Documentation:Nightly:Registration:RegistrationLibrary:RegLib C41 - Revision history

Meier at 16:23, 2 October 2013

2013-10-02T16:23:22Z

Meier: /* Download (from NAMIC MIDAS) */

2013-10-02T16:22:55Z

Download (from NAMIC MIDAS)

Meier: /* Registration Results */

2013-10-02T16:22:08Z

Registration Results

Meier: /* Registration Results */

2013-10-02T16:21:08Z

Registration Results

Meier at 16:18, 2 October 2013

2013-10-02T16:18:59Z

Meier: /* Procedure */

2013-10-02T16:13:11Z

Procedure

Meier: /* Procedure */

2013-10-02T16:11:51Z

Procedure

Meier at 16:06, 2 October 2013

2013-10-02T16:06:12Z

Show changes

Meier: Created page with ' = Slicer Registration Library Case #41: Mouse Brain MRI = === Input === {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0" |[[Image:RegLib_C41_Thumb1.png|15…'

2013-10-02T15:32:34Z

Created page with ' = Slicer Registration Library Case #41: Mouse Brain MRI = === Input === {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0" |[[Image:RegLib_C41_Thumb1.png|15…'

New page

= Slicer Registration Library Case #41: Mouse Brain MRI =
=== Input ===
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C41_Thumb1.png|150px|lleft|MRI baseline]]
|[[Image:RegArrow_NonRigid.png|100px|lleft]]
|[[Image:RegLib_C41_Thumb2.png|150px|lleft|MRI follow-up]]
|-
|fixed image 1/target MRI mouse #1
|
|moving image MRI mouse #2
|}

== Modules Used ==

== Description ==
Aim is to register the two brains of control mice to eachother.

=== Download ===
*DATA
**[[Media:RegLib_C41_DATA.zip‎|'''Registration Library Case 41 ''' (Data & Solution Xforms, zip file 81 MB) ]]
*Documentation:
**See detailed pipeline with parameter settings below

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

===Input Data===
*reference/fixed MRI: 0.1 x 0.1 x 0.1 mm, 192 x 256 x 192
*moving MRI: 0.1 x 0.1 x 0.1 mm, 192 x 256 x 192

===Registration Challenges===
*The original images are not in standard RAS space, the orientation has axial and sagittal planes flipped
*target image content is of low intensity and small compared to the surrounding tissue, making masking essential

== Procedure ==
[[Image:RegLib_C41_Reorient_transform.png|150px|lleft|transform to reorient volumes to RAS space]]
*'''Phase I: Reorient to RAS space'''
#The original images have their header orientation info in a nonstandard form. As a consequence the image loads with sagittal and axial views switched. To fix we create a reorientation transform
#in the ''Data'' module, right click on the "Scene" node and select "Insert Transform" from the pulldown menu
#In the the ''MRML Node Inspector" below, rename the new transform to "Xf0_reorient" or similar.
#place/drag the image inside the transform node.
#go to the ''Transforms'' module & select "Xf0_reorient" from the menu
#change the identity matrix as shown in the image on the right. To modify an entry, select it via mouseclick, then hit ENTER.
#when finished the 3 views should show, axial, sagittal and coronal views respectively (see result images).
#save
*'''Phase II: Bias Field correction'''
#go to the [http://www.slicer.org/slicerWiki/index.php/Modules:N4ITKBiasFieldCorrection-Documentation-3.6 N4 Bias Correction] module
#select 11_5202 as input and create a new volume as output, renamed to 11_5202_b
#increase iteration parameters to 50,40,40
#click Apply
#repeat for second image 11_5221
#save
*'''Phase III - Part 1: Brain Segmentation'''
#to obtain a usable mask for both images we first need to segment the two brains. You can use the mask for the first to speed up the second.
#go to the ''Editor'' module and select the "Draw" tool
#in each slice, trace the brain contours and close with the ENTER key
#save when finished
#repeat for the second brain. You can save time by duplicating the first mask and then manually align it to roughly match the second. Then resample.
*'''Phase III - Part 2: Brain mask for registration'''
#It is useful for the registration mask to include the outer edges of the brain. Hence we enlarge the mask slightly to extend past this boundary
#Go to the ''Editor'' module, select the "Master" and "Label" volume as for above
#Click on the "Dilation" icon
#check the "8-neighbor" box
#click apply 2-3 times, wait each time for the process to finish and verify that the labelmap mask does indeed grow.
#repeat for the other volume
#save under new name "_mask_dilated.nrrd" etc.
*'''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: 11_5202, Moving Image: 11_5221
##Registration phases: check boxes for ''Include Rigid registration phase'', ''Include Scale Versor3D registration phase'' ''Include Affine registration phase''.
##Output: Slicer Linear transform: create new, rename to "Xf1_Affine"
##Registration Parameters: increase ''Number Of Samples'' to 200,000
##Registration Parameters: reduce "Transform Scale" to 400
##Control Of Mask Processing Tab: check ''ROI'' box, for ''Input Fixed Mask'' and ''Input Moving Mask'' select the two dilated labelmaps from above
##Leave all other settings at default
##click apply
#go to ''Data'' module. You should see the "11_5221" volume moved inside the "Xf1.." transform node
*'''Phase V: Nonrigid Registration'''
#Go to the ''BRAINSFit'' module
##enter the following settings:
##Fixed Image: 11_5202, Moving Image: 11_5221
##Registration phases: from ''Initialize with previously generated transform', select "Xf2_..." node created before.
##Registration phases: check boxes for ''Include BSpline registration phase''
##Output: Slicer BSpline transform: create new, rename to "Xf2_BSpline5"
##Output Image Volume: create new, rename to "11_5221_Xf2"; ''Pixel Type'': "short"
##Registration Parameters: increase ''Number Of Samples'' to 200,000; ''Number of Grid Subdivisions'': 5,5,5
##Control Of Mask Processing Tab: check ''ROI'' box, for ''Input Fixed Mask'' and ''Input Moving Mask'' select the two dilated labelmaps from above
##Leave all other settings at default
##click apply
#Extend of nonrigid alignment will depend on the application. For better match the gridsize can be increased to 7x7x7 and higher, along with the number of sample points. Because larger grid sizes bear the risk of unstable and unfeasible deformations, an iterative approach with increasing DOF is recommended. Since the current version (3.6.1) of Slicer does not yet support concatenation of nonrigid transforms, such a stepwise approach implies multiple resampling of the moving volume and associated interpolation blurring.

