Projects:RegistrationLibrary:RegLib C32 - Revision history

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2017-07-10T17:45:54Z

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

Meier: /* Download */

2010-11-12T15:42:41Z

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Meier: /* Procedures */

2010-11-12T15:27:42Z

Procedures

Meier: /* Procedures */

2010-11-12T14:59:58Z

Procedures

Meier: /* Procedures */

2010-11-12T14:55:09Z

Procedures

Meier: /* Registration Results */

2010-11-11T22:39:59Z

Registration Results

Meier at 22:27, 11 November 2010

2010-11-11T22:27:24Z

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

2010-11-11T22:21:35Z

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= v3.6.1 [[Image:Slicer3-6Announcement-v1.png‎|150px]] Slicer Registration Library Case #32: Intra-subject Brain DTI =
=== Input ===
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C30_Thumb2.png|150px|lleft|this is the DTI Baseline scan, to be registered with the T1]]
|[[Image:RegLib_C30_Thumb3.png|150px|lleft|this is the DTI tensor image, in the same orientation as the DTI Baseline]]
|[[Image:RegArrow_NonRigid.png|100px|lleft]]
|[[Image:RegLib_C30_Thumb1.png|150px|lleft|this is the fixed reference image. All images are aligned into this space]]
|-
|fixed image 1/target DTI baseline
|fixed image 1/target DTI tensor
|
|moving image T1
|}

=== 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 '''Skull Stripping Module'''], [http://www.slicer.org/slicerWiki/index.php/Modules:N4ITKBiasFieldCorrection-Documentation-3.6 '''N4 MRI Bias Field Correction''']

===Objective / Background ===
This is a common case of a DTI exam with no T2 available as structural reference and a T1 that has strong field inhomogeneity. We wish to spatially align the DTI to the anatomical reference scan (T1-SPGR).

=== Download ===
*DATA
**[[Media:RegLib_C30_Data.zip‎|'''Registration Library Case 30 (registration set) ''' (Data & Solution Xforms, incl. DTI, zip file 18 MB) ]]
**[[Media:RegLib_C30_Data2.zip‎|'''Registration Library Case 30 (DWI+resampled DTI set) ''' (original DWI + resampled DTI only, zip file 53 MB) ]]
*PRESETS:
**[[Media:RegLib_C30_Presets.mrml‎|'''Registration Library Case 30: 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
**[[Media:RegLib_C30_DTI.ppt| Powerpoint Tutorial (.ppt PowerPoint file, MB)]]
**[[Media:RegLib_C30_DTI.pdf| Powerpoint Tutorial as PDF (PDF file MB)]]

=== Keywords ===
MRI, brain, head, intra-subject, DTI, T1, non-rigid,

===Input Data===
*reference/fixed : T1 , 1x1x1.1 mm voxel size, 256 x 256 x 193
*moving: DTI baseline: 2.5 x 2.5 x 2.5 mm, 128 x 112 x 44
*moving 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

===Registration Challenges===
*The DTI sequence (EPI) has a low resolution, a clipped FOV and distortions we seek to correct via non-rigid alignment
*the DTI baseline is similar in contrast to a T2, but we have only a T1 as structural reference

===Key Strategies===
*'''Slicer 3.6.1 recommended modules: [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BrainsFit]
*to align the DTI with the T1 we need 2 preprocessing steps: 1. reduce the bias field inhomogeneity in the reference T1 and 2. obtain a skull-stripping / brain mask for the T1
*The DWI is already isotropic and hence no resampling is required before obtaining the DTI
*the DTI-T2 registration includes non-rigid deformation to correct for the strong distortions from the EPI acquisition. Because of the nonrigid component a mask of the brain parenchyma helps greatly in obtaining a meaningful transform.
*The DTI estimation provides an automated mask for the DTI_baseline scan, but we have no mask for the T1. We can either obtain one through separate segmentation or by sending the DTI_mask through an additional registration step. We use the former here.
*thus the full pipeline is this:
:#Bias Field Correction of T1 -> T1_bc
:#Skull Stripping of T1_bc
:#DWI -> DTI estimation (incl. DTI_base and DT_mask output)
:#Affine registration of DTI_baseline to T1_bc, unmasked
:#non-rigid (BSpline) registration of DTI_baseline to T1_bc, masked, using above affine as starting pose
:#resample DTI with result Affine+BSpline transform

