Modules:LabelDiameterEstimation-Documentation-3.5 - Revision history

Nicole: /* Source code & documentation */

2010-01-15T23:12:01Z

Source code & documentation

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

2009-11-16T02:24:13Z

Quick Tour of Features and Use

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

2009-11-16T02:23:36Z

Quick Tour of Features and Use

Fedorov: /* Development */

2009-11-16T02:22:00Z

Development

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

2009-11-16T02:19:41Z

Quick Tour of Features and Use

Fedorov: /* Examples, Use Cases & Tutorials */

2009-11-16T02:19:28Z

Examples, Use Cases & Tutorials

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

2009-11-16T02:19:09Z

Quick Tour of Features and Use

Fedorov: /* References */

2009-11-16T02:17:54Z

References

Fedorov: /* References */

2009-11-16T02:17:05Z

References

Fedorov: /* Source code & documentation */

2009-11-16T02:07:18Z

Source code & documentation

@@ Line 85: / Line 85: @@
 Source code can accessed [http://viewvc.slicer.org/viewcvs.cgi/trunk/ChangeTrackerExtra/LabelDiameterEstimation/?root=NAMICSandBox here]
-[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.
+[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/ Links] to documentation generated by doxygen.
 == More Information ==

@@ Line 40: / Line 40: @@
 ** '''Input volume''' specifies the image with the label to be measured
 ** '''Output label image''' is a label image, which will have the computed diameters represented by distinctive labels. The diameters from the longest to the shortest are represented by consecutive labels from 1 to 3.
-** '''File to keep the output fiducials''' must be specified to store the endpoints of the diameters. After computation is completed, the fiducials can be loaded from the ''File -> Add data...'' menu. The fiducials are named as ''DA-0'' and ''DA-1'' for the endpoints of the longest diameter, ''DB'' and ''DC'' for the other two.
+** '''File to keep the output fiducials''' must be specified to store the endpoints of the diameters. After computation is completed, the fiducials can be loaded from the ''File -> Add data...'' menu. The fiducials are named as ''DA-0'' and ''DA-1'' for the endpoints of the longest diameter, ''DB-0''/''DB-1'' and ''DC-0''/''DC-1'' for the other two.
 * '''Advanced parameters'''

@@ Line 40: / Line 40: @@
 ** '''Input volume''' specifies the image with the label to be measured
 ** '''Output label image''' is a label image, which will have the computed diameters represented by distinctive labels. The diameters from the longest to the shortest are represented by consecutive labels from 1 to 3.
-** '''File to keep the output fiducials''' must be specified to store the endpoints of the diameters. After computation is completed, the fiducials can be loaded from the ''File -> Add data...'' menu.
+** '''File to keep the output fiducials''' must be specified to store the endpoints of the diameters. After computation is completed, the fiducials can be loaded from the ''File -> Add data...'' menu. The fiducials are named as ''DA-0'' and ''DA-1'' for the endpoints of the longest diameter, ''DB'' and ''DC'' for the other two.
 * '''Advanced parameters'''

← Older revision		Revision as of 02:22, 16 November 2009
Line 63:		Line 63:

	== Development ==		== Development ==
		+
		+	Standing issues under development:
		+	* would be nice to have fiducials read automatically; currently not possible, since fiducials are not fully integrated with CLI
		+	* use measurements widgets instead of label images for diameter visualization; measurements are also not integrated with CLI, and are not yet feature-complete
		+	* update Acks tab to point to documentation and give credit to BSF

	===Dependencies===		===Dependencies===

@@ Line 37: / Line 37: @@
 * '''Control panel''' contains the following items
-** '''Label value''' specifies which label should be used for diameter computation. When your label image has multiple labels, you can choose which one you want to measure. The default value of 0 will force the module to treat all label values in [1,255] as a single label.
+** '''Label value''' specifies which label should be used for diameter computation. When your label image has multiple labels, you can choose which one you want to measure. The default value of 0 will force the module to treat all label values in (1,255) as a single label.
 ** '''Input volume''' specifies the image with the label to be measured
 ** '''Output label image''' is a label image, which will have the computed diameters represented by distinctive labels. The diameters from the longest to the shortest are represented by consecutive labels from 1 to 3.

@@ Line 27: / Line 27: @@
 ===Examples, Use Cases & Tutorials===
-This module was originally designed to calculate the dimensions of tumor, following the RECIST/WHO guidelines.
+This module was originally designed to calculate the dimensions of tumor, following the RECIST [1] and WHO guidelines.
 * '''Implementation details''' The module implements the following algorithm for calculating the dimensions of the label. First, the area of the label slice is computed in all the slices of the image that are passing through the label. This is done for the three orthogonal directions of the image. The largest area slice is found. ''The largest diameter (DA)'' is estimated by finding the two most distant points on the contour of the label cross-section. ''The second diameter (DB)'' is found by finding the two most distant points on the contour that lie on the line perpendicular to the first diameter. ''The third diameter (DC)'' is estimated by calculating the two points of intersection between the line perpendicular to the plane formed by ''DA'' and ''DB''passing through the point of their intersection, and the contour of the analyzed label.

