Difference between revisions of "Projects:DBP2:Harvard:Registration Documentation"

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= Same subject Registration =
 
 
Slicer 3 contains a number of different ways to register two images.  In this document we will examine the results of these modules on three different cases. The convention used will be (moving image) -> (fixed image) = (resulting moved image).  The cases are:
 
Slicer 3 contains a number of different ways to register two images.  In this document we will examine the results of these modules on three different cases. The convention used will be (moving image) -> (fixed image) = (resulting moved image).  The cases are:
 
* Registering a t2 weighted image to an arbitrary t1, then registering this transformed image back to the original t2.  Ideally this will produce a identical image.
 
* Registering a t2 weighted image to an arbitrary t1, then registering this transformed image back to the original t2.  Ideally this will produce a identical image.
 
* Registering a DTI baseline image to the corresponding realigned t2 weighted image, and vice-versa.  This is a realistic test of one of our (the PNL) everyday uses of registration.
 
* Registering a DTI baseline image to the corresponding realigned t2 weighted image, and vice-versa.  This is a realistic test of one of our (the PNL) everyday uses of registration.
 
* Registering a realigned t2 weighted image to another t2.
 
* Registering a realigned t2 weighted image to another t2.
 +
 +
=There and back registration=
  
 
==Slicer modules==
 
==Slicer modules==
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The image shows these side by side.  The are nearly the same except for the loss of fine detail.
 
The image shows these side by side.  The are nearly the same except for the loss of fine detail.
  
 +
 +
 +
===Linear===
 +
[[File:52-t2 lin.png|600px|thumb|left|Linear case 1: Minor shift at front, loss of detail.]]
 +
*53-t2 -> 31-t1 = lin1
 +
*lin1 -> 53-t2 = lin2
 +
 +
The image shows lin2 and 53-t2 side by side.  The image shows there appears to be some change beyond loss of detail, possibly a L-R shift in the front.
 +
 +
 +
===Rigid===
 +
[[File:53-t2 rig.png|600px|thumb|left|Rigid case 1: Significant loss of detail.]]
 +
*53-t2 -> 31-t1 = rig1
 +
*rig1 -> 53-t2 = rig2
 +
 +
Significant blurring, but every feature is in it's proper place.
 +
 +
===Deformable B-spline===
 +
[[File:53-t2 Bspline.png|600px|thumb|left|BSpline case 1: Frontal enlargement, rear upward shift, distortions throughout.]]
 +
*53-t2 -> 31-t1 = Bspline1
 +
*Bspline1 -> 53-t2 = Bspline2
 +
 +
Superior frontal enlargement, odd upward shifting in rear of brain,
 +
distortions everywhere.
 +
 +
 +
 +
===Diffeomorphic Demons===
 +
[[File:53-t2 demons.png|600px|thumb|left|Demons case 1: Many minor deformations, clipping of brain at top, roughly correct placement overall.]]
 +
*53-t2 -> 31-t1 = Demons1
 +
*Demons1 -> 52-t2 = Demons2
 +
 +
Multiple deformations. Much larger ventricles. Small errors everywhere,
 +
expansions, contractions, shifts.  Roughly in the same place overall.
 +
 +
 +
==Register Images Module==
 +
===Initial===
 +
[[File:53-t2 RV initial.png|600px|thumb|left|Initial case 1: Minor shift down and anterior]]
 +
[[File:53-t2 RV init histo.png|600px|thumb|left|Initial case 1: histograms of the two images.]]
 +
*53-t2 -> 31-t1 = init1
 +
*init1 -> 53-t2 = init2
 +
Huge shift in count values, rigid translation down ~4 pixels, left ~1 pixel.
 +
 +
 +
 +
===Rigid===
 +
[[File:53-t2 RV rigid.png|600px|thumb|left|Rigid case 1: Shift in grey values.]]
 +
*53-t2 -> 31-t1 = rigid1
 +
*rigid1 -> 53-t2 = rigid2
 +
Shift in grey values. Few other problems.
 +
 +
 +
===Affine===
 +
[[File:53-t2 RV affine.png|600px|thumb|left|Affine case 1: Slight posterior shift and grey value shift.]]
 +
*53-t2 -> 31-t1 = affine1
 +
*affine1 -> 53-t2 = affine2
 +
Again, shift in grey values, mostly okay otherwise.  Slight posterior shift.
 +
 +
===B-Spline===
 +
[[File:53-t2 RV bspline.png|600px|thumb|left|BSpline case 1: Minor distortions, grey value shifts.]]
 +
*53-t2 -> 31-t1 = Bspline1
 +
*Bspline1 -> 53-t2 = Bspline2
 +
Again grey values shift.  Minor distortion in frontal lobe and cerebellum.
 +
 +
= DTI Baseline to t2 registration =
 +
 +
==Slicer modules==
 +
 +
===affine===
 
