Projects:RegistrationLibrary:RegLib C27 - Revision history

Meier: /* Procedures */

2012-05-04T20:06:01Z

Procedures

Meier: /* Procedures */

2012-05-04T20:05:15Z

Procedures

Meier: /* Procedures */

2012-05-04T20:05:02Z

Procedures

Meier at 19:54, 4 May 2012

2012-05-04T19:54:04Z

Meier at 19:53, 4 May 2012

2012-05-04T19:53:37Z

Meier at 19:49, 4 May 2012

2012-05-04T19:49:28Z

Meier at 19:34, 4 May 2012

2012-05-04T19:34:46Z

Meier: /* Procedures */

2012-05-04T19:11:26Z

Procedures

Meier at 20:09, 24 September 2010

2010-09-24T20:09:59Z

Meier: /* Registration Results */

2010-09-24T19:56:19Z

Registration Results

@@ Line 41: / Line 41: @@
 === Procedures ===
 *'''Phase I: register FLAIR to T1'''
-#open the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit Registration: General Registration (BRAINS) module]
+#open the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit General Registration (BRAINS) module]
 ##''Fixed Image Volume'': T1
 ##''Moving Image Volume'': FLAIR
@@ Line 68: / Line 68: @@
 #Click: Apply
 *'''Phase IV:  Register DTI (unmasked)'''
-#open the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit |Registration: General Registration (BRAINS) module]
+#open the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit General Registration (BRAINS) module]
 ##''Fixed Image Volume'': FLAIR_Xf1
 ##''Moving Image Volume'': DWI_iso_baseline

@@ Line 41: / Line 41: @@
 === Procedures ===
 *'''Phase I: register FLAIR to T1'''
-#open the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit |Registration: General Registration (BRAINS) module]
+#open the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit Registration: General Registration (BRAINS) module]
 ##''Fixed Image Volume'': T1
 ##''Moving Image Volume'': FLAIR

@@ Line 41: / Line 41: @@
 === Procedures ===
 *'''Phase I: register FLAIR to T1'''
-#open the [ http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit |Registration: General Registration (BRAINS) module]
+#open the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit |Registration: General Registration (BRAINS) module]
 ##''Fixed Image Volume'': T1
 ##''Moving Image Volume'': FLAIR

← Older revision		Revision as of 19:54, 4 May 2012
Line 20:		Line 20:
	\|}		\|}

−	~~=== Modules ===~~
−	*'''Slicer 3.6.1 recommended modules: [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BrainsFit]'''

	===Objective / Background ===		===Objective / Background ===

@@ Line 3: / Line 3: @@
 [[Projects:RegistrationDocumentation:UseCaseInventory|Back to Registration Use-case Inventory]] <br>
-==<small>v3.6.1</small> [[Image:Slicer3-6Announcement-v1.png‎|150px]] Slicer Registration Library Exampe #27: Diffusion Weighted Image Volume: align with structural reference MRI ==
+==<small>updated for '''v4.1'''</small> [[Image:Slicer4_RegLibLogo.png|150px]] <br>Slicer Registration Library Exampe #27: Diffusion Weighted Image Volume: align with structural reference MRI ==
 === Input ===

