Difference between revisions of "Projects:RegistrationLibrary:RegLib C29"

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=== Procedures ===
 
=== Procedures ===
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*'''Phase I: LOAD DATA'''
+
*'''Phase I: Preprocessing: Build DWI mask + baseline'''
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#download example dataset
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#open the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/DiffusionWeightedMasking ''Modules:Diffusion:DiffusionWeightedImages:DiffusionWeightedVolumeMasking'' ] module
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#load into 3DSlicer 3.6.1 (Load Scene)
+
##''Input DWI Volume'': "DWI"
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#To convert the DWI into a DTI: use the ''Converters / DICOM to NRRD Converter'' module
+
##''Output Baseline Volume'':  ''Create New Volume'', rename to "DWI_baseline"
−
*'''Phase II: Register T2 to T1'''
+
##''Output Threshold Mask'': ''Create New Volume'', rename to "DWI_mask"
−
#open Registration : ''BrainsFit'' module
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##Leave other settings at default; click ''Apply''
−
##Registration Phases:  
+
*'''Phase II: Preprocessing: Convert DWI -> DTI'''
−
##select/check ''Include Rigid registration phase''
+
#open [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/DiffusionTensorEstimation "Diffusion Tensor Estimation" module] (menu: Diffusion:DiffusionWeightedImages: DiffusionTensorEstimation)
−
##select/check ''Include Affine registration phase''
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##''Input DWI Volume'': DWI_iso,  
−
##select a new transform ''Output Transform''
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##''Output DTI Volume'': create new, rename to "DTI_iso"
−
#Registration Parameters: increase ''Number Of Samples'' to 200,000
+
##''Output Baseline Volume'': create new, rename to "DWI_iso_baseline"
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#Leave all other settings at default
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#Click: Apply
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#click apply; runtime ca. 1-2 min.
+
*'''Phase III: register T2 to T1'''
−
#Resample T2 into T1 space
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#open the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit General Registration (BRAINS) module]
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##Open ''Resample Scalar/Vector/DWI Volume'' module (Filtering menu)
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##''Fixed Image Volume'': T1
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##Input Volume: T2, Reference Volume: T1
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##''Moving Image Volume'': T2
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##Output Volume: create new volume, rename to "T2_Xf1"
 
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##Interpolation Type: select ''ws'' (windowed sinc)
 
−
##Click Apply.
 
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##Upon completion, go to ''Volumes'' module to adjust window & level
 
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##Active Volume: select T2_Xf1
 
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##Open Display tab and adjust window & level, e.g. 1300/700
 
−
*'''Phase III:REGISTER DTI TO T2_Xf1'''
 
−
#open Registration : ''BrainsFit'' module
 
−
##Registration Phases:
 
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##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 ''Include Rigid registration phase''
 
−
###select ''Include Affine registration phase''
 
−
###select ''Include BSpline registration phase''
 
 
##Output Settings:  
 
##Output Settings:  
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###select a new transform "Slicer BSpline Transform", rename to "Xf2_DTI-T1_unmasked"
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###''Slicer BSpline Transform": none
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###select a new volume "Output Image Volume'', rename to "DT_base_Xf2"
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###''Slicer Linear Transform'': create new transform, rename to "Xf1_T2-T1"
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##Registration Parameters: increase ''Number Of Samples'' to 200,000
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###''Output Image Volume'': create new volume, rename to "T2_Xf1"
−
##Registration Parameters: set  ''Number Of Grid Subdivisions'' to 5,5,3
+
##''Registration Phases'': check boxes for ''Rigid'' and ''Affine''
 +
##''Main Parameters'':
 +
###''Number Of Samples'': 200,000
 
