for an ideal rod structure SMI=3. This is a dimensionless (non-metric) parameter.
:Refer to [[Media:1997-hildebrand-quantification-of-structure-model-index.pdf|'''this article''']] for more details.

[[File:MarchingCube.JPG|800px]] <br>
Image Source: Wikipedia, http://en.wikipedia.org/wiki/File:MarchingCubes.svg, Aug 2011

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====Other Method====
*'''Degree of Anisotropy (DA)''': A measure of how structure varies with orientation (i.e., if there is a preferred orientation). An isotropic structure, where properties are similar in all directions, would have DA=1 whereas an anisotropic structure has DA>1. Degree of anisotropy is defined as the ratio between the maximal and minimal radius of the mean intercept length (MIL) ellipsoid. The MIL is calculated by placing a series of parallel lines over the 3D image and taking the total length of the test lines divided by the number of bone-marrow interface. The MIL is calculated for a range of 3D directions and the MIL ellipsoid is calculated using a least square fit. This is a dimensionless (non-metric) parameter.
:Refer to [[Media:1984-characterization-of-microstructural-anisotropy-in-orthotropic-materials-using-a-second-rank-tensor.pdf|'''this article''']] for more details.

[[File:DAmethod.JPG|500px]] <br>
Image Source: C. Turner (1992), J. Biomech., 25, pp. 1-9.

*'''Connectivity Density (ConnD)''': A measure of the number of trabecular connections per unit volume. Measured using the Euler characteristic with controlled topological notes. Output units are 1/mm3.
:Refer to [[Media:1993-odgaard-quantification-of-connectivity-density.pdf|'''this article''']] for more details.

[[File:ConnD.jpg|300px]] <br>
This figure illustrates the concept of redundent trabeculae: a) a single trabeculae, b) two trabeculae, c) three trabeculae, and d) four trabeculae. Trabeculae are counted by "cutting trabeculae" until the structure is broken into two disconnected parts.<br>
Image Source: A. Odgaard and H.J.G. Gundersen (1993), Bone, 14, pp. 173-182.

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===Densitometric Measurements===
Densitometry parameters are measured on grayscale data.

====Descriptive Statistics (Mean, Median, SD) of Calibrated Voxel Values====
Bone mineral density (BMD) is defined as the volumetric density of calcium hydroxyapatite (CaHA) in a biological tissue in terms of g.cm-3. It is calibrated by means of phantoms with known density of CaHA. Bone mineral density can refer to two different measurements:

*'''Bone Mineral Density (BMD)''': A measure of the density of minerals within the whole bone. Measured by taking the average grayscale intensity of bone, marrow, and pore voxels, and converting it to hydroxyapatite (HA) mineral density. The combined density of a well-defined volume which contains a mixture of both bone and soft tissue, such as a selected volume of medullary trabecular bone in a femur or tibia, is measured as “bone mineral density”, or BMD. This parameter BMD relates to the amount of bone within a mixed bone-soft tissue region, but does not give information about the material density of the bone itself.

*'''Tissue Mineral Density (TMD)''': A measure of the density of minerals within the bone tissue. Measured by taking the average grayscale intensity of the bone only (usually suppressing 2 voxels at the edges to elimitate partial volume artifacts) and converting it to hydroxyapatite (HA) mineral density. The density measurement restricted to within the volume of calcified bone tissue, such as cortical bone, excluding surrounding soft tissue, is called “tissue mineral density” or TMD. By contrast to BMD, this gives us information about the material density of the bone itself, and ignores surrounding soft tissue.

*Refer to [[Media:2007-koller-calibration-of-micro-ct-data-for-quantifying-bone-mineral.pdf|'''this article''']] for more details.

Typically trabecular bone is assessed for BMD, averaging bone and marrow within the medullary volume of interest. By contrast, for cortical bone, TMD is measured. Note that in the case of trabecular bone, partial volume effect compromises the measurement of TMD except at very high micro-CT resolutions. As a general rule, resolution should be such that the thickness of a bone structure should equal 10 pixels or more, in order for TMD to be measured.