*DTI-baseline -> 53-t2 = aff3
 
*DTI-baseline -> 53-t2 = aff3
 
<nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki>
 
<nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki>
Line 23: Line 94:
  
 
===Linear===
 
===Linear===
−
[[File:52-t2 lin.png|600px|thumb|left|Linear case 1: Minor shift at front, loss of detail.]]
 
−
*53-t2 -> 31-t1 = lin1
 
−
*lin1 -> 53-t2 = lin2
 
−
 
−
The image shows lin2 and 53-t2 side by side.  The image shows there appears to be some change beyond loss of detail, possibly a L-R shift in the front.
 
  
 
*DTI-baseline -> 53-t2 = lin3
 
*DTI-baseline -> 53-t2 = lin3
Line 38: Line 104:
  
 
===Rigid===
 
===Rigid===
−
[[File:53-t2 rig.png|600px|thumb|left|Rigid case 1: Significant loss of detail.]]
 
−
*53-t2 -> 31-t1 = rig1
 
−
*rig1 -> 53-t2 = rig2
 
  
−
Significant blurring, but every feature is in it's proper place.
 
  
 
*DTI-baseline -> 53-t2 = rig3
 
*DTI-baseline -> 53-t2 = rig3
Line 52: Line 114:
 
Similar.
 
Similar.
  
−
===Deformable B-spline===
+
===B-Spline===
−
[[File:53-t2 Bspline.png|600px|thumb|left|BSpline case 1: Frontal enlargement, rear upward shift, distortions throughout.]]
 
−
*53-t2 -> 31-t1 = Bspline1
 
−
*Bspline1 -> 53-t2 = Bspline2
 
−
 
 
−
Superior frontal enlargement, odd upward shifting in rear of brain,
 
−
distortions everywhere.
 
  
 
*DTI-baseline -> 53-t2 = Bspline3
 
*DTI-baseline -> 53-t2 = Bspline3
Line 74: Line 130:
  
 
===Diffeomorphic Demons===
 
===Diffeomorphic Demons===
−
[[File:53-t2 demons.png|600px|thumb|left|Demons case 1: Many minor deformations, clipping of brain at top, roughly correct placement overall.]]
 
−
*53-t2 -> 31-t1 = Demons1
 
−
*Demons1 -> 52-t2 = Demons2
 
  
−
Multiple deformations. Much larger ventricles. Small errors everywhere,
 
−
expansions, contractions, shifts.  Roughly in the same place overall.
 
  
 
*DTI-baseline -> 53-t2 = Demons3
 
*DTI-baseline -> 53-t2 = Demons3
 
[[File:Basline-demons-t2.png|600px|thumb|left|Demons case 2: Terrible distortions everywhere, unclear what it was trying to match.]]
 
[[File:Basline-demons-t2.png|600px|thumb|left|Demons case 2: Terrible distortions everywhere, unclear what it was trying to match.]]
  
−
*53-t2 ->  
+
*53-t2 -> DTI-baseline = Demons 4
 +
 
 +
==Register Images module==
  
−
==Register Images Module==
 
 
===Initial===
 
===Initial===
−
[[File:53-t2 RV initial.png|600px|thumb|left|Initial case 1: Minor shift down and anterior]]
 
−
[[File:53-t2 RV init histo.png|600px|thumb|left|Initial case 1: histograms of the two images.]]
 
−
*53-t2 -> 31-t1 = init1
 
−
*init1 -> 53-t2 = init2
 
−
Huge shift in count values, rigid translation down ~4 pixels, left ~1 pixel.
 
−
 
 
*DTI-baseline -> t2 = init3
 
*DTI-baseline -> t2 = init3
 
<nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki>
 
<nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki>
Line 101: Line 147:
  
 
===Rigid===
 
===Rigid===
−
[[File:53-t2 RV rigid.png|600px|thumb|left|Rigid case 1: Shift in grey values.]]
 
