Projects:RegistrationLibrary:RegLib C33 v36 - Revision history

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2012-05-16T20:04:49Z

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Meier at 19:22, 16 May 2012

2012-05-16T19:22:23Z

Meier at 19:01, 16 May 2012

2012-05-16T19:01:15Z

Meier at 19:00, 16 May 2012

2012-05-16T19:00:29Z

Meier at 19:00, 16 May 2012

2012-05-16T19:00:01Z

Meier: Created page with '=== RegLib C36 Procedures for Slicer 3.6 === *'''Phase I: Load & Convert DICOM''' #run Dicom2NRRD converter for the DWI Dicom set. Output file: DWI.nrrd #load DWI.nrrd #load T1, …'

2012-05-16T18:59:16Z

Created page with '=== RegLib C36 Procedures for Slicer 3.6 === *'''Phase I: Load & Convert DICOM''' #run Dicom2NRRD converter for the DWI Dicom set. Output file: DWI.nrrd #load DWI.nrrd #load T1, …'

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=== RegLib C36 Procedures for Slicer 3.6 ===
*'''Phase I: Load & Convert DICOM'''
#run Dicom2NRRD converter for the DWI Dicom set. Output file: DWI.nrrd
#load DWI.nrrd
#load T1, FLAIR and T1Gd images via AddVolume...
#Subsample T1: The T1 is 512 x 512 x 176 (0.5 x 0.5 x 1) resolution, which is too large as a reference to sample the DTI into. So we generate a smaller, isotropic 1x1x1 version of the T1 that can serve as reference:
##Open ''Filtering/Resample Scalar Volume'' module
##Input: T1, Output: new volume, rename to T1_sub
##interpolation: ''Hamming''
##Spacing: 1,1,1
*'''Phase II: Check initial Alignment and anisotropy'''
#large initial misalignment and high voxel anisotropy can cause problems when registering and resampling the DTI. In such cases it is advisable to resample the DWI first into a more isotropic space and, if necessary, initially realign to a similar orientation as the T1 reference, '''before'' converting to DTI. In this example DWI is sufficiently aligned and has voxel dimensions of 1 x 1 x 2.6, which is borderline. Anisotropy ratios greater than 1:3 tend to benefit from initial resampling. In this case we proceed without.
*'''Phase III: convert DWI -> DTI''
#go to module: Diffusion / Utilities / Diffusion Tensor Estimation
#input: DWI, output : DTI, DTI_base and DTI_mask
#Input DWI Volume: DWI, Output DTI Volume: create new, rename to "DTI"
#Output Baseline: create new, rename to "DTI_base"
#Otsu Threshold Mask: create new, rename to "DTI_iso_mask"
#check boxes for ''Remove Islands'' and ''Apply Mask''
##leave defaults
*'''Phase IVa: Register DTI-T1 (unmasked)'''
#open Registration : ''BrainsFit'' module (presets: Xf1_DTI-T1_unmasked
##Registration Phases:
##set T1_sub as fixed and DTI_base as moving image
###select/check ''Include Affine registration phase''
###select/check ''Include BSpline registration phase''
##Output Settings:
###select a new transform "Slicer BSpline Transform", rename to "Xf1_DTI-T1_unmasked"
###select a new volume "Output Image Volume'', rename to "DTI_base_Xf1"
##Registration Parameters: increase ''Number Of Samples'' to 200,000
##Registration Parameters: set ''Number Of Grid Subdivisions'' to 5,5,3
##Leave all other settings at default
##click: Apply; (runtime < 1 min 10 sec. on MacPro Quad Core 2.4Ghz)
##result: the absence of the skull in the DTI causes significant and incorrect stretch of image in the I-S direction.
##we repeat with mask, using the above estimate to produce a mask for the T1
*'''Phase IVb: Build mask for T1: resample DTI_mask'''
#go to Filtering/Resample Scalar Vector DWI Volume
##Use provided presets or set the following:
##input: DTI_mask
##reference: T1_sub
##output: create new, rename to T1_sub_mask
##Transform node: Xf1_DTI-T1_unmasked
##Transforms order: check ''output-to-input''
##interpolation type: check "nn"
##click: ''Apply''
#Go to ''Volumes'' module
#select new "T1_sub_mask: volume, go to ''Info'' tab
#check the ''labelmap'' checkbox
*'''Phase IVc: Register DTI-T1 (masked)'''
#open Registration : ''BrainsFit'' module (presets: Xf1_DTI-T1_masked)
##settings as in Phase IVa above, except:
###select a new transform "Slicer BSpline Transform", rename to "Xf2_DTI-T1_masked"
###select a new volume "Output Image Volume'', rename to "DTI_base_Xf2"
##Mask Processing Mode: check "ROI"
##Input Fixed Mask: T1_mask
##Input Moving Mask: DTI_mask
##Apply. Runtime 45 sec.
##go to ''Volumes'' module to adjust window&level for new result "DTI_base_Xf2"
##alignment is now much improved
*'''Phase V: 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_sub''
##Transform Parameters: select transform "Xf2_DTI-T1_masked''
##check box: ''output-to-input''
##Leave all other settings at defaults
##Click Apply; runtime ~ 3 min.
*'''Phase VIa: Register FLAIR & T1 Gd: obtain masks'''
#we seek affine alignment only for FLAIR and T1Gd. As above, better results are achieved when masking non-brain parenchyma. To obtain masks for the FLAIR and T1Gd we proceed as above by resampling the DT_mask with the '''Xf2_DTI-T1''' transform and the respective image as reference.
#go to Filtering/Resample Scalar Vector DWI Volume
##input: DTI_mask
##reference: FLAIR
##output: create new, rename to FLAIR_mask
##Transform node: Xf2_DTI-T1_masked
##Transforms order: check ''output-to-input''
##interpolation type: check "nn"
##click: ''Apply''
#Go to ''Volumes'' module
#select new "FLAIR_mask: volume, go to ''Info'' tab
#check the ''labelmap'' checkbox
*'''Phase VIb: Mask for T1Gd'''
#ditto: we seek affine alignment only for T1Gd. Identical procedure as for FLAIR above:
#go to Filtering/Resample Scalar Vector DWI Volume
##input: DTI_mask
##reference: T1Gd
##output: create new, rename to T1Gd_mask
##Transform node: Xf2_DTI-T1_masked
##Transforms order: check ''output-to-input''
##interpolation type: check "nn"
##click: ''Apply''
#Go to ''Volumes'' module
#select new "T1Gd_mask: volume, go to ''Info'' tab
#check the ''labelmap'' checkbox
*'''Phase VIc: Register FLAIR & T1Gd'''
#open Registration : ''BrainsFit'' module (presets: Xf4_... and Xf5_...)
##Registration Phase: check box for "Affine" only
###select a new linear transform "Slicer Linear Transform", rename to "Xf4_FLAIR-T1_masked"
##Mask Processing Mode: check "ROI"
##Input Fixed Mask: T1_mask
##Input Moving Mask: FLAIR_mask
##Apply. Runtime ~45 sec.
#ditto for T1Gd