=== Registration Results===
shown are, from left to right, panels of '''axial''', '''sagittal''' and '''coronal''' views. 
[[Image:RegLib_C41_Reorient_before.png‎ |500px|original brain in non-RAS orientation]] original, not RAS 
[[Image:RegLib_C41_Reorient_after.png‎ |500px|original brain in proper RAS orientation]] original,after reorientation into RAS 

----

[[Image:RegLib_C41_unreg.gif‎ |500px|original unregistered brains]] original, not registered 
[[Image:RegLib_C41_affine.gif‎|500px| affine registered brains]] affine registered 
[[Image:RegLib_C41_BSpline.gif |500px|registered brains after 5x5x5 nonrigid BSpline alignment]] registered brains after 5x5x5 nonrigid BSpline alignment 
[[Image:RegLib_C41_defgrid.png |500px|deformation visualized by grid overlay]] deformation visualized by grid overlay 
 
=== Acknowledgments ===
Many thanks to ''Lili X. Cai'' from the [http://web.mit.edu/jasanofflab/ Jasanoff Laboratory at MIT] for sharing the Data and registration problem.

← Older revision		Revision as of 16:23, 2 October 2013
Line 1:		Line 1:
		+	[[Documentation/Nightly/Registration/RegistrationLibrary\|Back to Registration Library]] <br>
		+
	= Slicer Registration Library Case #41: Mouse Brain MRI =		= Slicer Registration Library Case #41: Mouse Brain MRI =
	=== Input ===		=== Input ===

@@ Line 22: / Line 22: @@
 == Download (from NAMIC MIDAS) ==
 <small>''Why 2 sets of files?  The "input data" mrb includes only the unregistered data to try the method yourself from start to finish. The full dataset includes intermediate files and results (transforms, resampled images etc.). If you use the full dataset we recommend to choose different names for the images/results you create yourself to distinguish the old data from the new one you generated yourself. ''</small>
-*[http://slicer.kitware.com/midas3/download/?items=xx '''RegLib_C41.mrb''': input data only, use this to run the tutorial from the start <small>(Slicer mrb file. 32 MB). </small>]
+*[http://slicer.kitware.com/midas3/download/?items=119689 '''RegLib_C41.mrb''': input data only, use this to run the tutorial from the start <small>(Slicer mrb file. 32 MB). </small>]
-*[http://slicer.kitware.com/midas3/download/?items=xx '''RegLib_C41_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify <small>(Slicer mrb file. 97 MB). </small>]
+*[http://slicer.kitware.com/midas3/download/?items=119688 '''RegLib_C41_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify <small>(Slicer mrb file. 97 MB). </small>]
 == Keywords ==

