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==v3.6.3 [[Image:Slicer3-6Announcement-v1.png‎|150px]] Slicer Registration Library Case #12: Intra-subject liver & kidney CT / MRI: preop-scan to intra-op scan ==
=== Input ===
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C12_Thumb1.png|150px|lleft|this is the fixed reference image. All images are aligned into this space]]
|[[Image:RegArrow_NonRigid.png|100px|lleft]]
|[[Image:RegLib_C12_Thumb2.png|150px|lleft|this is the moving image. The transform is calculated by matching this to the reference image]]
|-
|fixed image/target
|
|moving image
|}

=== Modules ===
'''Slicer 3.6.3''' recommended modules:
*[http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BrainsFit]
*

===Objective / Background ===
This is a typical case of image fusion from preop planning: we seek to align the preoperative MRI and CT (which have better tumor visibility) to the intra-operative CT.
=== Keywords ===
abdominal CT, abdominal MRI, liver, kidney, surgical planning, image fusion, tumor, nonrigid

===Input Data===
*reference/fixed : intra-operative CT, 1x1x5 mm voxel size, 512x512x41, axial
*moving 1: pre-operative MRI, 0.8x0.8x2.5 mm voxel size, 512x512x96, axial
*moving 2: pre-operative contrast CT, 0.9x0.9x5 mm voxel size, 512x512x42, axial

=== Overall Strategy ===
:#run rigid/affine registration (BRAINSfit) with initialization
:#run 7x7x7 nonrigid registration (BRAINSfit BSpline) using the above affine as input

=== Procedures ===
*'''Phase I: Register Rigid/Affine'''
#open Registration : ''BrainsFit'' module (presets: BRAINSfit_Xf1 or _Xf2
##Registration Phases:
###select/check ''Include Affine registration phase''
###for affine also select/check ''Include Scale Versor 3D'' and ''Include Affine'' registration phase''
##Registration Parameters: increase ''Number Of Samples'' to 200,000
###select a new transform "Linear Transform", rename to "Xf1_affine"
##Leave all other settings at default
*'''Phase II: [optional]: generate skull mask
#open ''Skull Stripper for Structural MRI'' Module (Extension module)
#increase ''Iterations" to 200 and ''Subdivisions'' to 12
#both results will have to be edited manually using the Editor module.
*'''Phase III: Register BSpline'''
#open Registration : ''BrainsFit'' module (presets: BRAINSfit_Xf3 or _Xf4
##select a new volume "Output Image Volume'', rename to "DTI_base_Xf1"
##Registration Parameters: increase ''Number Of Samples'' to 200,000
##Registration Parameters: set ''Number Of Grid Subdivisions'' to 7x7x7
##Leave all other settings at default
##if using masks, set the ''Mask Processing Mode'' to "ROI" and select the two labelmaps generated in phase II as Input Masks

=== Registration Results===
{| style="color:#bbbbbb; background-color:#333333;" cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C12_unreg.png|400px|center|unregistered]]
|original unregistered
|-
|[[Image:RegLib_C12_Xf1.gif|400px|center|rigid]]
|[[Image:RegLib_C12_Xf2.gif|400px|center|affine]]
|-
|rigid registered
|affine registered
|-
|[[Image:RegLib_C12_Xf3.gif|400px|center|BSpline (7x7x7) unmasked]]
|[[Image:RegLib_C12_Xf4.gif|400px|center|BSpline (7x7x7) masked]]
|-
|nonrigid registered (7x7x7 BSpline unmasked)
|nonrigid registered (7x7x7 BSpline '''masked''')
|}

===Download ===
*Data
**[[Media:RegLib_C12_Data.zip‎ ‎|'''RegLib_C12_Data''' , image data, resets & solution transforms (NRRD files, zip file 41 MB) ]]'''
*Presets
**[[Media:RegLib_C12_Presets.mrml‎|'''RegLib_C12_Presets''' Presets for BRAINSFIT registration (.mrml file 12 kB) ]]'''
**[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]

@@ Line 17: / Line 17: @@
 === Modules ===
 '''Slicer 3.6.3''' recommended modules:
-*[http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BrainsFit]
+*[https://www.slicer.org/wiki/Modules:BRAINSFit BrainsFit]
+*

Projects:RegistrationDocumentation:RegLib 12 LiverTumorAblation1 - Revision history

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

Meier: Created page with 'Back to ARRA main page Back to Registration main page [[Projects:RegistrationDocumentation:UseCaseInv…'

Meier: Created page with 'Back to ARRA main page
Back to Registration main page
[[Projects:RegistrationDocumentation:UseCaseInv…'