−
*53-t2 -> 31-t1 = rigid1
 
−
*rigid1 -> 53-t2 = rigid2
 
−
Shift in grey values. Few other problems.
 
−
 
 
*DTI-baseline -> t2 = rigid3
 
*DTI-baseline -> t2 = rigid3
 
<nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki>
 
<nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki>
Line 113: Line 154:
  
 
===Affine===
 
===Affine===
−
[[File:53-t2 RV affine.png|600px|thumb|left|Affine case 1: Slight posterior shift and grey value shift.]]
 
−
*53-t2 -> 31-t1 = affine1
 
−
*affine1 -> 53-t2 = affine2
 
−
Again, shift in grey values, mostly okay otherwise.  Slight posterior shift.
 
  
 
*DTI-baseline -> t2 = affine3
 
*DTI-baseline -> t2 = affine3
Line 125: Line 162:
  
 
===B-Spline===
 
===B-Spline===
−
[[File:53-t2 RV bspline.png|600px|thumb|left|BSpline case 1: Minor distortions, grey value shifts.]]
 
−
*53-t2 -> 31-t1 = Bspline1
 
−
*Bspline1 -> 53-t2 = Bspline2
 
−
Again grey values shift.  Minor distortion in frontal lobe and cerebellum.
 
  
 
*DTI-baseline -> t2
 
*DTI-baseline -> t2
Line 137: Line 170:
 
*t2 -> DTI-baseline
 
*t2 -> DTI-baseline
 
<nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki>
 
<nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki>
−
 
  
 
= Different subject registration =
 
= Different subject registration =

Revision as of 13:39, 23 April 2009

Home < Projects:DBP2:Harvard:Registration Documentation

Slicer 3 contains a number of different ways to register two images. In this document we will examine the results of these modules on three different cases. The convention used will be (moving image) -> (fixed image) = (resulting moved image). The cases are:

  • Registering a t2 weighted image to an arbitrary t1, then registering this transformed image back to the original t2. Ideally this will produce a identical image.
  • Registering a DTI baseline image to the corresponding realigned t2 weighted image, and vice-versa. This is a realistic test of one of our (the PNL) everyday uses of registration.
  • Registering a realigned t2 weighted image to another t2.

There and back registration

Slicer modules

Affine

Affine case 1: Minor loss of detail.
  • 53-t2 -> 31-t1 = aff1
  • aff1 -> 53-t2 = aff2

The image shows these side by side. The are nearly the same except for the loss of fine detail.


Linear

Linear case 1: Minor shift at front, loss of detail.
  • 53-t2 -> 31-t1 = lin1
  • lin1 -> 53-t2 = lin2

The image shows lin2 and 53-t2 side by side. The image shows there appears to be some change beyond loss of detail, possibly a L-R shift in the front.


Rigid

Rigid case 1: Significant loss of detail.
  • 53-t2 -> 31-t1 = rig1
  • rig1 -> 53-t2 = rig2

Significant blurring, but every feature is in it's proper place.

Deformable B-spline

BSpline case 1: Frontal enlargement, rear upward shift, distortions throughout.
  • 53-t2 -> 31-t1 = Bspline1
  • Bspline1 -> 53-t2 = Bspline2

Superior frontal enlargement, odd upward shifting in rear of brain, distortions everywhere.


Diffeomorphic Demons

Demons case 1: Many minor deformations, clipping of brain at top, roughly correct placement overall.
  • 53-t2 -> 31-t1 = Demons1
  • Demons1 -> 52-t2 = Demons2

Multiple deformations. Much larger ventricles. Small errors everywhere, expansions, contractions, shifts. Roughly in the same place overall.


Register Images Module

Initial

Initial case 1: Minor shift down and anterior
Initial case 1: histograms of the two images.
  • 53-t2 -> 31-t1 = init1
  • init1 -> 53-t2 = init2

Huge shift in count values, rigid translation down ~4 pixels, left ~1 pixel.


Rigid

Rigid case 1: Shift in grey values.
  • 53-t2 -> 31-t1 = rigid1
  • rigid1 -> 53-t2 = rigid2

Shift in grey values. Few other problems.


Affine

Affine case 1: Slight posterior shift and grey value shift.
  • 53-t2 -> 31-t1 = affine1
  • affine1 -> 53-t2 = affine2

Again, shift in grey values, mostly okay otherwise. Slight posterior shift.

