Difference between revisions of "Projects:RegistrationLibrary:RegLib C04"

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==Slicer Registration Library Case 04: Intra-subject Brain MR of Multiple Sclerosis: Multi-contrast series for lesion change assessment ==
 
==Slicer Registration Library Case 04: Intra-subject Brain MR of Multiple Sclerosis: Multi-contrast series for lesion change assessment ==
 
{| 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:RLib02_SPGR.png|150px|lleft|this is the fixed reference image. All images are aligned into this space]]  
+
|[[Image:Reglib_C04_Thumb_PD1.jpg|150px|lleft|this is the fixed reference image. All images are aligned into this space]]  
−
|[[Image:RLib02_SPGR+ICC.png|150px|lleft|this is a passive image to which the calculated transform is applied. It is a label-map in the same space as the moving FLAIR image]]
+
|[[Image:RReglib_C04_Thumb_T21.jpg|150px|lleft|this is a passive image to which the calculated transform is applied. It is a label-map in the same space as the moving FLAIR image]]
 +
|[[Image:RReglib_C04_Thumb_Gd1.jpg|150px|lleft|this is a passive image to which the calculated transform is applied. It is a label-map in the same space as the moving FLAIR image]]
 
|[[Image:Arrow_left_gray.jpg|100px|lleft]]  
 
|[[Image:Arrow_left_gray.jpg|100px|lleft]]  
−
|[[Image:RLib02_FLAIR_150.png|150px|lleft|this is the moving image. The transform is calculated by matching this to the reference image]]
+
|[[Image:Reglib_C04_Thumb_PD2.jpg|150px|lleft|this is the moving image. The transform is calculated by matching this to the reference image]]
−
|[[Image:RLib02_FLAIR+LesionSeg_150.png|150px|lleft|this is a passive image to which the calculated transform is applied. It is a label-map in the same space as the moving FLAIR image]]
+
|[[Image:Reglib_C04_Thumb_T22.jpg|150px|lleft|this is a passive image to which the calculated transform is applied. It is a label-map in the same space as the moving FLAIR image]]
 +
|[[Image:Reglib_C04_Thumb_Gd2.jpg|150px|lleft|this is a passive image to which the calculated transform is applied. It is a label-map in the same space as the moving FLAIR image]]
 
|align="left"|LEGEND<br><small><small>
 
|align="left"|LEGEND<br><small><small>
 
[[Image:Button_red_fixed.jpg|20px|lleft]]  this indicates the reference image that is fixed and does not move. All other images are aligned into this space and resolution<br>
 
[[Image:Button_red_fixed.jpg|20px|lleft]]  this indicates the reference image that is fixed and does not move. All other images are aligned into this space and resolution<br>
 
[[Image:Button_green_moving.jpg|20px|lleft]]  this indicates the moving image that determines the registration transform.  <br>
 
[[Image:Button_green_moving.jpg|20px|lleft]]  this indicates the moving image that determines the registration transform.  <br>
−
[[Image:Button_purple_mask.jpg|20px|lleft]] this indicates images that serve as masks, i.e. they focus the active registration onto a specific area.<br>
 
 
[[Image:Button_blue_tag.jpg|20px|lleft]] this indicates images that passively move into the reference space, i.e. they have the transform applied but do not contribute to the calculation of the transform.
 
[[Image:Button_blue_tag.jpg|20px|lleft]] this indicates images that passively move into the reference space, i.e. they have the transform applied but do not contribute to the calculation of the transform.
 