=== Procedures ===
*note: for guidance on obtaining the DTI estimate from the DWI see [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorEstimation-Documentation-3.6 here] or the tutorials for [[Projects:RegistrationLibrary:RegLib_C27| Library case #27]]
*'''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
##Output: create new volume, rename to T1_bc
##Use presets or set parameters: ''BSpline grid'': 2,2,2 ; ''Shrink Factor'': 4
##Click: Apply
##the bias-corrected image will be of type 'float'; to save memory convert to 'uint':
#Open ''Cast Image'' module
##Input: T1_bc, Output: T1_bc
##Output Type: unsigned short
*'''Phase III: Skull Stripping'''
#Open "Skull Skull Stripper for Structural MR'': This is an extension module. If you have never used it before you need to load it first via the extension manager
##Click on the gear wheel icon to the right of the ''Modules'' menu. Select the ''Skull Stripper'' module and click download and install. Save prelim. work and then restart Slicer to load
##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 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
##use presets ''Xf1_DTI-T1_masked_Aff1'' or enter the following settings:
##Fixed Image: T1_bc, Moving Image: DTI_base
##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_DTI-T1_masked"
##Registration Parameters: increase ''Number Of Samples'' to 200,000
##Control Of Mask Processing Tab: check ''ROI'' box, ''Input Fixed Mask'' : T1_mask; ''Input Moving Mask'': DTI_mask
##Leave all other settings at default
##click apply; runtime ca. 1-2 min.
#go to ''Data'' module. You will see the "DTI_base" 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
##use presets ''Xf2_DTI-T1_BSpl'' or enter the following settings:
##Fixed Image: T1_bc, Moving Image: DTI_base
##Registration phases: check boxes for ''Include BSpline registration phase''
##Output: Slicer BSpline transform: create new, rename to "Xf2_DTI-T1_BSpl"
##Output Image Volume: create new, rename to "DTI_base_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'' : T1_mask; ''Input Moving Mask'': DTI_mask
##Leave all other settings at default
##click apply; runtime ca. 1-2 min.
*'''Phase VI: Resample DTI'''
#Open the ''Resample DTI Volume'' module (found under: All Modules)
##Input Volume: select DTI
##Output Volume: select ''New DTI Volume'', rename to ''DTI_Xf2''
##Reference Volume: select ''T1''
##Transform Parameters: select transform "Xf2_DTI-T1''
##check box: ''output-to-input''
##Leave all other settings at defaults
##Click Apply; runtime 3-4 min.
#Go to the ''Volumes'' module, select the newly produced ''DTI_Xf2'' volume
#under the ''Display'' tab, select ''Color Orientation'' from the ''Scalar Mode'' menu
#set ''T1'' as background and new ''DTI_Xf2'' volume as foreground
#Set fade slider to see DTI overlay onto the SPGR image

for more details see the tutorial(s) under Downloads

=== Registration Results===
[[Image:RegLib_C30_AGif_reg.gif‎ |500px|Registered DTI superimposed on T1]] registered

@@ Line 25: / Line 25: @@
 === Download ===
 *DATA
-**[[Media:RegLib_C32_Data.zip‎|'''Registration Library Case 32 (registration set)  '''<small> (Data & Solution Xforms, incl. DTI,  zip file 18 MB) </small>]]
+**[[Media:RegLib_C32_Data.zip‎|'''Registration Library Case 32 (registration set)  '''<small> (Data & Solution Xforms, incl. DWI and DTI,  zip file 35 MB) </small>]]
 *PRESETS:
 **[[Media:RegLib_C32_Presets.mrml‎|'''Registration Library Case 32:  Parameter Presets''' <small> (presets for bias correction, mask generation,  registration & resampling) 12kB, load via ''ImportScene..'') </small>]]

@@ Line 78: / Line 78: @@
 ##Click on the gear wheel icon to the right of the ''Modules'' menu. Select the ''Skull Stripper'' module and click download and install. Save prelim. work and then restart Slicer to load
 ##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 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
@@ Line 83: / Line 91: @@
 ## enter the following settings:
 ##Fixed Image: DTI_base, Moving Image: T1_bc
 ##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"