@@ Line 106: / Line 106: @@
 [[Image:RegLib_C41_unregistered.gif|500px|original unregistered brains]] original, not registered<br>
-[[Image:RegLib_C41_registered_Affine|500px| affine registered brains]] affine registered<br>
+[[Image:RegLib_C41_registered_Affine.gif|500px| affine registered brains]] affine registered<br>
 [[Image:RegLib_C41_registered_BSpline.gif|500px|registered brains after 5x5x5 nonrigid BSpline alignment]] registered brains after 5x5x5 nonrigid BSpline alignment<br>
 <br>

@@ Line 100: / Line 100: @@
 === Registration Results===
 shown are, from left to right, panels of '''axial''', '''sagittal''' and '''coronal''' views. <br>
-[[Image:RegLib_C41_Reorient_before.png‎ |500px|original brain in non-RAS orientation]] original, not RAS<br>
+[[Image:RegLib_C41_original.png|500px|original brain in non-RAS orientation]] original, not RAS<br>
-[[Image:RegLib_C41_Reorient_after.png‎ |500px|original brain in proper RAS orientation]] original,after reorientation into RAS<br>
+[[Image: RegLib_C41_RASoriented.png‎ |500px|original brain in proper RAS orientation]] original,after reorientation into RAS<br>
 ----
-[[Image:RegLib_C41_unreg.gif‎ |500px|original unregistered brains]] original, not registered<br>
+[[Image:RegLib_C41_unregistered.gif|500px|original unregistered brains]] original, not registered<br>
-[[Image:RegLib_C41_affine.gif‎|500px| affine registered brains]] affine registered<br>
+[[Image:RegLib_C41_registered_Affine|500px| affine registered brains]] affine registered<br>
-[[Image:RegLib_C41_BSpline.gif |500px|registered brains after 5x5x5 nonrigid BSpline alignment]] registered brains after 5x5x5 nonrigid BSpline alignment<br>
+[[Image:RegLib_C41_registered_BSpline.gif|500px|registered brains after 5x5x5 nonrigid BSpline alignment]] registered brains after 5x5x5 nonrigid BSpline alignment<br>
 <br>
 === Acknowledgments ===
 Many thanks to ''Lili X. Cai''  from the [http://web.mit.edu/jasanofflab/  Jasanoff Laboratory at MIT] for sharing the Data and registration problem.

@@ Line 31: / Line 31: @@
 *reference/fixed MRI: 0.1 x 0.1 x 0.1 mm, 192 x 256 x 192
 *moving MRI: 0.1 x 0.1 x 0.1 mm, 192 x 256 x 192
 == Procedure ==
-#'''Reorient to RAS space''':
+#'''Reorient to RAS space''': ([[Media:RegLib_C41_2_RASfix.mov|Movie/screencast for this step]])
 ##go to the [[Documentation/Nightly/Modules/Data| ''Data'']] module
 ###right click on the "Scene" node and select "Insert Transform" from the pulldown menu
@@ Line 43: / Line 50: @@
 ###you should see the images in the position as shown in the results below, with the eyes looking up in the axial (red) and left in the sagittal (yellow)  view.
 ##save intermediate results
-#'''Bias Correction''': Correct for local intensity inhomogeneities [[Media: RegLib_C06_2_BiasCorrection.mov|(screencast for this step)]]
+#'''Bias Correction''': Correct for local intensity inhomogeneities  ([[Media:RegLib_C41_1_BiasCorrection.mov|Movie/screencast for this step]])
 ##Open the [[Documentation/Nightly/Modules/Editor| ''Editor'']] module  (we first build a rough mask for better filtering results)
 ###select "mouse1" as input image, accept the default colormap settings.
@@ Line 59: / Line 66: @@
 ##repeat for the "mouse2" image. Same settings
 ##save intermediate results
-#''Build Registration Masks''': we now rebuild masks for the registration. You could also use the masks generated above, but we will generate more accurate ones with relatively little effort. Note that registration masks need not be overly accurate but should include the main boundaries of the structure of interest, in this case the brain. We seek a method that will let us generate such a mask quickly and without excessive manual editing.
+#''Build Registration Masks''': we now rebuild masks for the registration. You could also use the masks generated above, but we will generate more accurate ones with relatively little effort. Note that registration masks need not be overly accurate but should include the main boundaries of the structure of interest, in this case the brain. We seek a method that will let us generate such a mask quickly and without excessive manual editing.  ([[Media:RegLib_C41_3_BuildMask1.mov|Movie/screencast for this step]])
 ##Open the [[Documentation/Nightly/Modules/Editor| ''Editor'']] module  (we first build a rough mask for better filtering results)
 ###select "mouse1" as input image, accept the default colormap settings. Create a new label map (do not use the one already generated above)
@@ Line 67: / Line 74: @@
 ###left click inside the brain in any of the 3 views. Wait a few seconds for the effect to run and the display to update. You will see speckled segmentation overlay being added for each click. Do not worry about the speckled nature of the result at this point, we will fix that later. What we want is points to cover largely the extent of the brain in all dimensions. Use all 3 views to place seeds. See the screencast for details. Once you have most of the brain covered, proceed with next step below.
 ###select the "Dilate" tool [[Image:DilateEffectIcon.png|30px]]. Click the "Apply" button 2-3 times until the mask closes the gaps and encloses all of the brain and a bit beyond
-###repeat for the "mouse2" image
+###repeat for the "mouse2" image:  ([[Media:RegLib_C41_3_BuildMask2.mov|Movie/screencast for this step]])
-#'''Affine Registration''': open the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
+#'''Affine Registration''': open the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]].  ([[Media:RegLib_C41_4_Register.mov|Movie/screencast for this step]])
 ##''Input Images: Fixed Image Volume'': mouse1_N4
 ##''Input Images: Moving Image Volume'': mouse2_N4