</small></small>
 
</small></small>
 
|-
 
|-
−
|[[Image:Button_red_fixed.jpg|40px|lleft]]  T1 SPGR
+
|[[Image:Button_red_fixed.jpg|40px|lleft]]  PD axial
−
|[[Image:Button_purple_mask.jpg|40px|lleft]]  mask
+
|[[Image:Button_red_fixed.jpg|40px|lleft]]  T2 axial
 +
|[[Image:Button_green_moving.jpg|40px|lleft]]  T1-GdDTPA
 
|
 
|
−
|[[Image:Button_green_moving.jpg|40px|lleft]] T2 FLAIR
+
|[[Image:Button_green_moving.jpg|40px|lleft]] PD axial
−
|[[Image:Button_blue_tag.jpg|40px|lleft]] segmentation
+
|[[Image:Button_blue_tag.jpg|40px|lleft]] T2 axial
 +
|[[Image:Button_blue_tag.jpg|40px|lleft]] T1-GdDTPA
 
|-
 
|-
−
|1mm isotropic<br> 256 x 256 x 146<br>RAS
+
|0.9375 x 0.9375 x 3 mm axial<br> 256 x 256 x 51<br>RAS
−
|1mm isotropic<br> 256 x 256 x 146<br>RAS
+
|0.9375 x 0.9375 x 3 mm axial<br> 256 x 256 x 51<br>RAS
 +
|0.9375 x 0.9375 x 5 mm axial<br> 256 x 256 x 24<br>RAS
 
|
 
|
−
|1.2mm isotropic<br> 256 x 256 x 116<br>RAS
+
|0.9375 x 0.9375 x 3 mm axial<br> 256 x 256 x 54<br>RAS
−
|1.2mm isotropic<br> 256 x 256 x 116<br>RAS
+
|0.9375 x 0.9375 x 3 mm axial<br> 256 x 256 x 54<br>RAS
 +
|0.9375 x 0.9375 x 5 mm axial<br> 256 x 256 x 24<br>RAS
 
|}
 
|}
 
===Objective / Background ===
 
===Objective / Background ===
−
This scenario occurs in many forms whenever we wish to align all the series from a single MRI exam/session into a common space. Alignment is necessary because the subject likely has moved in between series.  
+
This scenario occurs in many forms whenever we wish to assess change in a series of multi-contrast MRI. The follow-up scan(s) are to be aligned with the baseline, but also the different series within each exam need to be co-registered, since the subject may have moved between acquisitions. Hence we have a set of nested registrations. This particular exam features a dual echo scan (PD/T2), where the two structural scans are aligned by default. The post-contrast T1-GdDTPA scan however is not necessarily aligned with the dual echo. Also the post-contrast scan is taken with a clipped field of view (FOV) and a lower axial resolution, with 4mm slices and a 1mm gap (which we treat here as a de facto 5mm slice).
 
=== Keywords ===
 
=== Keywords ===
−
MRI, brain, head, intra-subject, FLAIR, T1, defacing, masking, labelmap, segmentation
+
MRI, brain, head, intra-subject, multiple sclerosis, MS, multi-contrast, change assessment, dual echo, nested registration
  
 
===Input Data===
 
===Input Data===
−
*[[Image:Button_red_fixed_white.jpg|20px]]reference/fixed : T1 SPGR , 1x1x1 mm voxel size, sagittal, RAS orientation.  
+
*[[Image:Button_red_fixed_white.jpg|20px]]reference/fixed : PD baseline exam , 0.9375 x 0.9375 x 3 mm voxel size, axial acquisition, RAS orientation.  
−
*[[Image:Button_green_moving_white.jpg|20px]] moving: T2 FLAIR 1.2x1.2x1.2 mm voxel size, sagittal, RAS orientation.
+
*[[Image:Button_red_fixed_white.jpg|20px]]reference/fixed : T2 baseline exam , 0.9375 x 0.9375 x 3 mm voxel size, axial acquisition, RAS orientation.  
−
*[[Image:Button_purple_mask_white.jpg|20px]]mask: skull stripping labelmap obtained from SPGR, serves as mask
+
*[[Image:Button_green_moving_white.jpg|20px]] moving: T1-GdDTPA  baseline exam 0.9375 x 0.9375 x 5 mm voxel size, axial acquisition.
−
*[[Image:Button_blue_tag_white.jpg|20px]]tag: segmentation labelmap obtained from FLAIR.
+
*[[Image:Button_green_moving_white.jpg|20px]] moving: PD follow-up exam 0.9375 x 0.9375 x 3 mm voxel size, axial acquisition.
−
*Content preview: Have a quick look before downloading:  Does your data look like this?  [[Media:Lighbox_SPGR.jpg|SPGR Lighbox]] , [[Media:Lighbox_FLAIR.jpg|FLAIR Lighbox]]
+
*[[Image:Button_blue_tag_white.jpg|20px]]tag: T2 follow-up exam 0.9375 x 0.9375 x 3 mm voxel size, axial acquisition.
 +
*[[Image:Button_green_moving_white.jpg|20px]] moving:T1-GdDTPA  follow-up exam0.9375 x 0.9375 x 5 mm voxel size, axial acquisition.
  
