Modules:ChangeTracker-Documentation - Revision history

Fedorov: /* Quick Tour of Features and Use */

2008-12-22T23:51:10Z

Quick Tour of Features and Use

Fedorov: /* Dependencies */

2008-12-22T23:50:21Z

Dependencies

Fedorov: /* Dependencies */

2008-12-22T23:49:47Z

Dependencies

Fedorov: /* Dependencies */

2008-12-22T23:48:25Z

Dependencies

Fedorov: /* Dependencies */

2008-12-22T23:43:35Z

Dependencies

Fedorov: /* Quick Tour of Features and Use */

2008-12-22T23:33:36Z

Quick Tour of Features and Use

Fedorov: /* Quick Tour of Features and Use */

2008-12-22T23:33:13Z

Quick Tour of Features and Use

Fedorov: /* Quick Tour of Features and Use */

2008-12-22T23:30:33Z

Quick Tour of Features and Use

Kikinis: /* Quick Tour of Features and Use */

2008-12-22T19:23:33Z

Quick Tour of Features and Use

Fedorov: /* Quick Tour of Features and Use */

2008-12-22T16:50:53Z

Quick Tour of Features and Use

@@ Line 65: / Line 65: @@
 {|
 |We provide two metrics -- intensity-based and deformation-based -- to quantify tumor progression (see details in this [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1430 paper]). Choose the metric you would like to use.
-|[[Image:ChangeTracker_Step4.png|thumb|450px|Step 4: Metric selection]]
+|[[Image:ChangeTracker_Step4.png|thumb|250px|Step 4: Metric selection]]
 |}

@@ Line 85: / Line 85: @@
 {|
-|The module is using [http://slicer.spl.harvard.edu/slicerWiki/index.php/Modules:LinearRegistration-Documentation Rigid Registration module] through the CommandLineModule shared object invocation. Note, that there are two distinct rigid registration modules in Slicer, which have identical functionality: "Linear registration" and "Rigid registration". Both of these modules should be available in your build, but "Rigid registration" *must* be available for ChangeTracker to function properly. You can verify the availability of the module manually by looking at the list of modules in the registration category.
+|ChangeTracker is using [http://slicer.spl.harvard.edu/slicerWiki/index.php/Modules:LinearRegistration-Documentation Rigid Registration module] through the CommandLineModule shared object invocation. Note, that there are two distinct rigid registration modules in Slicer, which have identical functionality: "Linear registration" and "Rigid registration". Both of these modules should be available in your build, but "Rigid registration" *must* be available for ChangeTracker to function properly. You can verify the availability of the module manually by looking at the list of modules in the registration category.
 |[[Image:rigid_registration_module.png|thumb|200px|Checking availability of Rigid registration module (click to zoom in)]]
 |}

@@ Line 85: / Line 85: @@
 {|
-|The module is using [http://slicer.spl.harvard.edu/slicerWiki/index.php/Modules:LinearRegistration-Documentation Rigid Registration module] through the CommandLineModule shared object invocation. Note, that there are two distinct rigid registration modules in Slicer, which have identical functionality: "Linear registration" and "Rigid registration". Both of these modules should be available in your build, but "Rigid registration" *must* be available for ChangeTracker to function properly. You can verify this by
+|The module is using [http://slicer.spl.harvard.edu/slicerWiki/index.php/Modules:LinearRegistration-Documentation Rigid Registration module] through the CommandLineModule shared object invocation. Note, that there are two distinct rigid registration modules in Slicer, which have identical functionality: "Linear registration" and "Rigid registration". Both of these modules should be available in your build, but "Rigid registration" *must* be available for ChangeTracker to function properly. You can verify the availability of the module manually by looking at the list of modules in the registration category.
 |[[Image:rigid_registration_module.png|thumb|200px|Checking availability of Rigid registration module (click to zoom in)]]
 |}

@@ Line 85: / Line 85: @@
 {|
-|The module is using [http://slicer.spl.harvard.edu/slicerWiki/index.php/Modules:LinearRegistration-Documentation Rigid Registration module] through the CommandLineModule shared object invocation. Note, that there are two distinct rigid registration modules in Slicer, which have identical functionality: "Linear registration" and "Rigid registration". Both of these modules should be available in your build. You can verify this by
+|The module is using [http://slicer.spl.harvard.edu/slicerWiki/index.php/Modules:LinearRegistration-Documentation Rigid Registration module] through the CommandLineModule shared object invocation. Note, that there are two distinct rigid registration modules in Slicer, which have identical functionality: "Linear registration" and "Rigid registration". Both of these modules should be available in your build, but "Rigid registration" *must* be available for ChangeTracker to function properly. You can verify this by
-|[[Image:rigid_registration_module.png|thumb|250px|Checking availability of Rigid registration module]]
+|[[Image:rigid_registration_module.png|thumb|200px|Checking availability of Rigid registration module (click to zoom in)]]
 |}

@@ Line 84: / Line 84: @@
 ===Dependencies===
-The module is using [http://slicer.spl.harvard.edu/slicerWiki/index.php/Modules:LinearRegistration-Documentation Rigid Registration module] through the CommandLineModule shared object invocation
+{|
 ===Known bugs===

