Difference between revisions of "Image Registration for MRg Prostate Biopsy"

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== Intro and Disclaimer ==
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=Summary=
  
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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.
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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.
  
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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.
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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.
  
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== General instructions ==
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=Build instructions=
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{|style="text-align:left;" border="0"
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|
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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.
  
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* 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:
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|[[Image:BRAINSFitIGT_build_option.png]]
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<pre>
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|-
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/workspace/fedorov/Slicer/Stable-Release/Slicer3-superbuild/Slicer3-build/Slicer3
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|}
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</pre>
 
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* log on to opel with X forwarding enabled:
 
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<pre>
 
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ssh -XY opel
 
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</pre>
 
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* the code is also available on the cart workstation at SPL. Log in using "develop" account (email me fedorov AT bwh) if you need the password. Use the Slicer icon on the desktop to launch Slicer with BRAINSFitIGT.
 
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* 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]
 
  
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== WARNINGS ==
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=Usage instructions=
  
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Do not's ...
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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].
  
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* 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)
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Before registering pre-procedural prostate T2w MRI, the following workflow is advised:
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* do not use your home directory for Slicer temporary storage -- it will fill up quickly, and Slicer will not work correctly
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# prepare approximate contouring of the prostate gland in the pre-procedural T2w image
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# 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".
  
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== Processing Steps ==
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Next, proceed with the registration steps as described below.
  
 
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## create a new label image
 
## 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")
 
## trace the approximate boundary of the prostate capsule in each image using "Draw" tool (let's say, they are called "preop-label" "intraop-label")
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# Perform bias correction on the intraop image
 
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## go to "N4ITK MRI Bias Correction" module
 
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## ''Parameters: Input image = "intraop" or "preop" image, Mask image = "intraop-label" or "preop-label", Output volume = create new volume and name it "preop-N4"/"intraop-N4"''
 
  
 
'''2. Registration step'''
 
'''2. Registration step'''
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|[[Image:ProstateRegistration-RegStep.png|thumb|280px|Fields that need to be selected for the '''Registration step'' of the workflow are highlighted]]
 
|[[Image:ProstateRegistration-RegStep.png|thumb|280px|Fields that need to be selected for the '''Registration step'' of the workflow are highlighted]]
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|[[Image:ProstateRegistration-RegStep_phases.png|thumb|280px|Registration phases to use]]
 
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== Testing Data ==
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=References=
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Example datasets of prostate MRI acquired before and during Mr-guided biopsy procedures are available on the cart workstation at SPL:
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* 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
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* load a training dataset by clicking on File --> Load Scene... --> Prostate_registration_training
 
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* there should be three training datasets: Case003, Case 004. Case005
 
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* choose e.g. Case004/RegistrationScene.mrml
 
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* nomenclature:
 
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** t2ax = preoperative prostate image data
 
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** t2ax-intraop = intraoperative prostate image data
 
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The same training data is also available on SPL network in /projects/igtcases/ProstateBx_cases/Training/
 

Latest revision as of 17:20, 10 July 2017

Home < Image Registration for MRg Prostate Biopsy

Summary

BRAINSFitIGT code is a 3D Slicer module based on the 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

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.

BRAINSFitIGT build option.png

Usage instructions

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 Slicer 3.6 training page.

Before registering pre-procedural prostate T2w MRI, the following workflow is advised:

  1. prepare approximate contouring of the prostate gland in the pre-procedural T2w image
  2. apply N4 inhomogeneity correction (using 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.

1. Preparation step: start Slicer, load the images (let's say, they are called "preop.nrrd" and "intraop.nrrd"). Do the following:

  1. Contour the object you want to register in both images
    1. go to Slicer Editor module
    2. create a new label image
    3. 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

  1. Choose Registration -> BRAINSFitIGT module
    1. Parameters: Fixed image volume = "intraop-N4", Moving image volume = "preop-N4", Input fixed mask = "intraop-label", Input moving mask = "preop-label", Slicer BSpline transform = create a new transform and name it "bspline-REG-tfm", Output image volume = create a new volume and name it "preop-REG"
    2. Upon completion of registration, inspect the result and check if it makes sense
Fields that need to be selected for the 'Registration step of the workflow are highlighted
Registration phases to use

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
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