 
===Registration Challenges===
 
===Registration Challenges===
−
*the amount of misalignment to be small. Subject did not leave the scanner in between the two acquisitions, but we have some head movement.
+
*we have multiple nested transforms: each exam is co-registered within itself, and then the exams are aligned to eachother
−
*we know the underlying structure/anatomy did not change, but the two distinct acquisition types may contain different amounts of distortion
+
*potential pathology change can affect the registration
−
*the T1 high-resolution had a "defacing" applied, i.e. part of the image containing facial features was removed to ensure anonymity. The FLAIR is lower resolution and contrast and did not need this. The sharp edges and missing information in part of the image may cause problems.
+
*anisotropic voxel size causes difficulty in rotational alignment
−
*we have a skull stripping label map of the fixed image (T1) that we can use to mask out the non-brain part of the image and prevent it from actively participating in the registration.
+
*clipped FOV and low tissue contrast of the post-contrast scan
−
*we have one or more label-maps attached to the moving image that we also want to align.
 
−
*the different series have different dimensions, voxel size and field of view. Hence the choice of which image to choose as the reference becomes important. The additional image data present in one image but not the other may distract the algorithm and require masking.
 
−
*hi-resolution datasets may have defacing applied to one or both sets, and the defacing-masks may not be available
 
−
*the different series have different contrast. The T1 contains good contrast between white (WM) and gray matter (GM) , and pathology appears as hypointense. The FLAIR on the other hand shows barely any WM/GM contrast and the pathology appears very dominantly as hyperintense.
 
  
 
===Key Strategies===
 
===Key Strategies===
−
*we choose the SPGR as the anatomical reference. Unless there are overriding reasons, always use the highest resolution image as your fixed/reference, to avoid loosing data through the registration.
+
*we first register the post-contrast scans within each exam to the PD
−
*the defacing of the SPGR image introduces sharp edges that can be detrimental. We apply a multiresolution scheme at least. If this fails we mask that area or better still the brain. As a general rulle, if you have the mask available, use it.
+
*we also move the T2 exam within the same Xform
−
*because of the contrast differences and the defacing we use '''Mutual Information''' as the cost function.
+
*second we register the follow-up PD scan to the baseline PD
−
*because of the combined effects of rotational misalignment, defacing, pathology and contrast differences, we use a multi-resolution approach (Register Images MultiRes).
+
*we then nest the first alignment within the second
 +
*we compare T1Gd to T1Gd, which went through 2 transforms. We correct residual misalignment with a 3rd correction transform
 +
*because of the contrast differences and anisotropic resolution we use Mutual Information as cost function for better robustness
 +
*we adjust the expected translation and rotational parameter settings to the visual assessment of the input data (i.e. initial misalignment)
  
