Difference between revisions of "Projects:RegistrationLibrary:RegLib C03"

From NAMIC Wiki
Jump to: navigation, search
m (Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/")
 
(16 intermediate revisions by one other user not shown)
Line 3: Line 3:
 
[[Projects:RegistrationDocumentation:UseCaseInventory|Back to Registration Use-case Inventory]] <br>
 
[[Projects:RegistrationDocumentation:UseCaseInventory|Back to Registration Use-case Inventory]] <br>
  
== <small>v4.1</small> [[Image:Slicer363_banner.png|150px]] Slicer Registration Library Case #3: Diffusion Weighted Image Volume: align with structural reference MRI==
+
== <small>updated for '''v4.1'''</small> [[Image:Slicer4_RegLibLogo.png|150px]] <br>Slicer Registration Library Case #3: Diffusion Weighted Image Volume: align with structural reference MRI==
 
=== Input ===
 
=== Input ===
 
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
 
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
Line 16: Line 16:
 
|moving image 2b<br>DTI tensor
 
|moving image 2b<br>DTI tensor
 
|}
 
|}
 
=== Modules ===
 
*'''Slicer 4.1 recommended modules:  [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit BrainsFit]''', [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ResampleDTIVolume Resample DTI Volume], [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/DiffusionTensorEstimation Diffusion Tensor Estimation]
 
*[[Projects:RegistrationLibrary:RegLib_C03b|for the Slicer 3.6.3 version of this case see here]]
 
  
 
===Objective / Background ===
 
===Objective / Background ===
 
Goal is to align the DTI image with the structural reference T2 scan that provides accuracte anatomical reference.  
 
Goal is to align the DTI image with the structural reference T2 scan that provides accuracte anatomical reference.  
*'''Alternate Versions:''' this example covers the most basic form of directly registering a DTI + baseline to a T2. There is another (more advanced) version that show how to address additional issues of a strong initial rotation and strong voxel-anisotropy for the raw DWI image acquired.  [[Projects:RegistrationLibrary:RegLib_C03B|You will find the advanced version here]].
 
  
=== Part I : registration only ===
+
=== Slicer 4.1 Modules Used ===
This assumes you have the following: 1) a T2 reference image, 2) a DTI baseline image and  3) the DTI volume (both obtained from the  [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/DiffusionTensorEstimation Diffusion Tensor Estimation module]).
+
*[https://www.slicer.org/wiki/Documentation/4.1/Modules/BRAINSFit BrainsFit]
 +
*[https://www.slicer.org/wiki/Documentation/4.1/Modules/ResampleDTIVolume Resample DTI Volume]
 +
*[https://www.slicer.org/wiki/Documentation/4.1/Modules/DiffusionTensorEstimation Diffusion Tensor Estimation]
 +
 
 +
=== Alternate Versions ===
 +
*this example covers the most basic form of directly registering a DTI + baseline to a T2. There is another (more advanced) version that show how to address additional issues of a strong initial rotation and strong voxel-anisotropy for the raw DWI image acquired.  [[Projects:RegistrationLibrary:RegLib_C03B|You will find the advanced version here]].
 +
*[[Projects:RegistrationLibrary:RegLib_C03_v3|for the Slicer 3.6.3 version of this case see here]]
 +
 
 +
===Download ===
 +
*Image Data:
 +
**[[Media:RegLib_C03_Data.zip‎|'''RegLib_C03_Data''': main registration package: register DTI <small> (Data, Transforms, solutions, zip file 115 MB) </small>]]
 +
 
 +
=== Procedure ===
 +
This assumes you have the following: 1) a T2 reference image, 2) a DTI baseline image and  3) the DTI volume (both obtained from the  [https://www.slicer.org/wiki/Documentation/4.1/Modules/DiffusionTensorEstimation Diffusion Tensor Estimation module]).
 
*Image Data:
 
*Image Data:
**[[Media:RegLib_C03_Data.zip‎|'''RegLib_C03_Data''': main registration package: register DTI <small> (Data,Presets, Transforms, zip file 61 MB) </small>]]
 
 
*'''Overview''':
 
*'''Overview''':
::#Using  [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit General Registraion (BRAINS)]''', register DTI_baseline to T2 (affine+nonrigid) w/o masking
+
::#Using  [https://www.slicer.org/wiki/Documentation/4.1/Modules/BRAINSFit General Registraion (BRAINS)]''', register DTI_baseline to T2 (affine+nonrigid) w/o masking
:#Resample the DTI with above transform with the  [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ResampleDTIVolume Resample DTI Volume] module
+
:#Resample the DTI with above transform with the  [https://www.slicer.org/wiki/Documentation/4.1/Modules/ResampleDTIVolume Resample DTI Volume] module
#open  [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit Registration : ''General Registration (BRAINS)'']  module  
+
#open  [https://www.slicer.org/wiki/Modules:BRAINSFit Registration : ''General Registration (BRAINS)'']  module  
 
##''Input Images'': fixed = T2 , moving = DTI_base
 
##''Input Images'': fixed = T2 , moving = DTI_base
 
##''Output Settings'':  
 
##''Output Settings'':  
Line 45: Line 52:
 
##click: ''Apply''; runtime < 1 min.
 