@@ Line 95: / Line 95: @@
 ##enter the following settings:
 ##Fixed Image: DTI_base, Moving Image: T1_bc
 ##Registration phases: check boxes for  ''Include BSpline registration phase''
 ##Output: Slicer BSpline transform: create new, rename to "Xf2_T1-DTI_BSpl"
@@ Line 102: / Line 103: @@
 ##Leave all other settings at default
 ##click apply; runtime ca. 1-2 min.
-*'''Phase VI: Resample DTI'''
+*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.
-#Open the ''Resample DTI Volume'' module (found under: All Modules)
+#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 ''T1'' as background and new  ''DTI_Xf2'' volume as foreground
+#set ''DTI'' as background and the new  "T1_bc_Xf2" volume as foreground
-#Set fade slider to see DTI overlay onto the SPGR image
+#Set fade slider to see DTI overlay onto the SPGR image, you should see alignment similar to the result shown below.
 === Registration Results===
 [[Image:RgLib_C32_AGif_reg.gif‎ |500px|Registered T1 superimposed on DTI]] registered<br>
 <br>

@@ Line 119: / Line 119: @@
 === Registration Results===
-[[Image:RegLib_C32_AGif_reg.gif‎ |500px|Registered T1 superimposed on DTI]] registered<br>
+[[Image:RgLib_C32_AGif_reg.gif‎ |500px|Registered T1 superimposed on DTI]] registered<br>
 <br>

@@ Line 18: / Line 18: @@
 === 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 '''Skull Stripping Module'''],   [http://www.slicer.org/slicerWiki/index.php/Modules:N4ITKBiasFieldCorrection-Documentation-3.6 '''N4 MRI Bias Field Correction''']
+*'''Slicer 3.6.1 recommended modules:'''  [https://www.slicer.org/wiki/Modules:BRAINSFit '''BrainsFit'''],   [https://www.slicer.org/wiki/Modules:SkullStripperModule '''Skull Stripping Module'''],   [https://www.slicer.org/wiki/Modules:N4ITKBiasFieldCorrection-Documentation-3.6 '''N4 MRI Bias Field Correction''']
 ===Objective / Background ===
@@ Line 45: / Line 45: @@
 ===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]
 *to align the DTI and the T1 we need 2 preprocessing steps: 1. reduce the bias field inhomogeneity in the reference T1 and 2. obtain a skull-stripping / brain mask for the T1
 *The DWI is already isotropic and hence no resampling is required before obtaining the DTI
@@ Line 58: / Line 58: @@
 === Procedures ===
-*note: for guidance on obtaining the DTI estimate from the DWI see [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorEstimation-Documentation-3.6 here] or the tutorials for [[Projects:RegistrationLibrary:RegLib_C27| Library case #27]]
+*note: for guidance on obtaining the DTI estimate from the DWI see [https://www.slicer.org/wiki/Modules:DiffusionTensorEstimation-Documentation-3.6 here] or the tutorials for [[Projects:RegistrationLibrary:RegLib_C27| Library case #27]]
 *'''Phase I: LOAD DATA'''
 #download example dataset

@@ Line 81: / Line 81: @@
 #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
-##use presets ''Xf1_DTI-T1_masked_Aff1'' or enter the following settings:
+## enter the following settings:
-##Fixed Image: T1_bc, Moving Image: DTI_base
+##Fixed Image: DTI_base, Moving Image: T1_bc
-##Registration phases: check boxes for  ''Include Rigid registration phase'', ''Include Scale Versor3D registration phase''  ''Include Affine registration phase''
+##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_DTI-T1_masked"
+##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'' : T1_mask; ''Input Moving Mask'': DTI_mask
+##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 will see the "DTI_base" volume moved inside the "Xf1.." transform node
+#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
-##use presets ''Xf2_DTI-T1_BSpl'' or enter the following settings:
+##enter the following settings:
-##Fixed Image: T1_bc, Moving Image: DTI_base
+##Fixed Image: DTI_base, Moving Image: T1_bc
 ##Registration phases: check boxes for  ''Include BSpline registration phase''
-##Output: Slicer BSpline transform: create new, rename to "Xf2_DTI-T1_BSpl"
+##Output: Slicer BSpline transform: create new, rename to "Xf2_T1-DTI_BSpl"
-##Output Image Volume:  create new, rename to "DTI_base_Xf2"; ''Pixel Type'': "short"
+##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'' : T1_mask; ''Input Moving Mask'': DTI_mask
+##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.

