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= v3.6.1 [[Image:Slicer3-6Announcement-v1.png‎|150px]] Slicer Registration Library Case #34: Mouse Brain MRI =
=== Input ===
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C34_Thumb1.png|150px|lleft|MRI baseline]]
|[[Image:RegArrow_NonRigid.png|100px|lleft]]
|[[Image:RegLib_C34_Thumb2.png|150px|lleft|MRI follow-up]]
|-
|fixed image 1/target MRI mouse 1
|
|moving image MRI mouse 2
|}

=== Modules ===
*'''Slicer 3.6.1 recommended modules:''' [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit '''BrainsFit'''], [http://www.slicer.org/slicerWiki/index.php/Modules:SkullStripperModule '''Fast Marching Segmentation'''], [http://www.slicer.org/slicerWiki/index.php/Modules:N4ITKBiasFieldCorrection-Documentation-3.6 '''Histogram Matching''']

===Objective / Background ===
Aim is to register the brain of a 5 days old mouse (Post Natal Day 5, PND5) with an atlas.
=== Download ===
*DATA
**[[Media:RegLib_C34_Data.zip‎|'''Registration Library Case 34 ''' (Data & Solution Xforms, zip file 90 MB) ]]
*PRESETS:
**[[Media:RegLib_C34_Presets.mrml‎|'''Registration Library Case 34: Parameter Presets''' (presets for bias correction, mask generation, registration & resampling) 12kB, load via ''ImportScene..'') ]]
**[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]
*Documentation:
**See detailed pipeline with parameter settings below

=== Keywords ===
MRI, brain, mouse, masking, non-human, non-rigid,

===Input Data===
*reference/fixed: DTI baseline: 2.5 x 2.5 x 2.5 mm, 128 x 112 x 44
*reference/fixed: DTI tensor: : 2.5 x 2.5 x 2.5 mm, 128 x 112 x 44 x 9 (tensor), original: DWI 256 x 256 x 41 x 36 directions
*moving : T1 , 1x1x1.1 mm voxel size, 256 x 256 x 193

===Registration Challenges===
*The original images have very unusual dynamic range which can cause problems with modules that expect a minimal dynamic range in absolute terms
*target image content is of lower intensity than the surrounding tissue, making masking essential

===Key Strategies===
*'''Slicer 3.6.1 recommended modules: [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BrainsFit]