##Leave all other settings at default
 
##Leave all other settings at default
−
##click: Apply; runtime < 1 min.
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##click: Apply; runtime < 10 sec (MacPro QuadCore 2.4GHz)
−
*'''Phase IV: Resample DTI_mask'''
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*'''Phase IV: Register DTI (masked)'''
−
**we use the above Xform to produce a mask for the T1.
+
#open the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit General Registration (BRAINS) module]
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#Open ''Resample Scalar/Vector/DWI Volume'' module
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##''Fixed Image Volume'': FLAIR_Xf1
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##Input Volume: DTI_mask; Output volume: create new volume, rename to "DTI_mask_Xf2"
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##''Moving Image Volume'': DWI_iso_baseline
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##Transform Node: "Xf2_DTI-T1_unmasked"
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##Output Settings:
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##select/check:  ''output-to-input''
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###''Slicer BSpline Transform": create new transform, rename to "Xf2_DTI-T1"
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##Interpolation Type: select: '''nn'''
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###''Slicer Linear Transform'': none
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##click: Apply
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###''Output Image Volume'': create new volume,  rename to DWI_baseline_Xf2
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*'''Phase V:REGISTER DTI TO T2_Xf1 with masking'''
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##''Regstration Phases'': check boxes for ''Rigid'',  ''Affine'' and ''BSpline''
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#open Registration : ''BrainsFit'' module
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##''Main Parameters'':
−
##Registration Phases: as before: rigid, affine, BSpline
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###''Number Of Samples'': 200,000
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##set T2_Xf1 as fixed and DTI_baseline as moving image
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###''B-Spline Grid Size'': 5,5,3
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##All parameters as in Phase III
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##''Mask Option'': select ''ROIAUTO'' button
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##Output BSpline Transform: create new , rename to "Xf3_DTI-T1_masked"
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###''(ROIAUTO) Output fixed mask'': create new volume
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##Output Volume: create new, rename to "DTI_base_Xf3"
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###''(ROIAUTO) Output moving mask'': create new volume
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##Control of Mask Processing
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##Leave all other settings at default
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###select/check: ''ROI'' (rightmost box)
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##click: Apply; runtime 1-2 min (MacPro QuadCore 2.4GHz)
−
###Input Fixed Mask: select "DTI_mask_Xf2"
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*'''Phase V: Resample DTI'''
−
###Input Moving Mask: select "DTI_mask"
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#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)
−
##click: Apply; runtime < 1 min.
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##''Input Volume'': DTI
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*'''Phase VI: Resample DTI'''
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##''Output Volume'': create new DTI Volume, rename to ''DTI_Xf2''
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#Load the combined transform (''Add Data'')
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##''Reference Volume'': T2_Xf1
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#Open the ''Resample DTI Volume'' module (found under: All Modules)
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##''Transform Node'': select "Xf2_DTI-T1'' created above
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##Input Volume: select DTI
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##check box: ''displacement''
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##Output Volume: select ''New DTI Volume'', rename to ''DTI_Xf2''
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#leave all other settings at defaults
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##Reference Volume: select ''T1''
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#Click Apply; runtime ~ 3 min.
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##Transform Parameters: select transform "Xf2_DTI-T1''
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#set T1 or FLAIR as background and the new  ''DTI_Xf2'' volume as foreground
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##check box: ''output-to-input''
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#Move fade slider to see DTI overlay onto the structural image
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##Leave all other settings at defaults
 
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##Click Apply; runtime < 1 min.
 
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#Go to the ''Volumes'' module, select the newly produced ''DTI_Xf2'' volume
 
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#under the ''Display'' tab, select ''Color Orientation'' from the ''Scalar Mode'' menu
 
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#set ''T1'' as background and new  ''DTI_Xf2'' volume as foreground
 
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#Set fade slider to see DTI overlay onto the SPGR image
 
−
 
 
−
for more details see the tutorial(s) under Downloads
 
  
 
=== Registration Results===
 
=== Registration Results===
 
[[Image:RegLib_C29_registered.gif|500px|Registered DTI superimposed on SPGR and T2]] registered (cycles show T1 and T2 and color DTI overlay)<br>
 
[[Image:RegLib_C29_registered.gif|500px|Registered DTI superimposed on SPGR and T2]] registered (cycles show T1 and T2 and color DTI overlay)<br>
 
<br>
 
<br>

Revision as of 22:04, 4 May 2012

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v3.6.1 Slicer3-6Announcement-v1.png Slicer Registration Library Case #29: Intra-subject Brain DTI

Input

this is the fixed reference image. All images are aligned into this space lleft this is the T2 reference image, serves as target to the DTI baseline, but is itself aligned to the SPGR lleft this is the DTI Baseline scan, to be registered with the T2 this is the DTI tensor image, in the same orientation as the DTI Baseline
fixed image/target
T1 SPGR 		moving image 1
T2 		moving image 2a
DTI baseline 		moving image 2b
DTI tensor

Modules

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.