##click: ''Apply''; runtime < 1 min.
 
#Resample DTI
 
#Resample DTI
#Open the  [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ResampleDTIVolume Resample DTI Volume] module (found under: All Modules)
+
#Open the  [https://www.slicer.org/wiki/Documentation/4.1/Modules/ResampleDTIVolume Resample DTI Volume] module (found under: All Modules)
 
##Input Volume: select DTI
 
##Input Volume: select DTI
##Output Volume: select ''create new Diffusion Tensor Volume'',and rename it to ''DTI_Xf2''
+
##Output Volume: select ''create new Diffusion Tensor Volume'',and rename it to ''DTI_Xf1''
 
##Reference Volume: select ''T2''
 
##Reference Volume: select ''T2''
##Transform Parameters: select transform "Xf2_DTI-T2_masked'', ''Deformation Field'': none ; check the ''displacement'' checkbox
+
##Transform Parameters: select transform node "Xf1_DTI-T2_BSpline", for  ''Deformation Field'': none ; '''check the ''displacement'' checkbox'''
 
##Leave all other settings at defaults
 
##Leave all other settings at defaults
 
##Click Apply; runtime ~ 2 min.
 
##Click Apply; runtime ~ 2 min.
#Go to the ''Volumes'' module, select the newly produced ''DTI_Xf2'' volume
+
#set ''T2'' as background and new  ''DTI_Xf1'' volume as foreground
#under the ''Display'' tab, select ''Color Orientation'' from the ''Scalar Mode'' menu
+
#fade between back- and foreground to see DTI overlay onto the T2 image. Note that you can also fade via holding the OPTION+CMD keys (mac) + dragging left mouse.
#set ''T2'' as background and new  ''DTI_Xf2'' volume as foreground
 
#fade between back- and foreground to see DTI overlay onto the T2 image
 
  
=== Registration Results===
+
=== Registration Results (click to enlarge) ===
 
{| style="color:#bbbbbb; background-color:#333333;" cellpadding="10" cellspacing="0" border="0"
 
{| style="color:#bbbbbb; background-color:#333333;" cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C03_AGif_registered.gif|400px|left]]  
+
|[[Image:RegLib_C03_baseline_unregistered.gif|400px|left]]
 +
|[[Image:RegLib_C03_baseline_registered.gif|400px|left]]
 +
|[[Image:RegLib_C03_DTI_registered.gif|400px|left]]  
 
|-
 
|-
 +
|baseline & T2 before registration
 
|baseline to T2 after affine+nonrigid alignment
 
|baseline to T2 after affine+nonrigid alignment
 +
|DTI and T2 before & after registration
 
|}
 
|}
 
 
  
 
=== Keywords ===
 
=== Keywords ===
 
MRI, brain, head, intra-subject, DTI, DWI
 
MRI, brain, head, intra-subject, DTI, DWI
 
===Download ===
 
*Image Data:
 
**[[Media:RegLib_C03_Data.zip‎|'''RegLib_C03_Data''': main registration package: register DTI <small> (Data,Presets, Transforms, zip file 61 MB) </small>]]
 
**[[Media:RegLib_C03_Data_preproc.zip‎|'''RegLib_C03_Data_preproc''':preprocessing package: resample T2, resample & align DWI, convert to DTI  <small> (raw and resampled DWI, zip file 228 MB) </small>]]
 
**[[Media:RegLib_C03_DATA_results.zip‎|RegLib_C03_DATA_results: resampled DTI <small> (registered DTI, zip file 39 MB) </small>]]
 
*Presets:
 
**[[Media:RegLib_C03_Presets.mrml|'''Presets''' for BRAINSfit registration & resampling <small> (Data, Solution, zip file 12 kB) </small>]]
 
**[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]
 
*Documentation
 
**[[Media:RegLib_C03_DTI.ppt|'''Tutorial'''  <small> (.ppt file 2 MB) </small>]]
 
**[[Media:RegLib_C03_DTI.pdf|'''Tutorial as PDF''' <small> (PDF file 2 MB) </small>]]
 
 
===Input Data===
 
*reference/fixed : T2w axial, 0.4mm resolution in plane, 3mm slices
 
*moving: Baseline image of acquired DTI volume, corresponds to T2w MRI , 0.9375 x 0.9375 x 1.4 mm voxel size, oblique
 
*Tensor data of DTI volume, oblique, same orientation as Baseline image. The result Xform will be applied to this volume. The original DWI has 26 directions, the extracted DTI volume has 9 scalars, i.e. 256 x 256 x 36 x 9
 
  
 
