Projects:RegistrationLibrary:RegLib C03B - Revision history

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Meier: /* Procedures Part I : Preprocessing */

2012-05-03T16:28:38Z

Procedures Part I : Preprocessing

Meier: /* Procedures Part I : Preprocessing */

2012-04-27T18:55:57Z

Procedures Part I : Preprocessing

Meier: /* Procedures Part I : Preprocessing */

2012-04-27T18:44:35Z

Procedures Part I : Preprocessing

Meier: /* Procedures Part I : Preprocessing */

2012-04-27T18:43:27Z

Procedures Part I : Preprocessing

Meier: /* Procedures Part I : Preprocessing */

2012-04-27T18:37:13Z

Procedures Part I : Preprocessing

Meier: /* Procedures Part I : Preprocessing */

2012-04-27T17:11:55Z

Procedures Part I : Preprocessing

Meier: moved Projects:RegistrationLibrary:RegLib C03 2 to Projects:RegistrationLibrary:RegLib C03B

2012-04-27T15:37:24Z

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== v3.6.3 [[Image:Slicer363_banner.png|150px]] Slicer Registration Library Case #3B: Diffusion Weighted Image Volume: align with structural reference MRI (ADVANCED/EXTENDED)==
<big> Note that this is the complex/advanced version of this case, which includes preprocessing like resampling the DWI, DTI estimation etc. [[Projects:RegistrationLibrary:RegLib_C03|A simpler version showing only the registration + DTI resampling is here.]] </big>
=== Input ===
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C03_Reference_axial.png|150px|lleft|this is the fixed T2 reference image. All images are aligned into this space]]
|[[Image:RegArrow_NonRigid.png|100px|lleft]]
|[[Image:RegLib_C03_Baseline_axial.png|150px|lleft|this is the DTI Baseline scan, to be registered with the T2]]
|[[Image:RegLib_C03_DTIVol_axial.png|150px|lleft|this is the DTI tensor image, in the same orientation as the DTI Baseline]]
|-
|fixed image/target T2
|
|moving image 2a DTI baseline
|moving image 2b DTI tensor
|}

=== Modules ===
*'''Slicer 3.6.3 recommended modules: [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BrainsFit]''', [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleDTIVolume-Documentation-3.6 Resample DTI Volume], [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorEstimation-Documentation-3.6 Diffusion Tensor Estimation]
*[[Projects:RegistrationLibrary:RegLib_C03b|for the Slicer 3.6.3 version of this case see here]]

===Objective / Background ===
While this example shares a typical objective of DTI processing, it covers additional issues of a strong initial rotation and strong voxel-anisotropy for the raw DWI image acquired. Goal is to align the DTI image with the structural reference T2 scan that provides accuracte anatomical reference.

=== Keywords ===
MRI, brain, head, intra-subject, DTI, DWI

===Download ===
*Image Data:
**[[Media:RegLib_C03_Data.zip‎|'''RegLib_C03_Data''': main registration package: register DTI (Data,Presets, Transforms, zip file 61 MB) ]]
**[[Media:RegLib_C03_Data_preproc.zip‎|'''RegLib_C03_Data_preproc''':preprocessing package: resample T2, resample & align DWI, convert to DTI (raw and resampled DWI, zip file 228 MB) ]]
**[[Media:RegLib_C03_DATA_results.zip‎|RegLib_C03_DATA_results: resampled DTI (registered DTI, zip file 39 MB) ]]
*Presets:
**[[Media:RegLib_C03_Presets.mrml|'''Presets''' for BRAINSfit registration & resampling (Data, Solution, zip file 12 kB) ]]
**[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]
*Documentation
**[[Media:RegLib_C03_DTI.ppt|'''Tutorial''' (.ppt file 2 MB) ]]
**[[Media:RegLib_C03_DTI.pdf|'''Tutorial as PDF''' (PDF file 2 MB) ]]

===Input Data===
*reference/fixed : T2w axial, 0.4mm resolution in plane, 3mm slices
*moving: Baseline image of acquired DTI volume, corresponds to T2w MRI , 0.9375 x 0.9375 x 1.4 mm voxel size, oblique
*Tensor data of DTI volume, oblique, same orientation as Baseline image. The result Xform will be applied to this volume. The original DWI has 26 directions, the extracted DTI volume has 9 scalars, i.e. 256 x 256 x 36 x 9

