Difference between revisions of "Projects:RegistrationLibrary:RegLib C29"
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#click apply; runtime ca. 1-2 min. | #click apply; runtime ca. 1-2 min. | ||
#Resample T2 into T1 space | #Resample T2 into T1 space | ||
− | ##Open ''Resample Scalar/Vector/DWI Volume'' module | + | ##Open ''Resample Scalar/Vector/DWI Volume'' module (Filtering menu) |
− | + | ##Input Volume: T2, Reference Volume: T1 | |
− | + | ##Output Volume: create new volume, rename to "T2_Xf1" | |
− | # | + | ##Interpolation Type: select ''ws'' (windowed sinc) |
− | + | ##Click Apply. | |
− | + | *'''Phase III:REGISTER DTI TO T2_Xf1''' | |
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− | |||
− | *'''Phase | ||
#open Registration : ''BrainsFit'' module | #open Registration : ''BrainsFit'' module | ||
##Registration Phases: | ##Registration Phases: | ||
− | ##set | + | ##set T2_Xf1 as fixed and DTI_baseline as moving image |
##select/check ''Include Rigid registration phase'' | ##select/check ''Include Rigid registration phase'' | ||
##select/check ''Include Affine registration phase'' | ##select/check ''Include Affine registration phase'' | ||
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##select "Include Affine registration phase" | ##select "Include Affine registration phase" | ||
#Output Settings: | #Output Settings: | ||
− | ##select a new transform "Slicer BSpline Transform" | + | ##select a new transform "Slicer BSpline Transform", rename to "Xf2_DTI-T1'' |
##select a new volume "Output Image Volume'' | ##select a new volume "Output Image Volume'' | ||
#Registration Parameters: increase ''Number Of Samples'' to 200,000 | #Registration Parameters: increase ''Number Of Samples'' to 200,000 | ||
#Leave all other settings at default | #Leave all other settings at default | ||
#click apply; runtime ca. 3 min. | #click apply; runtime ca. 3 min. | ||
− | *'''Phase IV | + | *'''Phase IV: Resample DTI''' |
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#Load the combined transform (''Add Data'') | #Load the combined transform (''Add Data'') | ||
#Open the ''Resample DTI Volume'' module (found under: All Modules) | #Open the ''Resample DTI Volume'' module (found under: All Modules) | ||
##Input Volume: select DTI | ##Input Volume: select DTI | ||
− | ##Output Volume: select ''New DTI Volume'', rename to '' | + | ##Output Volume: select ''New DTI Volume'', rename to ''DTI_Xf2'' |
− | ##Reference Volume: select '' | + | ##Reference Volume: select ''T1'' |
− | ##Transform Parameters: select | + | ##Transform Parameters: select transform "Xf2_DTI-T1'' |
##check box: ''output-to-input'' | ##check box: ''output-to-input'' | ||
##Leave all other settings at defaults | ##Leave all other settings at defaults | ||
##Click Apply; runtime ca. 3-4 min. | ##Click Apply; runtime ca. 3-4 min. | ||
− | #Go to the ''Volumes'' module, select the newly produced '' | + | #Go to the ''Volumes'' module, select the newly produced ''DTI_Xf2'' volume |
#under the ''Display'' tab, select ''Color Orientation'' from the ''Scalar Mode'' menu | #under the ''Display'' tab, select ''Color Orientation'' from the ''Scalar Mode'' menu | ||
− | #set '' | + | #set ''T1'' as background and new ''DTI_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 | ||
Revision as of 19:41, 14 September 2010
Home < Projects:RegistrationLibrary:RegLib C29Back to ARRA main page
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Contents
v3.6.1 Slicer Registration Library Case #29: Intra-subject Brain DTI
Input
fixed image/target T1 SPGR |
moving image 1 T2 |
moving image 2a DTI baseline |
moving image 2b DTI tensor |
Modules
- Slicer 3.6.1 recommended modules: BrainsFit
Objective / Background
This is a classic case of a multi-sequence MRI exam we wish to spatially align to the anatomical reference scan (T1-SPGR). The scan of interest is the DTI image to be aligned for surgical planning/reference.
Keywords
MRI, brain, head, intra-subject, DTI, T1, T2, non-rigid, tumor, surgical planning
Input Data
- reference/fixed : T1 SPGR , 0.5x0.5x1 mm voxel size, 512 x 512 x 176
- moving 1: T2 0.5x0.5x1.5 mm voxel size, 512 x 512 x 92
- moving 2a: DTI baseline: 1 x 1 x 3 mm, 256 x 256 x 41
- moving 2b: 1 x 1 x 3 mm, 256 x 256 x 41 x 9 (tensor), original: DWI 256 x 256 x 41 x 32 directions
Registration Challenges
- The DTI sequence (EPI) contains string distortions we seek to correct via non-rigid alignment
- the DTI baseline is similar in contrast to a T2, albeit at much lower resolution
- we have different amounts of voxel-anisotropy
- a direct registration of the DTI_baseline to the SPGR will fail, hence a 2-step approach is required
Key Strategies
- Slicer 3.6.1 recommended modules: BrainsFit
- we use an 2-step approach: 1) we first co-register the T2 with the SPGR T1. 2) we register the DTI baseline to the T2 (the T1 provides insufficient similarity), 3) combine this with the Affine1 transform obtained from registering the T2 to the T1. affine transform with 12 DOF (rather than a rigid one) to address distortion differences between the two protocols; 4) resample the DTI volume with the new transform
Procedures
- Phase I: LOAD DATA
- download example dataset
- load into 3DSlicer 3.6.1 (Load Scene)
- To convert the DWI into a DTI: use the Converters / DICOM to NRRD Converter module
- Phase II: Register T2 to SPGR
- open Registration : BrainsFit module
- Registration Phases:
- select/check Include Rigid registration phase
- select/check Include Affine registration phase
- select a new transform Output Transform
- Registration Parameters: increase Number Of Samples to 200,000
- Leave all other settings at default
- click apply; runtime ca. 1-2 min.
- Resample T2 into T1 space
- Open Resample Scalar/Vector/DWI Volume module (Filtering menu)
- Input Volume: T2, Reference Volume: T1
- Output Volume: create new volume, rename to "T2_Xf1"
- Interpolation Type: select ws (windowed sinc)
- Click Apply.
- Phase III:REGISTER DTI TO T2_Xf1
- open Registration : BrainsFit module
- Registration Phases:
- set T2_Xf1 as fixed and DTI_baseline as moving image
- select/check Include Rigid registration phase
- select/check Include Affine registration phase
- select/check Include BSpline registration phase
- select Initialize with CenterofHeadAlign
- select Include Rigid registration phase
- select "Include Affine registration phase"
- Output Settings:
- select a new transform "Slicer BSpline Transform", rename to "Xf2_DTI-T1
- select a new volume "Output Image Volume
- Registration Parameters: increase Number Of Samples to 200,000
- Leave all other settings at default
- click apply; runtime ca. 3 min.
- Phase IV: Resample DTI
- Load the combined transform (Add Data)
- 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 ca. 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
Registered DTI superimposed on SPGR and T2 registered (cycles show T1 and T2 and color DTI overlay)
Download
- DATA
- PRESETS:
- TUTORIALS: