Vervet Atlas Construction:Debugging bspline registration - Revision history

Fedorov: /* Experiment 3 */

2009-11-24T20:51:07Z

Experiment 3

2009-11-24T20:48:12Z

Experiment 4

2009-11-24T20:42:55Z

Detailed description

2009-11-24T00:25:42Z

Detailed description

2009-11-24T00:22:19Z

Detailed description

2009-11-24T00:21:06Z

Detailed description

2009-11-24T00:19:50Z

Detailed description

2009-11-24T00:15:16Z

Detailed description

2009-11-24T00:13:45Z

Detailed description

2009-11-23T23:59:12Z

Detailed description

@@ Line 100: / Line 100: @@
 |}
-===Experiment 3===
+===Experiment3===
-Register MOVING/MOVING_ROI to FIXED2/FIXED_ROI. Initialize with INITIAL_TFM. Note that the only difference from the previous experiment is the fixed image. Per Hans' suggestion, use histogram matching (add --histogramMatching flag to BRAINSFit).
+Register MOVING/MOVING_ROI to FIXED2/FIXED_ROI. Initialize with INITIAL_TFM. Per Hans' suggestion, use histogram matching (add --histogramMatching flag to BRAINSFit -- the only difference vs Experiment2).
 {|

@@ Line 108: / Line 108: @@
 ===Experiment 4===
-Perform bias correction on the moving image prior to registration. Register MOVING_BIAS_CORRECTED/MOVING_ROI to FIXED2/FIXED_ROI. Initialize with INITIAL_TFM.
+Perform bias correction on the moving image prior to registration. Register MOVING_BIAS_CORRECTED/MOVING_ROI to FIXED2/FIXED_ROI. Initialize with INITIAL_TFM. No histogram matching applied.
 {|
 |[[Image:vervet_bspline_registered4.jpg|thumb|400px|REGISTERED4]]
 |}

@@ Line 98: / Line 98: @@
 {|
 |[[Image:vervet_bspline_registered2.jpg|thumb|400px|REGISTERED2]]
 |}

@@ Line 14: / Line 14: @@
 * MOVING_ROI.nrrd: brain mask for the moving image
 * INITIAL_TFM.tfm: affine transform aligning MOVING with FIXED
-* Everything in one package together with the Slicer scene:
+* [[Media:VervetBSplineDebugging.tgz|Everything in one package]] (together with the Slicer scene)
 The following screeshots demonstrate good initial alignment of the images with the initial affine transformation, and the outline of ROIs. Also note that FIXED1 and FIXED2 are very similar within ROI.

@@ Line 24: / Line 24: @@
-* '''Experiment1''': register MOVING/MOVING_ROI to FIXED1/FIXED_ROI. Initialize with INITIAL_TFM. Command line:
+===Experiment1===
 <pre>
 #!/bin/bash
@@ Line 57: / Line 62: @@
 |}
-* '''Experiment2''': register MOVING/MOVING_ROI to FIXED2/FIXED_ROI. Initialize with INITIAL_TFM Command line:
+===Experiment2===
 <pre>
 #!/bin/bash

@@ Line 16: / Line 16: @@
 * Everything in one package together with the Slicer scene:
-The following screeshots demonstrate good initial alignment of the images with the initial affine transformation, and the outline of ROIs.
+The following screeshots demonstrate good initial alignment of the images with the initial affine transformation, and the outline of ROIs. Also note that FIXED1 and FIXED2 are very similar within ROI.
 {|
 |[[Image:fixed1.jpg|thumb|300px|FIXED1]]
@@ Line 54: / Line 54: @@
 {|
-|[[Image:vervet_bspline_registered1.jpg|thumb|400px|Registered1]]
+|[[Image:vervet_bspline_registered1.jpg|thumb|400px|REGISTERED1]]
 |}
@@ Line 87: / Line 87: @@
 {|
-|[[Image:vervet_bspline_registered2.jpg|thumb|400px|Registered2]]
+|[[Image:vervet_bspline_registered2.jpg|thumb|400px|REGISTERED2]]
 |}

@@ Line 52: / Line 52: @@
 $CMD
 </pre>
 * '''Experiment2''': register MOVING/MOVING_ROI to FIXED2/FIXED_ROI. Initialize with INITIAL_TFM Command line:
@@ Line 81: / Line 85: @@
 $CMD
 </pre>