=== Overall Strategy ===
:#Resample T2 reference to isotropic voxel size
:#Manually reorient DWI into orientation of T2
:#Resample DWI into new space and into isotropic voxel size
:#Convert DWI -> DTI, incl. mask & baseline extraction
:#Register DTI_baseline to T2 (affine+nonrigid) w/o masking
:#Resample DTI_mask with above transform to build mask for T2
:#Repeat registration above, this time incl. masks and with higher BSpline grid size
:#Resample DTI with above transform
=== Procedures Part I : Preprocessing ===
*'''Note:''' if not interested in the preprocessing steps, download only the main dataset and skip phase I-III.
*'''Phase I: resample T2 to isotropic voxel size'''
##original T2 has 0.5 x 0.5 x 3 mm voxel size, which we resample to 1.2 x 1.2 x 1.2 mm (you may set 1x1x1 if you have sufficient RAM)
##open [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleVolume-Documentation-3.6 ''Filtering / Resample Scalar Volume''] module
##Spacing: enter 1,1,1
##Interpolation: check ''hamming''
##Input Volume: select T2raw, Output Volume: create new, rename to "T2"
##click: Apply
*'''Phase II: Manually align DWI_raw to T2'''
#open [http://www.slicer.org/slicerWiki/index.php/Modules:Data-Documentation-3.6 ''Data''] module
#in MRML tree, select the "Scene" node, then right click & select "Insert Transform Node"
#click on ''MRML Node Inspector'' and rename Xform node to "Xf0_DWI_init"
#drag DWI_raw into the "Xf0_DWI_init" node
#go to "Transforms" module
#select T2 as background and DWI_raw as foreground, set fading slider halfway
#manually adjust transform to align the two volumes, particularly LR rotation and IS translation
#Save
#go to [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleScalarVectorDWIVolume-Documentation-3.6 ''Filtering / Resample Scalar/Vector/DWI''] module
#Input Volume: "DWI_raw", Reference Volume: "T2", Output Volume: "create new Diffusion Weighted Volume", rename to "DWI_Xf0"
#Transform Node: select "Xf0_DWI_Init"
#Click: Apply
#this will correct both the initial misalignment and the anisotropy
#save new DWI_Xf0 to disk
#depending on RAM of your machine, consider deleting the original DWI_raw node
*'''Phase III: DWI -> DTI'''
#open [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorEstimation-Documentation-3.6 "Diffusion Tensor Estimation"] module
#Input DWI Volume: DWI_Xf0, Output DTI Volume: create new, rename to "DTI"
#Output Baseline: create new, rename to "DTI_base"
#Otsu Threshold Mask: create new, rename to "DTI_mask"
#Estimation Parameters: reduce ''Otsu Omega Threshold" to 0.3
#check boxes for ''Remove Islands'' and ''Apply Mask''
#Click: Apply
=== Procedures Part II : Registration ===
*'''Phase IV: Register DTI (unmasked)'''
#open [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit Registration : ''General Registration (BRAINS)''] module
##''Input Images'': fixed = T2 , moving = DTI_base
##''Output Settings'':
###''Slicer BSpline Transform'' (create new transform, rename to: "Xf1_DTbase-T2_BSpline")
###''Slicer Linear Transform'' none
###''Output Image Volume'' (create new volume, rename to: "DTIbaseline_Xf1"
##''Registration Phases'': select/check ''Rigid'' , ''Rigid+Scale'', ''Affine'', ''BSpline''
##''Main Parameters'':
###increase ''Number Of Samples'' to 200,000
###set ''B-Spline Grid Size'' to 5,5,5
##Leave all other settings at default
##click: ''Apply''; runtime < 1 min.
*'''Phase V: Resample DTI_mask''' (presets: DTI_mask_Xf1)
**we use the above Xform to produce a mask for the T2.
#Open '' [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleScalarVectorDWIVolume-Documentation-3.6 ''Filtering / Resample Scalar/Vector/DWI''] module
##Input Volume: DTI_mask; Output volume: create new volume, rename to "DTI_mask_Xf1"
##Transform Node: "Xf1_DTI-T2_unmasked"
##select/check: ''output-to-input''
##Interpolation Type: select: '''nn'''
##click: Apply
##Go to ''Volumes'' module, select the new "DTI_mask_Xf1", in the ''Info'' tab, check the ''Labelmap'' box
*'''Phase VI:REGISTER DTI TO T2 with masking'''
#open [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit Registration : ''BrainsFit''] module (presets: Xf2_DTI-T2_masked)
##set T2_Xf1 as fixed and DTI_baseline as moving image
###select/check ''Include Rigid registration phase''
###select/check ''Include ScaleVersor3D registration phase''
###select/check ''Include Affine registration phase''
###select/check ''Include BSpline registration phase''
##Output BSpline Transform: create new , rename to "Xf2_DTI-T2_masked"
##Output Volume: create new, rename to "DTI_base_Xf2"
##Registration Parameters: increase ''Number Of Samples'' to 200,000
##Registration Parameters: set ''Number Of Grid Subdivisions'' to 7,7,5
##Control of Mask Processing
###select/check: ''ROI'' (rightmost box)
###Input Fixed Mask: select "DTI_mask_Xf1"
###Input Moving Mask: select "DTI_mask"
##Leave all other settings at default
##click: Apply; runtime < 1 min.
*'''Phase VII: Resample DTI'''
#Load the combined transform (''Add Data'')
#Open the [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleDTIVolume-Documentation-3.6 ''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 ''T2''
##Transform Parameters: select transform "Xf2_DTI-T2_masked''
##check box: ''output-to-input''
##Leave all other settings at defaults
##Click Apply; runtime ~ 2 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 T2 image

