Image Registration for MRg Prostate Biopsy - Revision history

Grundlett: Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

2017-07-10T17:20:07Z

Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

Fedorov: /* Usage instructions */

2014-06-27T19:56:13Z

Usage instructions

Fedorov: /* Build instructions */

2012-08-21T23:51:04Z

Build instructions

Fedorov at 21:55, 1 June 2012

2012-06-01T21:55:28Z

Fedorov: /* Summary */

2012-03-28T16:01:50Z

Summary

Fedorov at 15:59, 28 March 2012

2012-03-28T15:59:30Z

Fedorov: moved Image registration with BRAINSFitIGT to Image Registration for MRg Prostate Biopsy: use a more descriptive title that correspond to the purpose of this page

2012-03-28T14:15:00Z

moved Image registration with BRAINSFitIGT to Image Registration for MRg Prostate Biopsy: use a more descriptive title that correspond to the purpose of this page

Fedorov: /* Intro and Disclaimer */

2010-09-17T14:44:35Z

Intro and Disclaimer

Fedorov at 14:25, 17 September 2010

2010-09-17T14:25:43Z

Fedorov at 14:10, 17 September 2010

2010-09-17T14:10:43Z

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 {|style="text-align:left;" border="0"
+|
-You must compile 3D Slicer version 3 from source. General build instructions and prerequisites can be found here: http://www.slicer.org/slicerWiki/index.php/Slicer3:Build_Instructions. You should also enable BRAINSFitIGT module in the CMake options, as shown in the screnshot.
+You must compile 3D Slicer version 3 from source. General build instructions and prerequisites can be found here: https://www.slicer.org/wiki/Slicer3:Build_Instructions. You should also enable BRAINSFitIGT module in the CMake options, as shown in the screnshot.
 |[[Image:BRAINSFitIGT_build_option.png]]
@@ Line 20: / Line 20: @@
 Before registering pre-procedural prostate T2w MRI, the following workflow is advised:
 # prepare approximate contouring of the prostate gland in the pre-procedural T2w image
-# apply N4 inhomogeneity correction (using [http://www.slicer.org/slicerWiki/index.php/Modules:N4ITKBiasFieldCorrection-Documentation-3.6 this module of Slicer]) to the pre-procedural image, in case it was acquired using endorectal coil. While performing inhomogeneity correction, use the prostate mask prepared in the previous step. The recommended number of iterations is "500,400,300".
+# apply N4 inhomogeneity correction (using [https://www.slicer.org/wiki/Modules:N4ITKBiasFieldCorrection-Documentation-3.6 this module of Slicer]) to the pre-procedural image, in case it was acquired using endorectal coil. While performing inhomogeneity correction, use the prostate mask prepared in the previous step. The recommended number of iterations is "500,400,300".
 Next, proceed with the registration steps as described below.

@@ Line 39: / Line 39: @@
 |[[Image:ProstateRegistration-RegStep.png|thumb|280px|Fields that need to be selected for the '''Registration step'' of the workflow are highlighted]]
 |-
 |}

@@ Line 8: / Line 8: @@
 {|style="text-align:left;" border="0"
+|
-You must compile 3D Slicer version 3 from source. General build instructions and prerequisites can be found here: http://www.slicer.org/slicerWiki/index.php/Slicer3:Build_Instructions. You should also enable BRAINSFit module in the CMake options, as shown in the screnshot.
+You must compile 3D Slicer version 3 from source. General build instructions and prerequisites can be found here: http://www.slicer.org/slicerWiki/index.php/Slicer3:Build_Instructions. You should also enable BRAINSFitIGT module in the CMake options, as shown in the screnshot.
 |[[Image:BRAINSFitIGT_build_option.png]]

← Older revision		Revision as of 21:55, 1 June 2012
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	\|-		\|-
	\|}		\|}
		+
		+	=References=
		+	* Fedorov A, Tuncali K, Fennessy FM, Hata N, Wells WM, Kikinis R, Tempany CM, Tokuda J, Hata N, Wells WM, et al. Image registration for targeted MRI-guided transperineal prostate biopsy. Journal of Magnetic Resonance Imaging. 2012 May 2009 http://www.ncbi.nlm.nih.gov/pubmed/22645031

@@ Line 1: / Line 1: @@
 =Summary=
-BRAINSFitIGT code is a 3D Slicer module based on the [http://wiki.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSFit] code originally developed by Hans Johnson and his team at U.Iowa. BRAINSFitIGT has been modified and customized to support registration of prostate preoperative MRI to intraoperative MRI during image-guided biopsy procedures. This module is NOT included in the binary distribution of 3D Slicer: you need to compile Slicer version 3 from source code to access it. This page explains how to compile and use this module.
+BRAINSFitIGT code is a 3D Slicer module based on the [http://wiki.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSFit] code originally developed by Hans Johnson and his team at U.Iowa. BRAINSFitIGT has been modified and customized to support registration of prostate preoperative MRI to intraoperative MRI during MR-guided biopsy procedures. This module is NOT included in the binary distribution of 3D Slicer: you need to compile Slicer version 3 from source code to access it. This page explains how to compile and use this module.
 BRAINSFitIGT module has been developed specifically to register pre-procedural T2w MRI that are typically using endorectal coil to intra-procedural MRI that do not use endorectal coil.
 =Build instructions=