@@ Line 56: / Line 56: @@
 ##click: Apply; runtime < 10 sec (MacPro QuadCore 2.4GHz)
 *'''Phase II: Resample DWI to isotropic voxel size'''
-#go to ''Filtering / Resample Scalar/Vector/DWI'' module
+#go to [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ResampleScalarVectorDWIVolume ''ResampleScalarVectorDWIVolume'' module] (''All Modules'' menu)
-#Input Volume: "DWI", Reference Volume: "T1", Output Volume: "create new Diffusion Weighted Volume", rename to "DWI_iso"
+##''Input Volume'': "DWI",
-#Click: Apply
+##''Output Volume'': "create new Diffusion Weighted Volume", rename to "DWI_iso"
 #save new DWI_iso to disk
 #depending on RAM of your machine, consider deleting the original DWI node
 *'''Phase III:  DWI -> DTI'''
-#open "Diffusion Tensor Estimation" module
+#open [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/DiffusionTensorEstimation "Diffusion Tensor Estimation" module] (menu: Diffusion:DiffusionWeightedImages: DiffusionTensorEstimation)
-#Input DWI Volume: DWI_iso, Output DTI Volume: create new, rename to "DTI_iso"
+##''Input DWI Volume'': DWI_iso,
-#Output Baseline: create new, rename to "DTI_iso_base"
+##''Output DTI Volume'': create new, rename to "DTI_iso"
-#Otsu Threshold Mask: create new, rename to "DTI_iso_mask"
+##''Output Baseline Volume'': create new, rename to "DWI_iso_baseline"
 #Click: Apply
 *'''Phase IV:  Register DTI (unmasked)'''
-#open Registration : ''BrainsFit'' module (presets: Xf2_DTI-FLAIR_unmasked)
+#open the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit |Registration: General Registration (BRAINS) module]
-##Registration Phases:
+##''Fixed Image Volume'': FLAIR_Xf1
-##set FLAIR as fixed and DTI_iso_base as moving image
+##''Moving Image Volume'': DWI_iso_baseline
 ##Output Settings:
-###select a new transform "Slicer BSpline Transform", rename to "Xf1_DTI-FLAIR_unmasked"
+###''Slicer BSpline Transform": create new transform, rename to "Xf2_DTI-T1"
-###select a new volume "Output Image Volume'', rename to "DT_iso_base_Xf1"
+###''Slicer Linear Transform'': none
-##Registration Parameters: increase ''Number Of Samples'' to 200,000
+###''Output Image Volume'': create new volume,  rename to DWI_iso_baseline_Xf2
-##Registration Parameters: set  ''Number Of Grid Subdivisions'' to 5,5,3
+##''Regstration Phases'': check boxes for ''Rigid'',  ''Affine'' and ''BSpline''
 ##Leave all other settings at default
-##click: Apply; runtime < 1 min.
+##click: Apply; runtime <1 min (MacPro QuadCore 2.4GHz)
 *'''Phase V: Resample DTI'''
-#Open the ''Resample DTI Volume'' module (found under: All Modules)
+#Open the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ResampleDTI ''Resample DTI Volume'' module]  (under ''All Modules'' menu; note this is distinct from the ResampleScalarVectorDWIVolume used above)
-##Input Volume: select DTI_iso
+##''Input Volume'': DTI_iso
-##Output Volume: select ''New DTI Volume'', rename to ''DTI_iso_Xf2''
+##''Output Volume'': create new DTI Volume, rename to ''DTI_iso_Xf2''
-##Reference Volume: select ''T1''
+##''Reference Volume'': T1
-##Transform Parameters: select transform "Xf2_DTI-FLAIR_unmasked''
+##''Transform Node'': select "Xf2_DTI-T1'' created in phase 4 above
-##check box: ''output-to-input''
+##check box: ''displacement''
-##Leave all other settings at defaults
+#leave all other settings at defaults
-##Click Apply; runtime ~ 3 min.
+#Click Apply; runtime ~ 3 min.
-#Go to the ''Volumes'' module, select the newly produced ''DTI_Xf2'' volume
+#set T1 or FLAIR as background and the new  ''DTI_Xf2'' volume as foreground
-#under the ''Display'' tab, select ''Color Orientation'' from the ''Scalar Mode'' menu
+#Move fade slider to see DTI overlay onto the structural image
 === Registration Results===
@@ Line 107: / Line 103: @@
 *Data
 **[[Media:RegLib_C27_Data.zip‎ ‎|'''RegLib_C27_Data''' DWI, DTI, T1, FLAIR, Presets & solution transforms  <small> (NRRD files, zip file 145 MB) </small>]]'''
-*Presets
+*Documentation (for Slicer Version 3.6, but procedure is the same)
 **[[Media:RegLib_C27_Tutorial.ppt‎|'''RegLib_C27_Tutorial.ppt''' step-by-step tutorial Powerpoint<small> (.ppt file 2.6MB) </small>]]'''
 **[[Media:RegLib_C27_Tutorial.pdf‎|'''RegLib_C27_Tutorial.pdf''' step-by-step tutorial PDF<small> (.pdf file 3.8MB) </small>]]'''

@@ Line 33: / Line 33: @@
 *moving: Baseline image of acquired DTI volume, corresponds to T2w MRI , 1.96 x 1.96 x 3 mm voxel size, oblique,  128 x 128 x 40
 *moving: Tensor data of DTI volume, oblique, same orientation as Baseline image. The result Xform will be applied to this volume. The original DWI has 64 directions, the extracted DTI volume has 9 scalars, i.e. 128 x 128 x 40 x 9
 === Registration Results===

@@ Line 36: / Line 36: @@
 === Registration Results===
-[[Image:RegLib_C27_AGif_reg_T1.gif|40px|lleft|DTI resampled to T1]]
+[[Image:RegLib_C27_AGif_reg_T1.gif|400px|lleft|DTI resampled to T1]]
 [[Image:RegLib_C27_AGif_reg_FLAIR.gif|400px|lleft|DTI resampled to FLAIR]]