for more details see the tutorial(s) under Downloads above

=== Registration Results===
{| style="color:#bbbbbb; background-color:#333333;" cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C03_AGif_registered.gif|400px|left]]
|-
|baseline to T2 after affine+nonrigid alignment
|}

=== Discussion: Key Strategies ===
*the two images have identical contrast, hence we could consider "sharper" cost functions, such as NormCorr or MeanSqrd. But because of the strong distortions and lower resolution of the moving image, Mutual Information is recommended as the most robust metric.
*often anatomical labels are available from the reference scan. It would be less work to align the anatomical reference with the DTI, since that would circumvent having to resample the complex tensor data into a new orientation. However the strong distortions are better addressed by registering the other direction, i.e. move the DTI into the anatomical reference space.
*in this example the initial alignment of the two scans is very poor. The strongly oblique orientation of the DWI makes an initial manual alignment step necessary. This step should occur '''before''' converting to the DTI to avoid interpolation artifacts.

=== Acknowledgments ===

@@ Line 19: / Line 19: @@
 === Modules ===
-*'''Slicer 3.6.3 recommended modules:  [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BrainsFit]''', [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleDTIVolume-Documentation-3.6 Resample DTI Volume], [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorEstimation-Documentation-3.6 Diffusion Tensor Estimation]
+*'''Slicer 3.6.3 recommended modules:  [https://www.slicer.org/wiki/Modules:BRAINSFit BrainsFit]''', [https://www.slicer.org/wiki/Modules:ResampleDTIVolume-Documentation-3.6 Resample DTI Volume], [https://www.slicer.org/wiki/Modules:DiffusionTensorEstimation-Documentation-3.6 Diffusion Tensor Estimation]
 *[[Projects:RegistrationLibrary:RegLib_C03b|for the Slicer 3.6.3 version of this case see here]]
@@ Line 56: / Line 56: @@
 :#Resample DTI with above transform
 === Procedures Part I : Preprocessing ===
-*'''Slicer 4.1 recommended modules:  [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit BrainsFit]''', [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ResampleDTIVolume Resample DTI Volume], [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/DiffusionTensorEstimation Diffusion Tensor Estimation]
+*'''Slicer 4.1 recommended modules:  [https://www.slicer.org/wiki/Documentation/4.1/Modules/BRAINSFit BrainsFit]''', [https://www.slicer.org/wiki/Documentation/4.1/Modules/ResampleDTIVolume Resample DTI Volume], [https://www.slicer.org/wiki/Documentation/4.1/Modules/DiffusionTensorEstimation Diffusion Tensor Estimation]
 *'''Note:''' if not interested in the preprocessing steps, download only the main dataset and skip phase I-III.
 *'''Phase I: resample T2 to isotropic voxel size'''
 ##original T2 has 0.5 x 0.5 x 3 mm voxel size, which we resample to 1.2 x 1.2 x 1.2 mm (you may set 1x1x1 if you have sufficient RAM)
-##open  [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ ''Modules:AllModules:ResampleScalarVolume''] module
+##open  [https://www.slicer.org/wiki/Documentation/4.1/Modules/ ''Modules:AllModules:ResampleScalarVolume''] module
 ##''Spacing'': enter 1,1,1
 ##''Interpolation'': check ''hamming''
@@ Line 76: / Line 76: @@
 ##Save generated volume as "DWI_mask.nrrd"
 *'''Phase IIb: Build Masks: T2 mask'''
-#open the  [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/SimpleRegionGrowingSegmentation ''Modules:Segmentation:SimpleRegionGrowing''] module
+#open the  [https://www.slicer.org/wiki/Documentation/4.1/Modules/SimpleRegionGrowingSegmentation ''Modules:Segmentation:SimpleRegionGrowing''] module
 ##set ''Smoothing iterations'' : 0
 ##set ''number of iterations'' : 1
@@ Line 87: / Line 87: @@
 ##''Output Volume:'' "T2_iso_mask"
