Projects:SlicerFAQ:DWI Registration - Revision history

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

2017-07-10T17:44:17Z

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

Meier at 22:02, 17 November 2010

2010-11-17T22:02:27Z

Meier at 22:01, 17 November 2010

2010-11-17T22:01:50Z

Meier at 17:46, 11 November 2010

2010-11-11T17:46:57Z

Meier: /* Overall Strategy */

2010-11-11T17:44:40Z

Overall Strategy

Meier: /* Overall Strategy */

2010-11-11T17:43:27Z

Overall Strategy

Meier: /* Overall Strategy */

2010-11-11T17:41:58Z

Overall Strategy

Meier: /* Overall Strategy */

2010-11-11T17:28:13Z

Overall Strategy

Meier: /* Overall Strategy */

2010-11-11T17:27:24Z

Overall Strategy

Meier: /* Overall Strategy */

2010-11-11T17:22:24Z

Overall Strategy

@@ Line 9: / Line 9: @@
 === Overall Strategy ===
 #if voxel size ratios are 1.5 or greater:
-##Resample the T2 reference to isotropic voxel size:[http://www.slicer.org/slicerWiki/index.php/Modules:ResampleVolume-Documentation-3.6 ''Resample Volume'' module] or [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleScalarVectorDWIVolume-Documentation-3.6 ''Resample Scalar/Vector/DWI Volume'' module]
+##Resample the T2 reference to isotropic voxel size:[https://www.slicer.org/wiki/Modules:ResampleVolume-Documentation-3.6 ''Resample Volume'' module] or [https://www.slicer.org/wiki/Modules:ResampleScalarVectorDWIVolume-Documentation-3.6 ''Resample Scalar/Vector/DWI Volume'' module]
-##Resample the DWI (not DTI)  to isotropic voxel size: [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleScalarVectorDWIVolume-Documentation-3.6 ''Resample Scalar/Vector/DWI Volume'' module]. Note that depending on the size of the original DWI, the isotropic volumes can become very large files. Make sure you have sufficient RAM and disk space available.
+##Resample the DWI (not DTI)  to isotropic voxel size: [https://www.slicer.org/wiki/Modules:ResampleScalarVectorDWIVolume-Documentation-3.6 ''Resample Scalar/Vector/DWI Volume'' module]. Note that depending on the size of the original DWI, the isotropic volumes can become very large files. Make sure you have sufficient RAM and disk space available.
-#Extract the baseline and DTI from the isotropic DWI:  [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorEstimation-Documentation-3.6 ''Diffusion Tensor Estimation'' module]. Also select to generate a mask image.
+#Extract the baseline and DTI from the isotropic DWI:  [https://www.slicer.org/wiki/Modules:DiffusionTensorEstimation-Documentation-3.6 ''Diffusion Tensor Estimation'' module]. Also select to generate a mask image.
 #Register the DWI baseline scan to the reference. Preferred structural reference is a T2-weighted scan. If no T2 is available use the next closest contrast.
-##If initial misalignment (rotation/translation) is significant (more than ~20% of the FOV), consider a preliminary manual alignment first, using the [http://www.slicer.org/slicerWiki/index.php/Modules:Transforms-Documentation-3.6 ''Transforms'' module]. If the final target is a T1 but a T2 is available, use the T2 as reference for the DWI, but then perform a second T2-T1 or T1-T2 registration.
+##If initial misalignment (rotation/translation) is significant (more than ~20% of the FOV), consider a preliminary manual alignment first, using the [https://www.slicer.org/wiki/Modules:Transforms-Documentation-3.6 ''Transforms'' module]. If the final target is a T1 but a T2 is available, use the T2 as reference for the DWI, but then perform a second T2-T1 or T1-T2 registration.
-##try [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit ''BRAINSfit'' module] as first method of choice
+##try [https://www.slicer.org/wiki/Modules:BRAINSFit ''BRAINSfit'' module] as first method of choice
 ##masking is recommended for better results. We have a mask for the DWI but not the T2 reference. To obtain a mask for the reference
 ##*you can either perform a prelim. registration without masking, then apply this transform to the DWI mask
 ##*you can obtain a mask from another scan (e.g.T1, via the skull stripping or other segmentation tool) and perform a registration to the reference
 ##*you can try and obtain a mask for the reference directly, via
-#Resample the DTI tensor with above transform, using the dedicated   [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleDTIVolume-Documentation-3.6 ''Resample DTIVolume'' module].
+#Resample the DTI tensor with above transform, using the dedicated   [https://www.slicer.org/wiki/Modules:ResampleDTIVolume-Documentation-3.6 ''Resample DTIVolume'' module].
 === Procedures ===

@@ Line 110: / Line 110: @@
 #set ''T1'' as background and new  ''DTI_Xf2'' volume as foreground
 #Set fade slider to see DTI overlay onto the T2 image
-=== Special Caveats ===
+=== Caveats ===
 *In the BRAINSfit registration step
 **if images are not already closely aligned, check boxes to include "Rigid" & "ScaleVersor3D" phases