=== Procedures ===
*'''Phase I: LOAD DATA'''
#download example dataset
#load into 3DSlicer 3.6.1 (Load Scene)
:Note that the main data package does not contain the DWI. Please load separately from the second Data download package.
*'''Phase II: Bias Correction of T1'''
#open Filtering : ''N4ITK MRI Bias Field Correction'' module
##Input: T1
##use presets or choose the following settings: Input Volume: T1_bc ; Brain Mask: create new, rename to "T1_mask"; Subdivisions: 20, Dilation Radius: 1
*'''Phase IVa: Manual Initial Alignment'''
#the two datasets in this case have very large initial misalignment and also a clipped FOV, which makes it difficult for an automated initializer to find the proper position. This increases the likelihood for the automated registration to go awry. To avoid this we adjust the main (translational) misalignment manually. You may skip this step if your data has closer initial alignment
#Go to the ''Data'' module, right-click on the "Scene" node and select "Insert Transform Node"
#select the new transform node and then rename it to "Xf0_ManualInit_T1-DTI", in the ''MRML Node Inspector" (press return after typing)
#place the DTI_base image in the background and the T1_bc image in the foreground
#move the fade slider halfway to the middle so that you can see both volumes
#go to the ''Transforms'' module, move the translation sliders to move the T1 image on top of the DTI, or enter -20 for both LR and IS translation
#in the BRAINSfit module below, select this initialization as starting transform.
*'''Phase IV: Affine Registration'''
#you may be able to skip this step and perform affine + nonrigid registration in one step, however the stepwise approach gives you more insight and control
#Go to the ''BRAINSFit'' module
## enter the following settings:
##Fixed Image: DTI_base, Moving Image: T1_bc
##Registration phases: from ''Initialize with previously generated transform', select "Xf0_ManualInit" node created before.
##Registration phases: check boxes for ''Include Rigid registration phase'', ''Include Scale Versor3D registration phase'' ''Include Affine registration phase''. To combine with Phase V below also check the ''Include BSpline phase'' box.
##Output: Slicer Linear transform: create new, rename to "Xf1_T1-DTI_masked"
##Registration Parameters: increase ''Number Of Samples'' to 200,000
##Control Of Mask Processing Tab: check ''ROI'' box, ''Input Fixed Mask'' : DTI_mask; ''Input Moving Mask'': T1_mask
##Leave all other settings at default
##click apply; runtime ca. 1-2 min.
#go to ''Data'' module. You should see the "T1_bc " volume moved inside the "Xf1.." transform node
#select T1_bc as background and DTI_base as foreground and check the alignment via the toggle switch
*'''Phase V: Nonrigid Registration'''
#Go to the ''BRAINSFit'' module
##enter the following settings:
##Fixed Image: DTI_base, Moving Image: T1_bc
##Registration phases: from ''Initialize with previously generated transform', select "Xf1_..." node created before.
##Registration phases: check boxes for ''Include BSpline registration phase''
##Output: Slicer BSpline transform: create new, rename to "Xf2_T1-DTI_BSpl"
##Output Image Volume: create new, rename to "T1_bc_Xf2"; ''Pixel Type'': "short"
##Registration Parameters: increase ''Number Of Samples'' to 200,000; ''Number of Grid Subdivisions'': 3,3,3
##Control Of Mask Processing Tab: check ''ROI'' box, ''Input Fixed Mask'' : DTI_mask; ''Input Moving Mask'': T1_mask
##Leave all other settings at default
##click apply; runtime ca. 1-2 min.
*The result volume "T1_bc_Xf2" is the one we want, since the DTI remains stationary, there is no additional resampling required. Note that the final transform "Xf2_T1-DTI_BSpl" contains both the affine and nonrigid BSpline portions.
#To check alignment, go to the ''Volumes'' module, select the newly produced ''DTI'' volume
#under the ''Display'' tab, select ''Color Orientation'' from the ''Scalar Mode'' menu
#set ''DTI'' as background and the new "T1_bc_Xf2" volume as foreground
#Set fade slider to see DTI overlay onto the SPGR image, you should see alignment similar to the result shown below.

=== Registration Results===
[[Image:RegLib_C34_AGif_Model.gif‎ |500px|Surface model of original unregistered brains]] original, not registered 
[[Image:RegLib_C34_AGif_Unregistered.gif‎ |500px|original unregistered brains]] original, not registered 
[[Image:RegLib_C34_AGif_Affine.gif |500px| affine registered brains]] affine registered 
[[Image:RegLib_C34_AGif_BSpline.gif |500px|registered brains after 5x5x5 nonrigid BSpline alignment]] registered brains after 5x5x5 nonrigid BSpline alignment]