 ##Click Apply. Upon completion you should get a sparse segmentation of the WM (see picture)
-#go to [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/Editor ''Modules:Editor''] module
+#go to [https://www.slicer.org/wiki/Documentation/4.1/Modules/Editor ''Modules:Editor''] module
 ##if not chosen by default, select "T2_iso_mask" as labelmap to edit
 ##Select ''Dilation'' tool. Click ''Apply'' button several times (4-5x) until most of the brain is filled
@@ Line 100: / Line 100: @@
 #Save generated map as "T2_iso_mask.nrrd"
 *'''Phase III: Register DWI to T2_iso'''
-#open the [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit Registration : ''Modules:Registration:General Registration (BRAINS)'']  module
+#open the [https://www.slicer.org/wiki/Modules:BRAINSFit Registration : ''Modules:Registration:General Registration (BRAINS)'']  module
 ##''Input Images'': fixed = T2_iso , moving = DWI_baseline
 ##''Output Settings'':
@@ Line 117: / Line 117: @@
 ##click: ''Apply''; runtime < 1-3 min.
 *''Phase III:  Resample DTI'''
-#Open the  [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ResampleDTIVolume Resample DTI Volume] module (found under: All Modules)
+#Open the  [https://www.slicer.org/wiki/Documentation/4.1/Modules/ResampleDTIVolume Resample DTI Volume] module (found under: All Modules)
 ##Input Volume: select DTI
 ##Output Volume: select ''create new Diffusion Tensor Volume'',and rename it to ''DTI_Xf1''
@@ Line 128: / Line 128: @@
 *''Phase III:  DWI -> DTI'''
-#open [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorEstimation-Documentation-3.6 "Diffusion Tensor Estimation"] module
+#open [https://www.slicer.org/wiki/Modules:DiffusionTensorEstimation-Documentation-3.6 "Diffusion Tensor Estimation"] module
 #Input DWI Volume: DWI_Xf0, Output DTI Volume: create new, rename to "DTI"
 #Output Baseline: create new, rename to "DTI_base"
@@ Line 138: / Line 138: @@
 === Procedures Part II : Registration ===
 *'''Phase IV:  Register DTI (unmasked)'''
-#open  [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit Registration : ''General Registration (BRAINS)'']  module
+#open  [https://www.slicer.org/wiki/Modules:BRAINSFit Registration : ''General Registration (BRAINS)'']  module
 ##''Input Images'': fixed = T2 , moving = DTI_base
 ##''Output Settings'':
@@ Line 152: / Line 152: @@
 *'''Phase V: Resample DTI_mask''' (presets: DTI_mask_Xf1)
 **we use the above Xform to produce a mask for the T2.
-#Open '' [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleScalarVectorDWIVolume-Documentation-3.6 ''Filtering / Resample Scalar/Vector/DWI''] module
+#Open '' [https://www.slicer.org/wiki/Modules:ResampleScalarVectorDWIVolume-Documentation-3.6 ''Filtering / Resample Scalar/Vector/DWI''] module
 ##Input Volume: DTI_mask; Output volume: create new volume, rename to "DTI_mask_Xf1"
 ##Transform Node:  "Xf1_DTI-T2_unmasked"
@@ Line 160: / Line 160: @@
 ##Go to ''Volumes'' module, select the new "DTI_mask_Xf1", in the ''Info'' tab, check the ''Labelmap'' box
 *'''Phase VI:REGISTER DTI TO T2 with masking'''
-#open  [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit Registration : ''BrainsFit''] module (presets: Xf2_DTI-T2_masked)
+#open  [https://www.slicer.org/wiki/Modules:BRAINSFit Registration : ''BrainsFit''] module (presets: Xf2_DTI-T2_masked)
 ##set T2_Xf1 as fixed and DTI_baseline as moving image
 ###select/check ''Include Rigid registration phase''
@@ Line 178: / Line 178: @@
 *'''Phase VII: Resample DTI'''
 #Load the combined transform (''Add Data'')
-#Open the [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleDTIVolume-Documentation-3.6 ''Resample DTI Volume''] module (found under: All Modules)
+#Open the [https://www.slicer.org/wiki/Modules:ResampleDTIVolume-Documentation-3.6 ''Resample DTI Volume''] module (found under: All Modules)
 ##Input Volume: select DTI
 ##Output Volume: select ''New DTI Volume'', rename to ''DTI_Xf2''