@@ Line 41: / Line 41: @@
 {|
 |Use drop-down controls to choose the two scans where you would like to measure pathology development. Currently, we support analysis of the images that correspond to two time points. Extending of the module to accept more than two time points is the feature under development.
-|[[Image:ChangeTracker_Step1.png|thumb|450px|Step 1: Scan selection]]
+|[[Image:ChangeTracker_Step1.png|thumb|250px|Step 1: Scan selection]]
 |}

@@ Line 40: / Line 40: @@
 {|
-|Use drop-down controls to choose the two scans where you would like to measure pathology development.
+|Use drop-down controls to choose the two scans where you would like to measure pathology development. Currently, we support analysis of the images that correspond to two time points. Extending of the module to accept more than two time points is the feature under development.
 |[[Image:ChangeTracker_Step1.png|thumb|450px|Step 1: Scan selection]]
 |}
@@ Line 47: / Line 47: @@
 {|
-|Use the mouse pointer in combination with left button clicks to identify the bounding box enclosing pathology in three projections of the viewer. You can also use the mouse to adjust sliders defining the bounding box more precisely. If you made a mistake, click "Reset" button to start over.
+|Use the mouse pointer in combination with left button clicks to identify the bounding box enclosing pathology in three projections of the viewer. You can also use the mouse to adjust sliders defining the bounding box more precisely. If you made a mistake, click "Reset" button to start over. "Show VOI" button can be used to show/hide blue overlay of the region of interest of the the image slice views.
 |{|
 |[[Image:ChangeTracker_Step2_1.png|thumb|200px|Step 2: ROI selection]]
@@ Line 57: / Line 57: @@
 {|
-|Use threshold control slider to find the intensity that most closely approximates tumor volume. Tumor volume is rendered in the 3D viewer as you are choosing the appropriate threshold.
+|Use threshold control slider to find the intensity that most closely approximates tumor volume. Tumor volume is rendered in the 3D viewer as you are choosing the appropriate threshold, and is also visualized as semi-transparent label in the image slice viewers.
 |[[Image:ChangeTracker_Step3.png|thumb|450px|Step 3: Threshold selection]]
 |}

@@ Line 39: / Line 39: @@
 * '''Step 1: Define input scans'''
-<gallery widths="400px" perrow="2">
+{|
-Image:ChangeTracker_Step1.png|Step 1: Scan selection: Use drop-down controls to choose the two scans, where you want to measure pathology development.
+|Use drop-down controls to choose the two scans where you would like to measure pathology development.
-Image:ChangeTracker_Step2_1.png|Step 2: Define volume of interest: Use the mouse pointer in combination with left button clicks to identify the bounding box enclosing pathology in three projections of the viewer. You can also use the mouse to adjust sliders defining the bounding box more precisely. If you made a mistake, click "Reset" button to start over.
+|[[Image:ChangeTracker_Step1.png|thumb|450px|Step 1: Scan selection]]
-</gallery>
+|}
 {|
 |[[Image:ChangeTracker_Step2_1.png|thumb|200px|Step 2: ROI selection]]
-|[[Image:ChangeTracker_Step2_2.png|thumb|300px|Step 2: ROI visualization]]
+|[[Image:ChangeTracker_Step2_2.png|thumb|250px|Step 2: ROI visualization]]
 |}
 * '''Step 3: Select tumor segmentation threshold'''
-Use threshold control slider to find the intensity that most closely approximates tumor volume. Tumor volume is rendered in the 3D viewer as you are choosing the appropriate threshold.
+{|
+|Use threshold control slider to find the intensity that most closely approximates tumor volume. Tumor volume is rendered in the 3D viewer as you are choosing the appropriate threshold.
-[[Image:ChangeTracker_Step3.png|thumb|450px|Step 3: Threshold selection]]
+|[[Image:ChangeTracker_Step3.png|thumb|450px|Step 3: Threshold selection]]
 * '''Step 4: Define metric'''
-We provide two metrics -- intensity-based and deformation-based -- to quantify tumor progression (see details in this [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1430 paper]). Choose the metric you would like to use.
+{|
+|We provide two metrics -- intensity-based and deformation-based -- to quantify tumor progression (see details in this [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1430 paper]). Choose the metric you would like to use.
-[[Image:ChangeTracker_Step4.png|thumb|200px|Step 4: Metric selection]]
+|[[Image:ChangeTracker_Step4.png|thumb|450px|Step 4: Metric selection]]
 * '''Analysis/Results'''
-Results are reported as the change in tumor volume, separately for growth and shrinkage component. The quantitative results are reported in voxels and mm^3.
+{|
 Sensitivity of the analysis can be controlled by choosing Sensitive, Moderate, or Robust analysis approach (Robust being the most conservative). As you change the sensitivity, visualization and quantitative data are updated accordingly. Growth is shown in purple, and shrinkage -- in green color.
@@ Line 69: / Line 77: @@
 You can choose to display the original sampling grid, and view the coronal slice of the subject using the module controls.
-[[Image:ChangeTracker_Analysis.png|thumb|450px|Visualization of the analysis results]]
+|[[Image:ChangeTracker_Analysis.png|thumb|450px|Visualization of the analysis results]]
 == Development ==