=== Registration Results===

[[Image:RegLib_C33_Agif.gif|400px|lleft|DTI aligned with T1]]

===Download ===
*Data
**[[Media:RegLib_C33_Data.zip‎ ‎|'''RegLib_C33_Data''' DWI, DTI, T1, FLAIR, Presets & solution transforms (NRRD files, zip file 174 MB) ]]'''
**[[Media:RegLib_C33_Data_noDWI.zip‎ ‎|'''RegLib_C33_Data_noDWI''' subset of the above, contains DTI but w/o DWI and resampled DTI (NRRD files, zip file 86 MB) ]]'''
**[[Media:RegLib_C33_Data_Xforms.zip‎ ‎|'''RegLib_C33_Data Transforms & Presets only''' contains only result transforms and parameter presets (NRRD files, zip file 30 kB) ]]'''
*Presets
**[[Media:RegLib_C33_Presets.mrml‎|'''RegLib_C33_Presets''' Presets for FLAIR and DTI registration & DTI resampling (.mrml file 12 kB) ]]'''
**[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]

@@ Line 7: / Line 7: @@
 ===Download ===
 *Data
-**[[Media:RegLib_C33_Data.zip‎ ‎|'''RegLib_C33_Data''' DWI, DTI, T1, FLAIR, Presets & solution transforms  <small> (NRRD files, zip file 174 MB) </small>]]'''
+**[[Media:RegLib_C33_v36_Data.zip‎ ‎|'''RegLib_C33_Data''' DWI, DTI, T1, FLAIR, Presets & solution transforms  <small> (NRRD files, zip file 174 MB) </small>]]'''
-**[[Media:RegLib_C33_Data_noDWI.zip‎ ‎|'''RegLib_C33_Data_noDWI''' subset of the above, contains DTI but w/o DWI and resampled DTI <small> (NRRD files, zip file 86 MB) </small>]]'''
+**[[Media:RegLib_C33_v36_Data_noDWI.zip‎ ‎|'''RegLib_C33_Data_noDWI''' subset of the above, contains DTI but w/o DWI and resampled DTI <small> (NRRD files, zip file 86 MB) </small>]]'''
-**[[Media:RegLib_C33_Data_Xforms.zip‎ ‎|'''RegLib_C33_Data Transforms & Presets only''' contains only result transforms and parameter presets <small> (NRRD files, zip file 30 kB) </small>]]'''
+**[[Media:RegLib_C33_v36_Data_Xforms.zip‎ ‎|'''RegLib_C33_Data Transforms & Presets only''' contains only result transforms and parameter presets <small> (NRRD files, zip file 30 kB) </small>]]'''
 *Presets
 **[[Media:RegLib_C33_Presets.mrml‎|'''RegLib_C33_Presets''' Presets for FLAIR and DTI registration & DTI resampling <small> (.mrml file 12 kB) </small>]]'''
 **[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]
 === Overall Strategy ===
 :#DWI -> DTI, obtain mask +baseline

@@ Line 13: / Line 13: @@
 **[[Media:RegLib_C33_Presets.mrml‎|'''RegLib_C33_Presets''' Presets for FLAIR and DTI registration & DTI resampling <small> (.mrml file 12 kB) </small>]]'''
 **[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]
 === Procedures ===
 **'''Phase I: Load & Convert DICOM'''

← Older revision		Revision as of 19:01, 16 May 2012
Line 1:		Line 1:
	= RegLib C36 Procedures for Slicer 3.6 =		= RegLib C36 Procedures for Slicer 3.6 =
		+	[[Projects:RegistrationLibrary:RegLib_C33\| back to Slicer 4 version]]

	=== Registration Results===		=== Registration Results===

← Older revision		Revision as of 19:00, 16 May 2012
Line 1:		Line 1:
−	=== RegLib C36 Procedures for Slicer 3.6 ===	+	= RegLib C36 Procedures for Slicer 3.6 =

	=== Registration Results===		=== Registration Results===

@@ Line 1: / Line 1: @@
 === RegLib C36 Procedures for Slicer 3.6 ===
 *'''Phase I: Load & Convert DICOM'''
 #run Dicom2NRRD converter for the DWI Dicom set. Output file: DWI.nrrd
 #load DWI.nrrd
@@ Line 102: / Line 115: @@
 ##Apply. Runtime ~45 sec.
 #ditto for T1Gd