B-Spline

BSpline case 1: Minor distortions, grey value shifts.
  • 53-t2 -> 31-t1 = Bspline1
  • Bspline1 -> 53-t2 = Bspline2

Again grey values shift. Minor distortion in frontal lobe and cerebellum.

DTI Baseline to t2 registration

Slicer modules

affine

  • DTI-baseline -> 53-t2 = aff3

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]] Image shows the 53-t2 target image and the registered image side by side. DTI distortion remains but aligned well to ventricles in center.

  • 53-t2 -> DTI-baseline = aff4

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]] The registered image does not stretch to the full extent of the DTI at the midline, though the match is quite close more laterally.

Linear

  • DTI-baseline -> 53-t2 = lin3

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]] Middle is clearly matched, coronal slices look okay, sagittal shows DTI distortions remain.

  • 53-t2 -> DTI-baseline = lin4

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]] Brainstem and cerebellum matched well, normal DTI distortions still present.

Rigid

  • DTI-baseline -> 53-t2 = rig3

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]] Brainstem aligned, normal DTI distortions present.

  • 53-t2 -> DTI-baseline =rig4

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]] Similar.

B-Spline

  • DTI-baseline -> 53-t2 = Bspline3
BSpline case 2: Terrible distortion. Matches cortex to skull.

Fits the cortex on the baseline to the skull on the t2. Retry with a skull stripped t2.

  • 53-t2 -> DTI-baseline = Bspline4

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]

  • DTI-baseline-masked -> 53-t2-masked = Bspline3

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]] Bad registration, numerous deformations, midline shift in frontal lobe, right side deformations, cerebellum doesn't fit any more.

Diffeomorphic Demons

  • DTI-baseline -> 53-t2 = Demons3
Demons case 2: Terrible distortions everywhere, unclear what it was trying to match.
  • 53-t2 -> DTI-baseline = Demons 4

Register Images module

Initial

  • DTI-baseline -> t2 = init3

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]

  • t2 -> DTI-baseline = init4

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]

Rigid

  • DTI-baseline -> t2 = rigid3

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]

  • t2 -> DTI-baseline = rigid4

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]

Affine

  • DTI-baseline -> t2 = affine3

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]

  • t2 -> DTI-baseline = affine4

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]

B-Spline

  • DTI-baseline -> t2

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]] Slow process. Inferior frontal, temporal, stretched downwards. Cerebellum is terrible. Very top of the brain is stretched. Pretty bad overall.

  • t2 -> DTI-baseline

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]

Different subject registration

Slicer modules

Rigid

01053>01031rigid.png = not bad... different brains of different sizes, but seem to be aligned in the ventricles so output seems okay. output slightly blurry. bad initial leveling displays.

Linear

01053>01031linear.png = not bad... different brains of different sizes, but seem to be aligned in the ventricles so output seems okay.output slightly blurry. bad initial leveling displays.

Affine

01053>01031_affine.png = looks good in terms of size. odd warping of frontal lobe and cerebellum area, but otherwise good coregistration.

B-spline

01053>01031_bspline.png = looks good in terms of size. odd warping of frontal/temporal lobe and cerebellum area, but otherwise good coregistration.

Diffeomorphic Demons

01053>01031_demons.png = 10 minutes. Window/leveling initially off. Otherwise, it looks really good. Not much distortion.

Register Images module

Initial

01053>01031_RI_initial.png - looks like the original 01053 image, but shifted, which is expected. resolultion a little worse.

Rigid

01053>01031_RI_rigid.png - center ventricles are mostly aligned, but not perfectly. in axial view, brain is more crooked than in initial scan... especially in frontal lobe.

Affine

01053>01031_RI_affine.png - ventricles aligned well. sizing decent. looks how one would expect affine to look. not perfect subcortically. some distortion, esp in temporal lobe.

B-spline

01053>01031_RI_bspline.png - good result. ventricles aligned well, but temporal lobe size is not the same as the target image.

Pipe Rigid

01053>01031_RI_pipe_rigid.png - shifted version of the original image. decent registration in the ventricles.

Pipe Affine

01053>01031_RI_pipe_affine.png - decent coreg. a bit of distortion in the frontal and temporal lobes, esp around the corpus collosum.

pipe B-spline

01053>01031_RI_pipe_bspline.png - good coregistration, but pretty blurred. also, I would have expected the temporal lobe to be coregistered better.

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