@@ Line 1: / Line 1: @@
-== Intro and Disclaimer ==
+=Summary=
-BRAINSFitIGT code is a 3D Slicer module based on the [http://wiki.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSFit] code originally developed by Hans Johnson and his team at U.Iowa. BRAINSFitIGT has been modified and customized to support registration of prostate preoperative MRI to intraoperative MRI during image-guided biopsy procedures. It has been used to produce reasonable registration results for the last 7 or so biopsy cases. Quantitative evaluation of the accuracy is in progress.
+BRAINSFitIGT code is a 3D Slicer module based on the [http://wiki.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSFit] code originally developed by Hans Johnson and his team at U.Iowa. BRAINSFitIGT has been modified and customized to support registration of prostate preoperative MRI to intraoperative MRI during image-guided biopsy procedures. This module is NOT included in the binary distribution of 3D Slicer: you need to compile Slicer version 3 from source code to access it. This page explains how to compile and use this module.
-While using this code, please remember that it can change at any time, as I (Andrey Fedorov) am working to evaluate and improve it. It has not been evaluated for organs other than prostate. I will be interested to learn about your experience using it for new applications.
+BRAINSFitIGT module has been developed specifically to register pre-procedural T2w MRI that are typically using endorectal coil to intra-procedural MRI that do not use endorectal coil.
-'''Please treat all the training data provided to you for testing as non-public. You MUST check with me or with Dr. Noby Hata before you copy the data outside the SPL network or use it in any publication!'''
+=Build instructions=
-== General instructions ==
+|[[Image:BRAINSFitIGT_build_option.png]]
-* The software components used in this pipeline are not available in the standard Slicer distribution. Instead, the following binary '''available on opel.bwh.harvard.edu''' should be used:
+=Usage instructions=
-== WARNINGS ==
+You are supposed to be familiar with 3D Slicer. If this is not the case, familiarize yourself at least with the tutorials 1, 2, 4 and 5 from [http://wiki.slicer.org/slicerWiki/index.php/Slicer_3.6:Training Slicer 3.6 training page].
-Do not's ...
+Before registering pre-procedural prostate T2w MRI, the following workflow is advised:
-* do not make slice visible in 3D viewer: this will crash Slicer (this is a known problem specific to SPL fat nodes, there is no solution to fix it right now)
+Next, proceed with the registration steps as described below.
 {|style="text-align:left;" border="0"
@@ Line 37: / Line 32: @@
 ## create a new label image
 ## trace the approximate boundary of the prostate capsule in each image using "Draw" tool (let's say, they are called "preop-label" "intraop-label")
 '''2. Registration step'''
@@ Line 49: / Line 41: @@
 |-
 |}

← Older revision	Revision as of 14:15, 28 March 2012
(No difference)

← Older revision		Revision as of 14:44, 17 September 2010
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	While using this code, please remember that it can change at any time, as I (Andrey Fedorov) am working to evaluate and improve it. It has not been evaluated for organs other than prostate. I will be interested to learn about your experience using it for new applications.		While using this code, please remember that it can change at any time, as I (Andrey Fedorov) am working to evaluate and improve it. It has not been evaluated for organs other than prostate. I will be interested to learn about your experience using it for new applications.
		+
		+	'''Please treat all the training data provided to you for testing as non-public. You MUST check with me or with Dr. Noby Hata before you copy the data outside the SPL network or use it in any publication!'''

	== General instructions ==		== General instructions ==

← Older revision		Revision as of 14:25, 17 September 2010
Line 1:		Line 1:
		+	== Intro and Disclaimer ==
		+
		+	BRAINSFitIGT code is a 3D Slicer module based on the [http://wiki.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSFit] code originally developed by Hans Johnson and his team at U.Iowa. BRAINSFitIGT has been modified and customized to support registration of prostate preoperative MRI to intraoperative MRI during image-guided biopsy procedures. It has been used to produce reasonable registration results for the last 7 or so biopsy cases. Quantitative evaluation of the accuracy is in progress.
		+
		+	While using this code, please remember that it can change at any time, as I (Andrey Fedorov) am working to evaluate and improve it. It has not been evaluated for organs other than prostate. I will be interested to learn about your experience using it for new applications.
		+
	== General instructions ==		== General instructions ==

@@ Line 9: / Line 9: @@
 ssh -XY opel
 </pre>
 * You are supposed to be familiar with 3D Slicer. If this is not the case, familiarize yourself at least with the tutorials 1, 2, 4 and 5 from [http://wiki.slicer.org/slicerWiki/index.php/Slicer_3.6:Training Slicer 3.6 training page]
@@ Line 20: / Line 21: @@
 == Processing Steps ==
-{|
+{|style="text-align:left;" border="0"
 '''1. Preparation step''': start Slicer, load the images (let's say, they are called "preop.nrrd" and "intraop.nrrd"). Do the following:
 # Contour the object you want to register in both images
@@ Line 38: / Line 41: @@
 |-
 |}