@@ Line 68: / Line 68: @@
 ##click: ''Apply''
 ##Save generated volume as "T2_iso.nrrd"
-*'''Phase IIa: Build Masks: DWI mask'''
+*'''Phase IIa: Build DWI mask + baseline'''
 #open the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/DiffusionWeightedMasking ''Modules:Diffusion:DiffusionWeightedImages:DiffusionWeightedVolumeMasking'' ] module
 ##''Input DWI Volume'': "DWI_raw"

@@ Line 61: / Line 61: @@
 *'''Phase I: resample T2 to isotropic voxel size'''
 ##original T2 has 0.5 x 0.5 x 3 mm voxel size, which we resample to 1.2 x 1.2 x 1.2 mm (you may set 1x1x1 if you have sufficient RAM)
-##open [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleVolume-Documentation-3.6 ''Filtering / Resample Scalar Volume''] module
+##open  [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ ''Modules:AllModules:ResampleScalarVolume''] module
-##Spacing: enter 1,1,1
+##''Spacing'': enter 1,1,1
-##Interpolation: check ''hamming''
+##''Interpolation'': check ''hamming''
-##Input Volume: select T2raw,  Output Volume: create new, rename to "T2"
+##''Input Volume'': "T2_raw"
-##click: Apply
+##''Output Volume'': create new volume, rename to "T2_iso"
 *'''Phase IIa: Build Masks: DWI mask'''
 #open the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/DiffusionWeightedMasking ''Modules:Diffusion:DiffusionWeightedImages:DiffusionWeightedVolumeMasking'' ] module
@@ Line 72: / Line 74: @@
 ##''Output Threshold Mask'': ''Create New Volume'', rename to "DWI_mask"
 ##Leave other settings at default; click ''Apply''
 *'''Phase IIb: Build Masks: T2 mask'''
 #open the  [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/SimpleRegionGrowingSegmentation ''Modules:Segmentation:SimpleRegionGrowing''] module
@@ Line 81: / Line 84: @@
 ##set ''Seeds'': "create New fiducial List"
 ##in toolbar select ''Fiducial'' mouse mode. Then place 2 fiducials in the center of the brain within the deep gray or deep WM (picture). Avoid selecting CSF.
-##''Input Volume":  "T2_raw"
+##''Input Volume":  "T2_iso"
-##''Output Volume:'' "T2_mask"
+##''Output Volume:'' "T2_iso_mask"
 ##Click Apply. Upon completion you should get a sparse segmentation of the WM (see picture)
 #go to [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/Editor ''Modules:Editor''] module
-##if not chosen by default, select "T2_mask" as labelmap to edit
+##if not chosen by default, select "T2_iso_mask" as labelmap to edit
 ##Select ''Dilation'' tool. Click ''Apply'' button several times (4-5x) until most of the brain is filled
 ##Select brush tool, adjust radius, set label to 0 and remove portions extending beyond the brain. Do not worry about holes in CSF not filled or small regions, they will not affect the registration
@@ Line 92: / Line 95: @@
 ##''Majority Threshold'': 1
 ##''Background'': 0 ; ''Foreground'': 1
-##''Input Volume'': T2_mask
+##''Input Volume'': T2_iso_mask
-##''Output Volume'': T2_mask
+##''Output Volume'': T2_iso_mask
 ##click ''Apply''.
-#Save generated map as "T2_mask.nrrd"
+#Save generated map as "T2_iso_mask.nrrd"
-*'''Phase II: Manually align DWI_raw to T2'''
+*''Phase III:  DWI -> DTI'''
 #open [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorEstimation-Documentation-3.6 "Diffusion Tensor Estimation"] module
 #Input DWI Volume: DWI_Xf0, Output DTI Volume: create new, rename to "DTI"

