Documentation:Nightly:Registration:RegistrationLibrary:RegLib C42 - Revision history

Meier: /* Procedure */

2013-10-01T19:02:56Z

Procedure

Meier at 18:57, 1 October 2013

2013-10-01T18:57:52Z

Meier: /* Registration Results */

2013-10-01T18:55:24Z

Registration Results

Meier at 18:51, 1 October 2013

2013-10-01T18:51:47Z

Meier: Created page with '= Slicer Registration Library Case #42:
Intra-subject Brain MRI: serial assessment of brain development in autism = == Input == {| style="color:#bbbbbb; " cellpadding="10" c…'

2013-10-01T18:49:49Z

Created page with '= Slicer Registration Library Case #42: <br>Intra-subject Brain MRI: serial assessment of brain development in autism = == Input == {| style="color:#bbbbbb; " cellpadding="10" c…'

New page

= Slicer Registration Library Case #42: <br>Intra-subject Brain MRI: serial assessment of brain development in autism =
== Input ==
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C42_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_C42_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 Used ==

===Description ===
This is a typical case of change assessment.

=== Keywords ===
MRI, brain, head, intra-subject, T1, autism, change assessment, pediatric MRI

=== Procedures ===
*'''Phase I: Register Rigid/Affine'''
#open Registration : ''BrainsFit'' module (presets: BRAINSfit_Xf1 or _Xf2
##Input Parameters:
###Fixed: "Autism_T1_2yrs"
###Moving: "Autism_T1_4yrs"
##Registration Phases:
###select/check ''Include Rigid registration phase'' , ''Include Scale Versor 3D'' , ''Include Affine'', ''Include BSpline''
##Output Settings
###select a new "Slicer BSpline Transform", rename to "Xf3_Affine+BSpline" or similar "
###select a new volume "Output Image Volume'', rename to "Autism_T1_4yrs_Xf3", indicating that this is the result volume after being resampled with the Xf3 transform.
###Output Image Pixel Type: check "ushort". As a general rule, match the datatype of the input image, unless specific reason demands otherwise (e.g. you wish to avoid rounding of interpolation effects). The "float" datatype is 4-bytes per pixel and can produce unnecessary large files.
##Registration Parameters:
###increase ''Number Of Samples'' to 300,000
##Registration Parameters: set ''Number Of Grid Subdivisions'' to 5,5,5
##Leave all other settings at default
##click Apply
=== Registration Results===
{| style="color:#bbbbbb; background-color:#333333;" cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C42_unregistered.gif|400px|center|unregistered]]
|original unregistered
|-
|[[Image:RegLib_C42_affine.gif|400px|center|rigid]]
|[[Image:RegLib_C42_Xf2_registered.gif|400px|center|affine]]
|-
|affine registered
|nonrigid registered (5,5,5 BSpline unmasked)
|-
|[[Image:RegLib_C42_Xf2a_DeformOnly.gif|400px|center|BSpline (7x7x7) unmasked]]
|
|-
|visualization of the nonrigid deformation component only
|
|}

@@ Line 27: / Line 27: @@
 == Procedure ==
-*'''Phase I:  Register Rigid/Affine'''
+#'''Affine Registration''': open the  [[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']] module.
-#open Registration : ''BrainsFit'' module (presets: BRAINSfit_Xf1 or _Xf2
+##''Fixed Image Volume'': "Autism_T1_4yrs"
-##Input Parameters:
+##''Moving Volume'': "Autism_T1_2yrs"
-###Fixed: "Autism_T1_2yrs"
+##Registration phases: check boxes for ''Rigid" ,"Scale", "Affine"
-###Moving:  "Autism_T1_4yrs"
+##''Slicer Linear Transform'': select "create new transform", rename to "Xf1_Affine" or similar
-##Registration Phases:
+##leave rest at defaults. Click ''Apply''
-###select/check ''Include Rigid registration phase'' , ''Include Scale Versor 3D'' , ''Include Affine'', ''Include BSpline''
+##registration should take ~ 10 secs.
-##Output Settings
+##use fade slider to verify alignment; compare with result snapshots shown below. Alignment will not be perfect but should be better than before.
-###select a new "Slicer BSpline Transform", rename to "Xf3_Affine+BSpline" or similar "
+##note: you can also change the colormaps for the fixed and moving volumes to better judge the alignment: go to the  [[Documentation/Nightly/Modules/Volumes| ''Volumes'']] module and in the ''Display'' tab, select "green" and "magenta" as the respective colormaps for the two volumes (vhf, vhm)
-###select a new volume "Output Image Volume'', rename to "Autism_T1_4yrs_Xf3", indicating that this is the result volume after being resampled with the Xf3 transform.
+#'''Nonrigid Registration''': open the  [[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']].
-###Output Image Pixel Type: check "ushort". As a general rule, match the datatype of the input image, unless specific reason demands otherwise (e.g. you wish to avoid rounding of interpolation effects). The "float" datatype is 4-bytes per pixel and can produce unnecessary large files.
+##''Fixed/Moving Image Volume'': as above
-##Registration Parameters:
+##Registration phases: uncheck boxes for rigid, scale and affine and check box for  ''BSpline''
-###increase ''Number Of Samples'' to 300,000
+##Output: Slicer Linear transform: set to None
-##Registration Parameters: set  ''Number Of Grid Subdivisions'' to 5,5,5
+##Output: Slicer BSpline transform: create new, rename to "Xf2_BSpline" or similar
 ##Leave all other settings at default
-##click Apply
+##click apply
 == Registration Results==

@@ Line 12: / Line 12: @@
 |}
-== Modules Used ==
+== Modules used ==
 == Description ==
 This is a typical case of change assessment.
 === Keywords ===
 MRI, brain, head, intra-subject, T1, autism, change assessment, pediatric MRI
+== Procedure ==
 *'''Phase I:  Register Rigid/Affine'''
 #open Registration : ''BrainsFit'' module (presets: BRAINSfit_Xf1 or _Xf2
@@ Line 41: / Line 43: @@
 ##Leave all other settings at default
 ##click Apply
 [[Image:RegLib_C42_unregistered.gif|300px]] baseline and follow-up before registration (click to enlarge) <br>
 [[Image:RegLib_C42_affine.gif|300px]] after affine alignment. Note the residual shape differences (click to enlarge) <br>

@@ Line 42: / Line 42: @@
 ##click Apply
 === Registration Results===
-{| style="color:#bbbbbb; background-color:#333333;" cellpadding="10" cellspacing="0" border="0"
-|[[Image:RegLib_C42_unregistered.gif|400px|center|unregistered]]
+[[Image:RegLib_C42_unregistered.gif|300px]] baseline and follow-up before registration (click to enlarge) <br>
-|original unregistered
+[[Image:RegLib_C42_affine.gif|300px]] after affine alignment. Note the residual shape differences (click to enlarge) <br>
-|-
+[[Image:RegLib_C42_Xf2_registered.gif|300px]] after nonrigid BSpline registration (click to enlarge) <br>
-|[[Image:RegLib_C42_affine.gif|400px|center|rigid]]
+[[Image:RegLib_C42_Xf2a_DeformOnly.gif|300px]]| visualization of the nonrigid deformation component only <br>
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