[[File:BMD_TMD.JPG|500px]]

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← Older revision		Revision as of 23:02, 22 January 2021
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			[[Image:Redirect.jpg\|15px]] [[#top\|''Return to Contents'']] or [[Main_Page\|''Return to Main Page'']]

			=Student Reports=
			:* 2003 SA S Moser M Kuhn "Development of intra-modality image registration methods for assessment of micro-structural bone adaptation." [[Media:Moser_Kuhn_2003_FinalReport.pdf \| Download PDF]]
			:* 2003 DA C Mattmann A Kuhn "Site-specific measurement of micro-structural bone adaptation and prediction of adapting bone architecture." [[Media:SiteSpecificChange.pdf\| Download PDF]]
			:* 2004 DA F Hofer "Finite element modeling for in vivo micro-computed tomography data: high throughput characterization of bone mechanical properties." [[Media:DA Documentation FelixHofer FinalVersion.pdf\| Download PDF]]
			:* 2005 SA D Christen "Development of a fully immersive visualization cave environment for micro-computed tomography." [[Media:Christen_SA_Final_report_2005.pdf \| Download PDF]]
			:* 2005 USRP J Owoc "Generating an average image for shape variability determination." [[Media:VtkImageAverageFilter.doc \| Download Word Document]]
			:* 2006 USRP J Owoc "Introduction of scale factor to multi-resolution registration." [[Media:2006 Markin-Flanagan Final Report.pdf \| Download PDF Report]] or [[Media:AppAffineRegistration-UserDocumentation.pdf \| Download PDF User Documentation]]
			:* 2006 DA E Schwyter "Multi-modal registration of micro-CT and MR imaging for development of 3D models of articular joints."
			::[[Media:Oct2006_EtienneSchwyterFinalReport_p1.pdf \| Download PDF (part 1 of 5)]]
			::[[Media:Oct2006_EtienneSchwyterFinalReport_p2.pdf \| Download PDF (part 2 of 5)]]
			::[[Media:Oct2006_EtienneSchwyterFinalReport_p3.pdf \| Download PDF (part 3 of 5)]]
			::[[Media:Oct2006_EtienneSchwyterFinalReport_p4.pdf \| Download PDF (part 4 of 5)]]
			::[[Media:Oct2006_EtienneSchwyterFinalReport_p5.pdf \| Download PDF (part 5 of 5)]]
			:* 2006 Ronan Sicre "Three-dimensional visualization of shape differences." [[Media:Report_Ronan_SICRE.pdf \| Download PDF]]
			:* 2007 David Christen "Local Strain Mapping for Bone Microstructure Under Load" [[Media:David Christen DA final_report.pdf \| Download PDF]]
			:* 2007 Michael Hofmann "Image Guided Failure Assessment of Whole Bones Under Multiple Loading Conditions" [[Media:Michael Hofmann DA final report.pdf \| Download PDF]]
			:* 2007 Dan Baker "The Diagnosis of Osteoporosis Using Xtreme-CT Data: The Development of a Protocol" [[Media:Report Final Dec 7th.pdf \| Download PDF]]
			:* 2007 Jim DuMont "Study of Motion Artifacts and Their Compensation in Micro-Computed Tomography" [[Media:JamesDumontThesis.doc \| Download Word Document]]
			:* 2008 Olivia Norton "Cuda - Quick Guide" [[Media:cuda-quickguide.pdf \| Download PDF]]
			::* CUDA Programming Guide [[Media:NVIDIA_CUDA_Programming_Guide_2.0.pdf \| Download PDF ]]
			:* 2008 Dan Baker "Assessment of Radius Bone Strength in Torsion with the Finite Element Method - Report and Documentation" [[Media:ResearchFinalReport-1-.pdf \| Download PDF]]
			:* 2008 Mathieu Boute "Image processing strategies to extract landmark curves from CT projection data" [[Media:FINAL_REPORT_BOUTE.pdf \| Download PDF]]


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Books and References - Revision history

Yingzhu at 23:02, 22 January 2021

Yingzhu: Created page with "=Imaging= ==Essential Physics of Medical Imaging== *'''Ch 13 - Computed Tomography''' *Media:Essentialph..."

Yingzhu: Created page with "=Imaging= ==Essential Physics of Medical Imaging== '''Ch 13 - Computed Tomography''' Media:Essentialph..."