=== Discussion: Key Strategies ===
 
=== Discussion: Key Strategies ===
*the two images have identical contrast, hence we could consider "sharper" cost functions, such as NormCorr or MeanSqrd. But because of the strong distortions and lower resolution of the moving image, Mutual Information is recommended as the most robust metric.
+
*the strong EPI-based distortions of the DTI image make nonrigid registration necessary
*often anatomical labels are available from the reference scan. It would be less work to align the anatomical reference with the DTI, since that would circumvent having to resample the complex tensor data into a new orientation. However the strong distortions are better addressed by registering the other direction, i.e. move the DTI into the anatomical reference space.
+
*initial alignment & overlap is sufficient so that no "initialization" methods are necessary and registration can succeed without.
*in this example the initial alignment of the two scans is very poor. The strongly oblique orientation of the DWI makes an initial manual alignment step necessary. This step should occur '''before''' converting to the DTI to avoid interpolation artifacts.
+
*contrast & initial pose are similar enough for registration to succeed without any masking. However the DTI estimation procedure '''does''' provide an optional mask that is usually very helpful in registering cases with more "distracting" image content.   [[Projects:RegistrationLibrary:RegLib_C03_2| For an example see the extended version of this case here.]]
 +
*the DTI in this example is isotropic and hence can be resampled directly. If the DTI contains strong anisotropy of ratios 1:3 or greater, reorienting the DTI can lead to strong artifacts (e.g. in axial direction appear as blue cast in the color orientation view). In that case it is necessary to resample the DWI in the original orientation to an isotropic size before reorienting. It may also be advisable to first reorient the DWI and perform the DTI estimation afterwards.
  
 
=== Acknowledgments ===
 
=== Acknowledgments ===

Latest revision as of 17:29, 10 July 2017

Home < Projects:RegistrationLibrary:RegLib C03

Back to ARRA main page
Back to Registration main page
Back to Registration Use-case Inventory

updated for v4.1 Slicer4 RegLibLogo.png
Slicer Registration Library Case #3: Diffusion Weighted Image Volume: align with structural reference MRI

Input

this is the fixed T2 reference image. All images are aligned into this space 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
T2
moving image 2a
DTI baseline
moving image 2b
DTI tensor

Objective / Background

Goal is to align the DTI image with the structural reference T2 scan that provides accuracte anatomical reference.

Slicer 4.1 Modules Used

Alternate Versions

Download

Procedure

This assumes you have the following: 1) a T2 reference image, 2) a DTI baseline image and 3) the DTI volume (both obtained from the Diffusion Tensor Estimation module).

  • Image Data:
  • Overview:
  1. Using General Registraion (BRAINS), register DTI_baseline to T2 (affine+nonrigid) w/o masking
  1. Resample the DTI with above transform with the Resample DTI Volume module
  1. open Registration : General Registration (BRAINS) module
    1. Input Images: fixed = T2 , moving = DTI_base
    2. Output Settings:
      1. Slicer BSpline Transform (create new transform, rename to: "Xf1_DTbase-T2_BSpline")
      2. Slicer Linear Transform none
      3. Output Image Volume (create new volume, rename to: "DTIbaseline_Xf1"
    3. Registration Phases: select/check Rigid , Rigid+Scale, Affine, BSpline
    4. Main Parameters:
      1. increase Number Of Samples to 200,000
      2. set B-Spline Grid Size to 5,5,5
    5. Leave all other settings at default
    6. click: Apply; runtime < 1 min.
  2. Resample DTI
  3. Open the Resample DTI Volume module (found under: All Modules)
    1. Input Volume: select DTI
    2. Output Volume: select create new Diffusion Tensor Volume,and rename it to DTI_Xf1
    3. Reference Volume: select T2
    4. Transform Parameters: select transform node "Xf1_DTI-T2_BSpline", for Deformation Field: none ; check the displacement checkbox
    5. Leave all other settings at defaults
    6. Click Apply; runtime ~ 2 min.
  4. set T2 as background and new DTI_Xf1 volume as foreground
  5. fade between back- and foreground to see DTI overlay onto the T2 image. Note that you can also fade via holding the OPTION+CMD keys (mac) + dragging left mouse.

Registration Results (click to enlarge)

RegLib C03 baseline unregistered.gif
RegLib C03 baseline registered.gif
RegLib C03 DTI registered.gif
baseline & T2 before registration baseline to T2 after affine+nonrigid alignment DTI and T2 before & after registration

Keywords

MRI, brain, head, intra-subject, DTI, DWI

Discussion: Key Strategies

  • the strong EPI-based distortions of the DTI image make nonrigid registration necessary
  • initial alignment & overlap is sufficient so that no "initialization" methods are necessary and registration can succeed without.
  • contrast & initial pose are similar enough for registration to succeed without any masking. However the DTI estimation procedure does provide an optional mask that is usually very helpful in registering cases with more "distracting" image content. For an example see the extended version of this case here.
  • the DTI in this example is isotropic and hence can be resampled directly. If the DTI contains strong anisotropy of ratios 1:3 or greater, reorienting the DTI can lead to strong artifacts (e.g. in axial direction appear as blue cast in the color orientation view). In that case it is necessary to resample the DWI in the original orientation to an isotropic size before reorienting. It may also be advisable to first reorient the DWI and perform the DTI estimation afterwards.

Acknowledgments