 
=== Registration Results===
 
=== Registration Results===

Revision as of 21:53, 19 February 2010

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Slicer Registration Library Case 04: Intra-subject Brain MR of Multiple Sclerosis: Multi-contrast series for lesion change assessment

this is the fixed reference image. All images are aligned into this space this is a passive image to which the calculated transform is applied. It is a label-map in the same space as the moving FLAIR image this is a passive image to which the calculated transform is applied. It is a label-map in the same space as the moving FLAIR image lleft this is the moving image. The transform is calculated by matching this to the reference image this is a passive image to which the calculated transform is applied. It is a label-map in the same space as the moving FLAIR image this is a passive image to which the calculated transform is applied. It is a label-map in the same space as the moving FLAIR image LEGEND

lleft this indicates the reference image that is fixed and does not move. All other images are aligned into this space and resolution
lleft this indicates the moving image that determines the registration transform.
lleft this indicates images that passively move into the reference space, i.e. they have the transform applied but do not contribute to the calculation of the transform.

lleft PD axial lleft T2 axial lleft T1-GdDTPA lleft PD axial lleft T2 axial lleft T1-GdDTPA
0.9375 x 0.9375 x 3 mm axial
256 x 256 x 51
RAS 		0.9375 x 0.9375 x 3 mm axial
256 x 256 x 51
RAS 		0.9375 x 0.9375 x 5 mm axial
256 x 256 x 24
RAS 		0.9375 x 0.9375 x 3 mm axial
256 x 256 x 54
RAS 		0.9375 x 0.9375 x 3 mm axial
256 x 256 x 54
RAS 		0.9375 x 0.9375 x 5 mm axial
256 x 256 x 24
RAS

Objective / Background

This scenario occurs in many forms whenever we wish to assess change in a series of multi-contrast MRI. The follow-up scan(s) are to be aligned with the baseline, but also the different series within each exam need to be co-registered, since the subject may have moved between acquisitions. Hence we have a set of nested registrations. This particular exam features a dual echo scan (PD/T2), where the two structural scans are aligned by default. The post-contrast T1-GdDTPA scan however is not necessarily aligned with the dual echo. Also the post-contrast scan is taken with a clipped field of view (FOV) and a lower axial resolution, with 4mm slices and a 1mm gap (which we treat here as a de facto 5mm slice).

Keywords

MRI, brain, head, intra-subject, multiple sclerosis, MS, multi-contrast, change assessment, dual echo, nested registration

Input Data

  • Button red fixed white.jpgreference/fixed : PD baseline exam , 0.9375 x 0.9375 x 3 mm voxel size, axial acquisition, RAS orientation.
  • Button red fixed white.jpgreference/fixed : T2 baseline exam , 0.9375 x 0.9375 x 3 mm voxel size, axial acquisition, RAS orientation.
  • Button green moving white.jpg moving: T1-GdDTPA baseline exam 0.9375 x 0.9375 x 5 mm voxel size, axial acquisition.
  • Button green moving white.jpg moving: PD follow-up exam 0.9375 x 0.9375 x 3 mm voxel size, axial acquisition.
  • Button blue tag white.jpgtag: T2 follow-up exam 0.9375 x 0.9375 x 3 mm voxel size, axial acquisition.
  • Button green moving white.jpg moving:T1-GdDTPA follow-up exam0.9375 x 0.9375 x 5 mm voxel size, axial acquisition.

Registration Challenges

  • we have multiple nested transforms: each exam is co-registered within itself, and then the exams are aligned to eachother
  • potential pathology change can affect the registration
  • anisotropic voxel size causes difficulty in rotational alignment
  • clipped FOV and low tissue contrast of the post-contrast scan

Key Strategies

  • we first register the post-contrast scans within each exam to the PD
  • we also move the T2 exam within the same Xform
  • second we register the follow-up PD scan to the baseline PD
  • we then nest the first alignment within the second
  • we compare T1Gd to T1Gd, which went through 2 transforms. We correct residual misalignment with a 3rd correction transform
  • because of the contrast differences and anisotropic resolution we use Mutual Information as cost function for better robustness
  • we adjust the expected translation and rotational parameter settings to the visual assessment of the input data (i.e. initial misalignment)

Registration Results

Unregistered Data + segmentation labelmap Registration Result: FLAIR + segmentation aligned with SPGR

Download

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

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