Download

Link to User Guide: How to Load/Save Registration Parameter Presets

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 DWI sequence (EPI) contains strong distortions we seek to correct via non-rigid alignment
  • The DWI sequence also contains strong intensity inhomogeneity (coil bias)
  • 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
  • to align the DTI with the T1 we need 2 registration steps: 1.align the T2 with the T1 and 2. align the DTI with the T2. The DTI baseline scan has contrast most similar to the T2 and hence is best registered against the T2. However the structural reference scan with highest resolution and tissue contrast is the T1.
  • we therefore use the following approach: 1) we first co-register the T2 with the SPGR T1. 2) we register the DTI baseline to the registered/resampled T2; 3) resample the DTI volume with the new transform
  • the DTI-T2 registration includes non-rigid deformation to correct for the strong distortions from the EPI acquisition. Because of the nonrigid component a mask of the brain parenchyma helps greatly in obtaining a meaningful transform.
  • The DTI estimation provides an automated mask for the DTI_baseline scan, but we have no mask for the T2. We can either obtain one through separate segmentation or by sending the DTI_mask through an additional registration step. In this example we show the latter.
  • thus the full pipeline is this:
  1. Affine align T2-T1, incl. resampled T2 volume = T2r
  2. Affine+BSpline align of DTI_baseline to T2r (unmasked)
  3. Resample DTI_mask with above BSpline -> mask for the T2r
  4. repeat Affine+BSpline align of DTI_base to T2r, WITH masks
  5. resample DTI with result Affine+BSpline transform

Procedures

  • Phase I: Preprocessing: Build DWI mask + baseline
  1. open the Modules:Diffusion:DiffusionWeightedImages:DiffusionWeightedVolumeMasking module
    1. Input DWI Volume: "DWI"
    2. Output Baseline Volume: Create New Volume, rename to "DWI_baseline"
    3. Output Threshold Mask: Create New Volume, rename to "DWI_mask"
    4. Leave other settings at default; click Apply
  • Phase II: Preprocessing: Convert DWI -> DTI
  1. open "Diffusion Tensor Estimation" module (menu: Diffusion:DiffusionWeightedImages: DiffusionTensorEstimation)
    1. Input DWI Volume: DWI_iso,
    2. Output DTI Volume: create new, rename to "DTI_iso"
    3. Output Baseline Volume: create new, rename to "DWI_iso_baseline"
  2. Click: Apply
  • Phase III: register T2 to T1
  1. open the General Registration (BRAINS) module
    1. Fixed Image Volume: T1
    2. Moving Image Volume: T2
    3. Output Settings:
      1. Slicer BSpline Transform": none
      2. Slicer Linear Transform: create new transform, rename to "Xf1_T2-T1"
      3. Output Image Volume: create new volume, rename to "T2_Xf1"
    4. Registration Phases: check boxes for Rigid and Affine
    5. Main Parameters:
      1. Number Of Samples: 200,000
    6. Leave all other settings at default
    7. click: Apply; runtime < 10 sec (MacPro QuadCore 2.4GHz)
  • Phase IV: Register DTI (masked)
  1. open the General Registration (BRAINS) module
    1. Fixed Image Volume: FLAIR_Xf1
    2. Moving Image Volume: DWI_iso_baseline
    3. Output Settings:
      1. Slicer BSpline Transform": create new transform, rename to "Xf2_DTI-T1"
      2. Slicer Linear Transform: none
      3. Output Image Volume: create new volume, rename to DWI_baseline_Xf2
    4. Regstration Phases: check boxes for Rigid, Affine and BSpline
    5. Main Parameters:
      1. Number Of Samples: 200,000
      2. B-Spline Grid Size: 5,5,3
    6. Mask Option: select ROIAUTO button
      1. (ROIAUTO) Output fixed mask: create new volume
      2. (ROIAUTO) Output moving mask: create new volume
    7. Leave all other settings at default
    8. click: Apply; runtime 1-2 min (MacPro QuadCore 2.4GHz)
  • Phase V: Resample DTI
  1. Open the Resample DTI Volume module (under All Modules menu; note this is distinct from the ResampleScalarVectorDWIVolume used above)
    1. Input Volume: DTI
    2. Output Volume: create new DTI Volume, rename to DTI_Xf2
    3. Reference Volume: T2_Xf1
    4. Transform Node: select "Xf2_DTI-T1 created above
    5. check box: displacement
  2. leave all other settings at defaults
  3. Click Apply; runtime ~ 3 min.
  4. set T1 or FLAIR as background and the new DTI_Xf2 volume as foreground
  5. Move fade slider to see DTI overlay onto the structural image

Registration Results

Registered DTI superimposed on SPGR and T2 registered (cycles show T1 and T2 and color DTI overlay)

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