Projects:RegistrationLibrary:RegLib C42 - Revision history

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

2017-07-10T18:07:12Z

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

Meier: /* v3.6.1 150px Slicer Registration Library Case #42: Intra-subject Brain MRI: serial assessment of brain development in autism */

2011-08-12T13:38:52Z

v3.6.1 150px Slicer Registration Library Case #42: Intra-subject Brain MRI: serial assessment of brain development in autism

Meier: /* Registration Results */

2011-08-05T14:25:00Z

Registration Results

Meier: /* Registration Results */

2011-08-05T14:24:47Z

Registration Results

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

2011-08-05T14:16:14Z

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

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==v3.6.1 [[Image:Slicer3-6Announcement-v1.png‎|150px]] Slicer Registration Library Case #42: 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 ===
'''Slicer 3.6.3''' recommended modules:
*[http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BrainsFit]

===Objective / Background ===
This is a typical case of change assessment.
=== Keywords ===
MRI, brain, head, intra-subject, T1, tumor, change assessment, pediatric MRI

===Input Data===
*reference/fixed : T1 SPGR , 1x1x1 mm voxel size, 256x256x192 ,sagittal
*moving: T1 SPGR , 1x1x1 mm voxel size, 256x256x192 ,sagittal

=== Overall Strategy ===
:#run rigid/affine registration (BRAINSfit) without initialization (initial positions are sufficiently close)
:#run 5x5x5 nonrigid regista=ration (BRAINSfit BSpline) using the above affine as input

=== 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.gif|400px|center|BSpline (7x7x7) unmasked]]
|
|-
|visualization of the nonrigid deformation component only
|
|}

===Download ===
*Data
**[[Media:RegLib_C42_Data.zip‎ ‎|'''RegLib_C42_Data''' , image data, resets & solution transforms (NRRD files, zip file 16 MB) ]]'''
*Presets
**[[Media:RegLib_C42_RegPresets.mrml‎|'''RegLib_C42_Presets''' Presets for BRAINSFIT registration (.mrml file 12 kB) ]]'''
**[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]

@@ Line 3: / Line 3: @@
 [[Projects:RegistrationDocumentation:UseCaseInventory|Back to Registration Case Library]] <br>
-==<small>v3.6.1</small> [[Image:Slicer3-6Announcement-v1.png‎|150px]] Slicer Registration Library Case #42: <br>Intra-subject Brain MRI:  serial assessment of brain development in autism ==
+==<small>v3.6.3</small> [[Image:Slicer3-6Announcement-v1.png‎|150px]] 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"

@@ Line 60: / Line 60: @@
 |nonrigid registered (5,5,5 BSpline unmasked)
 |-
-|[[Image:RegLib_C42_Xf2a_DeformOnly.gif.|400px|center|BSpline (7x7x7) unmasked]]
+|[[Image:RegLib_C42_Xf2a_DeformOnly.gif|400px|center|BSpline (7x7x7) unmasked]]
+|
 |-

@@ 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]
 ===Objective / Background ===

Projects:RegistrationLibrary:RegLib C42 - Revision history

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

Meier: /* v3.6.1 150px Slicer Registration Library Case #42: Intra-subject Brain MRI: serial assessment of brain development in autism */

Meier: /* Registration Results */

Meier: /* Registration Results */

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…'