@@ Line 45: / Line 45: @@
 ** '''Orthogonality tolerance''' You should change this parameter only if the module does not give you a meaningful answer with the default value. The larger the tolerance is, the more non-perpendicular the diameters are allowed to be. This is related to the implementation details of the module. Try increasing the tolerance from 0.01 to 0.1 if the results don't make sense.
-The module also outputs numeric values for the lengths of the computed diameters. To see these numbers, open ''Log Viewer'', and select the first from top log record with the name  ''Label Diameter Estimation: standard output''. The reported numbers are the lenghts of the three diameters, the volume estimate calculated as ''A*B*C/2'', and the true label volume in mm^3.
+The module also outputs numeric values for the lengths of the computed diameters. To see these numbers, open ''Log Viewer'', and select the first from top log record with the name  ''Label Diameter Estimation: standard output''. The reported numbers are the lenghts of the three diameters, the volume estimate calculated as ''A*B*C/2'' (a formula suggested in the literature for estimating volume of hematomas from planimetric measurements [2]), and the true label volume in mm^3.
+|
 {|

← Older revision		Revision as of 02:17, 16 November 2009
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	[1] E. Eisenhauer, P. Therasse, J. Bogaerts, L. Schwartz, D. Sargent, R. Ford, J. Dancey, S. Arbuck, S. Gwyther, and M. Mooney, "New response evaluation criteria in solid tumours: Revised recist guideline (version 1.1)," European Journal of Cancer, vol. 45, no. 2, pp. 228-247, January 2009. [http://dx.doi.org/10.1016/j.ejca.2008.10.026 DOI]		[1] E. Eisenhauer, P. Therasse, J. Bogaerts, L. Schwartz, D. Sargent, R. Ford, J. Dancey, S. Arbuck, S. Gwyther, and M. Mooney, "New response evaluation criteria in solid tumours: Revised recist guideline (version 1.1)," European Journal of Cancer, vol. 45, no. 2, pp. 228-247, January 2009. [http://dx.doi.org/10.1016/j.ejca.2008.10.026 DOI]

−	[2] H. B. Huttner, T. Steiner, M. Hartmann, M. Kohrmann, E. Juettler, S. Mueller, J. Wikner, U. Meyding-Lamade, P. Schramm, S. Schwab, and P. D. Schellinger, "Comparison of abc/2 estimation technique to computer-assisted planimetric analysis in warfarin-related intracerebral parenchymal hemorrhage," Stroke, vol. 37, no. 2, pp. 404-408, February 2006. [http://dx.doi.org/10.~~116101~~.STR.0000198806.67472.5c DOI]	+	[2] H. B. Huttner, T. Steiner, M. Hartmann, M. Kohrmann, E. Juettler, S. Mueller, J. Wikner, U. Meyding-Lamade, P. Schramm, S. Schwab, and P. D. Schellinger, "Comparison of abc/2 estimation technique to computer-assisted planimetric analysis in warfarin-related intracerebral parenchymal hemorrhage," Stroke, vol. 37, no. 2, pp. 404-408, February 2006. [http://dx.doi.org/10.1161/01.STR.0000198806.67472.5c DOI]

← Older revision		Revision as of 02:17, 16 November 2009
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	===References===		===References===
		+
		+	[1] E. Eisenhauer, P. Therasse, J. Bogaerts, L. Schwartz, D. Sargent, R. Ford, J. Dancey, S. Arbuck, S. Gwyther, and M. Mooney, "New response evaluation criteria in solid tumours: Revised recist guideline (version 1.1)," European Journal of Cancer, vol. 45, no. 2, pp. 228-247, January 2009. [http://dx.doi.org/10.1016/j.ejca.2008.10.026 DOI]
		+
		+	[2] H. B. Huttner, T. Steiner, M. Hartmann, M. Kohrmann, E. Juettler, S. Mueller, J. Wikner, U. Meyding-Lamade, P. Schramm, S. Schwab, and P. D. Schellinger, "Comparison of abc/2 estimation technique to computer-assisted planimetric analysis in warfarin-related intracerebral parenchymal hemorrhage," Stroke, vol. 37, no. 2, pp. 404-408, February 2006. [http://dx.doi.org/10.116101.STR.0000198806.67472.5c DOI]

@@ Line 78: / Line 78: @@
 ===Source code & documentation===
-Source code can accessed [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/ExtractSubvolumeROI/ here]
+Source code can accessed [http://viewvc.slicer.org/viewcvs.cgi/trunk/ChangeTrackerExtra/LabelDiameterEstimation/?root=NAMICSandBox here]
 [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.