@@ Line 46: / Line 46: @@
 ##Open the [[Documentation/Nightly/Modules/Editor| ''Editor'']] module  (we first build a rough mask for better filtering results)
 ###select "mouse1" as input image, accept the default colormap settings.
-###select the "Threshold" tool. [[Image:ThresholdToolIcon.png|30px]].
+###select the "Threshold" tool. [[Image:ThresholdEffectIcon.png|30px]].
 ###drag the left side of the threshold range slider until most of the brain is included. Then click "Apply"
 ###select the "Dilate" tool. Click the "Apply" button 2-3 times until the mask encloses all of the brain and a bit beyond
@@ Line 62: / Line 62: @@
 ##Open the [[Documentation/Nightly/Modules/Editor| ''Editor'']] module  (we first build a rough mask for better filtering results)
 ###select "mouse1" as input image, accept the default colormap settings. Create a new label map (do not use the one already generated above)
-###select the "Magic Wand" tool. [[Image:MagicWandToolIcon.png|30px]].
+###select the "Magic Wand" tool. [[Image:MagicWandEffectIcon.png|30px]].
 ###change the default tolerance and size limits to: 800 and 8000, respectively
 ###check the "Fill Volume" checkbox to apply the effect in 3D.
 ###left click inside the brain in any of the 3 views. Wait a few seconds for the effect to run and the display to update. You will see speckled segmentation overlay being added for each click. Do not worry about the speckled nature of the result at this point, we will fix that later. What we want is points to cover largely the extent of the brain in all dimensions. Use all 3 views to place seeds. See the screencast for details. Once you have most of the brain covered, proceed with next step below.
-###select the "Dilate" tool. Click the "Apply" button 2-3 times until the mask closes the gaps and encloses all of the brain and a bit beyond
+###select the "Dilate" tool [[Image:DilateEffectIcon.png|30px]]. Click the "Apply" button 2-3 times until the mask closes the gaps and encloses all of the brain and a bit beyond
 ###repeat for the "mouse2" image
 #'''Affine Registration''': open the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]

@@ Line 33: / Line 33: @@
 == Procedure ==
 #'''Reorient to RAS space''':
 ##go to the [[Documentation/Nightly/Modules/Data| ''Data'']] module
@@ Line 41: / Line 39: @@
 ###place/drag both images inside the transform node.
 ##go to the  [[Documentation/Nightly/Modules/Transforms| ''Transforms'']] ' module & select "Xf0_reorient" from the menu
-###change the identity matrix as shown in the image here. To modify an entry, double-click the field, then edit and to confirm hit the ENTER key.
+###change the identity matrix as shown in the image here. To modify an entry, double-click the field, then edit and to confirm hit the ENTER key.[[Image:RegLib_C41_Reorient_transform.png|150px|lleft|transform to reorient volumes to RAS space]]
 ###switch the "1" in the 1st and last row to the last and first column, respectively. Change the sign of the "1" in the middle row to "-1"
 ###you should see the images in the position as shown in the results below, with the eyes looking up in the axial (red) and left in the sagittal (yellow)  view.