← Older revision		Revision as of 22:01, 17 November 2010
Line 110:		Line 110:
	#set ''T1'' as background and new ''DTI_Xf2'' volume as foreground		#set ''T1'' as background and new ''DTI_Xf2'' volume as foreground
	#Set fade slider to see DTI overlay onto the T2 image		#Set fade slider to see DTI overlay onto the T2 image
		+	=== Special Caveats ===
		+	*In the BRAINSfit registration step
		+	**if images are not already closely aligned, check boxes to include "Rigid" & "ScaleVersor3D" phases
		+	**always check boxes for "Affine" and "BSpline" phases
		+	**remember to select "Slicer BSpline Transform" and "Output Image Volume" in Output Settings
		+	**reduce default grid size settings to 5,5,5 or similar, depending on level of distortion
		+	**increase sample points to 200,000
		+	**registration will take 2-4 minutes, depending on CPU and grid size setting
		+	**upon completion: drag the result volume back out from the result transform node to avoid confusion: since the transform contains a BSpline, moving a volume inside the node will not show an effect
		+	**when using masks: remember that 2 masks for both fixed and moving are required. The moving mask usually comes from the DTI estimation, the fixed mask can be obtained separately or via a prior (unmasked) registration that then allows to resample the DTI mask and thus produce a fixed mask.
		+	*DTI resampling
		+	*if the DTI has voxel anisotropy of ratio 3 or greater, consider isotropic resampling of DWI first (see [[Projects:RegistrationLibrary:RegLib_C03\| case 3]] for details.
		+	**use the dedicated ''Resample DTI Volume'' node (under ''All Modules'')
		+	**in the 'Resample DTI Volume'', make sure to check the "output-to-input" box in the ''Transform Parameters'' box. This will execute the affine transform first and the BSpline second.
		+	**always set a ''Reference Volume''. This will be the T1 or T2 baseline to which the DTI is registered. Check the resolution of the reference: if the image is very large (e.g. 512 x 512 x 100 etc.) you may get memory problems trying to resample the 4D tensor volume. In that case first subsample the reference scan (e.g. to 1x1x1) and the resample the DTI into this new space
		+	**validate the resulting resampled DTI using ''Color Orientation'' in the Volumes/Display settings. Make sure the FOV is not clipped and there is no "color cast" indicating blurring artifacts from anisotropic DTI voxels.

@@ Line 22: / Line 22: @@
 === Procedures ===
-*'''Note:''' if not interested in the preprocessing steps, download only the main dataset and skip phase I-III.
+*'''Note:''' below the step-by-step cookbook from a typical DWI case in the [[Projects:RegistrationDocumentation:UseCaseInventory:BrainIntraDTI|'''Slicer Registration Case Library''']]. This assumes a T2 reference. If voxel anisotropy is not a concern, you may skip phases 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 x 1 x 1 mm

@@ Line 16: / Line 16: @@
 ##try [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit ''BRAINSfit'' module] as first method of choice
 ##masking is recommended for better results. We have a mask for the DWI but not the T2 reference. To obtain a mask for the reference
-::*you can either perform a prelim. registration without masking, then apply this transform to the DWI mask
+##*you can either perform a prelim. registration without masking, then apply this transform to the DWI mask
-::*you can obtain a mask from another scan (e.g.T1, via the skull stripping or other segmentation tool) and perform a registration to the reference
+##*you can obtain a mask from another scan (e.g.T1, via the skull stripping or other segmentation tool) and perform a registration to the reference
-::*you can try and obtain a mask for the reference directly, via
+##*you can try and obtain a mask for the reference directly, via
 #Resample the DTI tensor with above transform, using the dedicated   [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleDTIVolume-Documentation-3.6 ''Resample DTIVolume'' module].

@@ Line 10: / Line 10: @@
 *if voxel size ratios are 1.5 or greater:
 :#Resample the T2 reference to isotropic voxel size:[http://www.slicer.org/slicerWiki/index.php/Modules:ResampleVolume-Documentation-3.6 ''Resample Volume'' module] or [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleScalarVectorDWIVolume-Documentation-3.6 ''Resample Scalar/Vector/DWI Volume'' module]
-:#Resample the DWI (not DTI)  to isotropic voxel size: [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleScalarVectorDWIVolume-Documentation-3.6 ''Resample Scalar/Vector/DWI Volume'' module]
+:#Resample the DWI (not DTI)  to isotropic voxel size: [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleScalarVectorDWIVolume-Documentation-3.6 ''Resample Scalar/Vector/DWI Volume'' module]. Note that depending on the size of the original DWI, the isotropic volumes can become very large files. Make sure you have sufficient RAM and disk space available.
-:#Extract the baseline and DTI from the isotropic DWI:  [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorEstimation-Documentation-3.6 ''Diffusion Tensor Estimation'' module]
+:#Extract the baseline and DTI from the isotropic DWI:  [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorEstimation-Documentation-3.6 ''Diffusion Tensor Estimation'' module]. Also select to generate a mask image.
-#Manually reorient DWI into orientation of T2:
+#Register the DWI baseline scan to the reference. Preferred structural reference is a T2-weighted scan. If no T2 is available use the next closest contrast.
-:#Resample DWI into new space and into isotropic voxel size
+##If initial misalignment (rotation/translation) is significant (more than ~20% of the FOV), consider a preliminary manual alignment first, using the [http://www.slicer.org/slicerWiki/index.php/Modules:Transforms-Documentation-3.6 ''Transforms'' module]. If the final target is a T1 but a T2 is available, use the T2 as reference for the DWI, but then perform a second T2-T1 or T1-T2 registration.
-:#Convert DWI -> DTI, incl. mask & baseline extraction
+##try [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSfit-Documentation-3.6 ''BRAINSfit'' module] as first method of choice
-:#Register DTI_baseline to T2 (affine+nonrigid) w/o masking
+##masking is recommended for better results. We have a mask for the DWI but not the T2 reference. To obtain a mask for the reference
-:#Resample DTI_mask with above transform to build mask for T2
+::*you can either perform a prelim. registration without masking, then apply this transform to the DWI mask
-:#Repeat registration above, this time incl. masks and with higher BSpline grid size
+::*you can obtain a mask from another scan (e.g.T1, via the skull stripping or other segmentation tool) and perform a registration to the reference
-:#Resample DTI with above transform
+::*you can try and obtain a mask for the reference directly, via
 === Procedures ===