@@ Line 21: / Line 21: @@
 ===Objective / Background ===
-This is a common case of a DTI exam with no T2 available as structural reference and a T1 that has strong field inhomogeneity. We wish to spatially align the DTI to the anatomical reference scan (T1-SPGR).
+This is a common case of a DTI exam with no T2 available as structural reference and a T1 that has strong field inhomogeneity. In this particular case we seek the inverse alignment of the T1 with the DTI.
 === Download ===
 *DATA
-**[[Media:RegLib_C30_Data.zip‎|'''Registration Library Case 30 (registration set)  '''<small> (Data & Solution Xforms, incl. DTI,  zip file 18 MB) </small>]]
+**[[Media:RegLib_C32_Data.zip‎|'''Registration Library Case 32 (registration set)  '''<small> (Data & Solution Xforms, incl. DTI,  zip file 18 MB) </small>]]
-**[[Media:RegLib_C30_Data2.zip‎|'''Registration Library Case 30 (DWI+resampled DTI set)  '''<small> (original DWI + resampled DTI only, zip file 53 MB) </small>]]
+**[[Media:RegLib_C32_Data2.zip‎|'''Registration Library Case 32 (DWI+resampled DTI set)  '''<small> (original DWI + resampled DTI only, zip file 53 MB) </small>]]
 *PRESETS:
-**[[Media:RegLib_C30_Presets.mrml‎|'''Registration Library Case 30:  Parameter Presets''' <small> (presets for bias correction, mask generation,  registration & resampling) 12kB, load via ''ImportScene..'') </small>]]
+**[[Media:RegLib_C32_Presets.mrml‎|'''Registration Library Case 32:  Parameter Presets''' <small> (presets for bias correction, mask generation,  registration & resampling) 12kB, load via ''ImportScene..'') </small>]]
 **<small>[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]</small>
 *Documentation:
 **See detailed pipeline with parameter settings below
 === Keywords ===
@@ Line 39: / Line 37: @@
 ===Input Data===
-*reference/fixed : T1 , 1x1x1.1 mm voxel size, 256 x 256 x 193
+*reference/fixed: DTI  baseline: 2.5 x 2.5 x 2.5 mm, 128 x 112 x 44
-*moving: 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 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===
@@ Line 49: / Line 47: @@
 ===Key Strategies===
 *'''Slicer 3.6.1 recommended modules:  [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BrainsFit]
-*to align the DTI with the T1 we need 2 preprocessing steps: 1. reduce the bias field inhomogeneity in the reference T1 and 2. obtain a skull-stripping / brain mask for the T1
+*to align the DTI and the T1 we need 2 preprocessing steps: 1. reduce the bias field inhomogeneity in the reference T1 and 2. obtain a skull-stripping / brain mask for the T1
 *The DWI is already isotropic and hence no resampling is required before obtaining the DTI
-*the DTI-T2 registration includes non-rigid deformation to correct for the strong distortions from the EPI acquisition. Because of the nonrigid component a mask of the brain parenchyma helps greatly in obtaining a meaningful transform.
+*the T1-DTI registration includes non-rigid deformation to correct for the strong distortions from the EPI acquisition. Because of the nonrigid component a mask of the brain parenchyma helps greatly in obtaining a meaningful transform.
 *The DTI estimation provides an automated mask for the DTI_baseline scan, but we have no mask for the T1. We can either obtain one through separate segmentation or by sending the DTI_mask through an additional registration step. We use the former here.
 *thus the full pipeline is this:
@@ Line 57: / Line 55: @@
 :#Skull Stripping of T1_bc
 :#DWI -> DTI estimation (incl. DTI_base and DT_mask output)
-:#Affine registration of DTI_baseline to T1_bc, unmasked
+:#Affine registration of T1_bc to DTI_baseline , unmasked
-:#non-rigid (BSpline) registration of DTI_baseline to T1_bc, masked, using above affine as starting pose
+:#non-rigid (BSpline) registration of T1_bc to DTI_baseline, masked, using above affine as starting pose
 === Procedures ===
@@ Line 122: / Line 119: @@
 === Registration Results===
-[[Image:RegLib_C30_AGif_reg.gif‎ |500px|Registered DTI superimposed on T1]] registered<br>
+[[Image:RegLib_C32_AGif_reg.gif‎ |500px|Registered T1 superimposed on DTI]] registered<br>
 <br>

Projects:RegistrationLibrary:RegLib C32 - Revision history

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

Meier: /* Download */

Meier: /* Procedures */

Meier: /* Procedures */

Meier: /* Procedures */

Meier: /* Registration Results */

Meier at 22:27, 11 November 2010

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…'