@@ Line 16: / Line 16: @@
 === Modules ===
-*'''Slicer 3.6.1 recommended modules:'''  [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit '''BrainsFit'''],   [http://www.slicer.org/slicerWiki/index.php/Modules:FastMarchingSegmentation-Documentation-3.6 '''Fast Marching Segmentation'''],   [http://www.slicer.org/slicerWiki/index.php/Modules:HistogramMatching-Documentation-3.6 '''Histogram Matching'''],  [http://www.slicer.org/slicerWiki/index.php/Modules:ModelMaker-Documentation-3.6 '''Model Maker'''],
+*'''Slicer 3.6.1 recommended modules:'''  [https://www.slicer.org/wiki/Modules:BRAINSFit '''BrainsFit'''],   [https://www.slicer.org/wiki/Modules:FastMarchingSegmentation-Documentation-3.6 '''Fast Marching Segmentation'''],   [https://www.slicer.org/wiki/Modules:HistogramMatching-Documentation-3.6 '''Histogram Matching'''],  [https://www.slicer.org/wiki/Modules:ModelMaker-Documentation-3.6 '''Model Maker'''],
 ===Objective / Background ===
@@ Line 41: / Line 41: @@
 ===Key Strategies===
-*'''Slicer 3.6.1 recommended modules:  [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BrainsFit]
+*'''Slicer 3.6.1 recommended modules:  [https://www.slicer.org/wiki/Modules:BRAINSFit BrainsFit]
 === Procedures ===
@@ Line 48: / Line 48: @@
 #we first shift the intensity range to integer range [0,1000] and convert to unsigned short or something equivalent
 #one way to accomplish this in slicer is to perform a histogram matching with a reference volume that has a usable dynamic range
-#Load a reference volume and then use the [http://www.slicer.org/slicerWiki/index.php/Modules:HistogramMatching-Documentation-3.6 '''Histogram Matching'''] module to adjust the dynamic range
+#Load a reference volume and then use the [https://www.slicer.org/wiki/Modules:HistogramMatching-Documentation-3.6 '''Histogram Matching'''] module to adjust the dynamic range
-#use the [http://www.slicer.org/slicerWiki/index.php/Modules:CastImage-Documentation-3.6 '''Cast module'''] to convert the datatype to unsigned short.
+#use the [https://www.slicer.org/wiki/Modules:CastImage-Documentation-3.6 '''Cast module'''] to convert the datatype to unsigned short.
 #save the new volumes
 *'''Phase II: Brain Segmentation'''
 #to obtain a usable mask for both images we first need to segment the two brains
-#go to the [http://www.slicer.org/slicerWiki/index.php/Modules:FastMarchingSegmentation-Documentation-3.6 '''Fast Marching Segmentation'''] module
+#go to the [https://www.slicer.org/wiki/Modules:FastMarchingSegmentation-Documentation-3.6 '''Fast Marching Segmentation'''] module
 #select 2-3 fiducials within the brain (see example dataset .fcv files), set a target size of ~ 0.8 ml and click Apply.
 #save the two labelmaps for the MD1 and MD2 segmentations. These will serve as masks for registration and a guides for initial alignment
@@ Line 59: / Line 59: @@
 #if two datasets have large initial misalignment and also different image content and unusual intensities, this makes it difficult for an automated initializer to find the proper position. This increases the likelihood for the automated registration to go awry. To avoid this we adjust the main (translational) misalignment manually. You may skip this step if your data has closer initial alignment
 #for complex geometries a 3D model can be very helpful in judging alignment. Both VolumeRendering and surface models are viable options. Since we already have two brain segmentations we use these to build 2 surface models:
-# use the [http://www.slicer.org/slicerWiki/index.php/Modules:ModelMaker-Documentation-3.6 '''Model Maker'''] module to build two models for MD1 and MD2 brain segmentation
+# use the [https://www.slicer.org/wiki/Modules:ModelMaker-Documentation-3.6 '''Model Maker'''] module to build two models for MD1 and MD2 brain segmentation
 #Go to the ''Data'' module, right-click on the "Scene" node and select "Insert Transform Node"
 #select the new transform node and then rename it to "Xf1_ManualInit", in the ''MRML Node Inspector" (press return after typing)

@@ Line 94: / Line 94: @@
 === Registration Results===
-[[Image:RegLib_C34_AGif_Model.gif‎ |500px|Surface model of original unregistered brains]] original, not registered<br>
+[[Image:RegLib_C34_AGif_Model.gif‎ |200px|Surface model of original unregistered brains]] original, not registered<br>
 [[Image:RegLib_C34_AGif_Unregistered.gif‎ |500px|original unregistered brains]] original, not registered<br>
 [[Image:RegLib_C34_AGif_Affine.gif |500px| affine registered brains]] affine registered<br>
 [[Image:RegLib_C34_AGif_BSpline.gif |500px|registered brains after 5x5x5 nonrigid BSpline alignment]] registered brains after 5x5x5 nonrigid BSpline alignment]<br>
 <br>