@@ Line 74: / Line 74: @@
 *'''Phase IIb: Build Masks: T2 mask'''
 #open the  [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/SimpleRegionGrowingSegmentation ''Modules:Segmentation:SimpleRegionGrowing''] module
-##set ''Smoothing iterations" : 0
+##set ''Smoothing iterations'' : 0
-##set ''number of iterations" : 1
+##set ''number of iterations'' : 1
 ##set ''Multiplier'': 0.8
 ##set ''Neighborhood Radius'' : 5
@@ Line 82: / Line 82: @@
 ##in toolbar select ''Fiducial'' mouse mode. Then place 2 fiducials in the center of the brain within the deep gray or deep WM (picture). Avoid selecting CSF.
 ##''Input Volume":  "T2_raw"
-##''Output Volume: ''T2_mask"
+##''Output Volume:'' "T2_mask"
 ##Click Apply. Upon completion you should get a sparse segmentation of the WM (see picture)
 #go to [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/Editor ''Modules:Editor''] module

@@ Line 67: / Line 67: @@
 ##click: Apply
 *'''Phase IIa: Build Masks: DWI mask'''
 *'''Phase IIb: Build Masks: T2 mask'''
-#open the   [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/SimpleRegionGrowing ''Modules:Segmentation:SimpleRegionGrowing''] module
+#open the  [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/SimpleRegionGrowingSegmentation ''Modules:Segmentation:SimpleRegionGrowing''] module
 ##set ''Smoothing iterations" : 0
 ##set ''number of iterations" : 1
@@ Line 79: / Line 84: @@
 ##''Output Volume: ''T2_mask"
 ##Click Apply. Upon completion you should get a sparse segmentation of the WM (see picture)
-#go to  [http://www.slicer.org/slicerWiki/index.php/Modules:Data-Documentation-3.6 ''Modules:Editor''] module
+#go to [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/Editor ''Modules:Editor''] module
 ##if not chosen by default, select "T2_mask" as labelmap to edit
 ##Select ''Dilation'' tool. Click ''Apply'' button several times (4-5x) until most of the brain is filled
 ##Select brush tool, adjust radius, set label to 0 and remove portions extending beyond the brain. Do not worry about holes in CSF not filled or small regions, they will not affect the registration
-#Go to ''Modules:Filtering:Voting Binary Hole Filling Image Filter'' module
+#Open the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/VotingBinaryHoleFillingImageFilter ''Modules:Filtering:Voting Binary Hole Filling Image Filter''] module
 ##''Maximum Radius'': 7,7,7
 ##''Majority Threshold'': 1

← Older revision	Revision as of 15:37, 27 April 2012
(No difference)

Projects:RegistrationLibrary:RegLib C03B - Revision history

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

Meier: /* Procedures Part I : Preprocessing */

Meier: /* Procedures Part I : Preprocessing */

Meier: /* Procedures Part I : Preprocessing */

Meier: /* Procedures Part I : Preprocessing */

Meier: /* Procedures Part I : Preprocessing */

Meier: /* Procedures Part I : Preprocessing */

Meier: moved Projects:RegistrationLibrary:RegLib C03 2 to Projects:RegistrationLibrary:RegLib C03B

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…'