Documentation:Nightly:Registration:RegistrationLibrary:RegLib C46 - Revision history

Grundlett: Text replacement - "\[http:\/\/www\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

2019-11-27T02:34:45Z

Text replacement - "\[http:\/\/www\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

2013-10-01T13:47:09Z

Registration Results

2013-10-01T13:46:03Z

Registration Results

2013-10-01T13:30:56Z

Procedure

2013-10-01T13:30:35Z

Download (from NAMIC MIDAS)

2013-10-01T13:28:48Z

Procedure

2013-10-01T13:27:36Z

Procedure

2013-10-01T13:25:12Z

2013-09-30T20:49:26Z

2013-09-30T20:45:46Z

Registration Results

@@ Line 67: / Line 67: @@
 ##upon completion, read the transform files with an editor or prototyping platform (e.g. Matlab) and extract the displacements of interest
 ##The ITK transform files describe displacements at the grid nodes, many of which are outside the region of interest. Because BRAINSfit pads the grid with 1 voxel, the grid returned is actually 8x8x8. We use only the plane (*,*,4) for analysis and discard the y-direction displacements, which as expected are all zero.
-##for details on the ITK transform format see the [http://www.slicer.org/slicerWiki/index.php/Slicer-3-6-FAQ#What_is_the_Meaning_of_.27Fixed_Parameters.27_in_the_transform_file_.28.tfm.29_of_a_BSpline_registration_.3F '''FAQ''' here]
+##for details on the ITK transform format see the [[Slicer-3-6-FAQ#What_is_the_Meaning_of_.27Fixed_Parameters.27_in_the_transform_file_.28.tfm.29_of_a_BSpline_registration_.3F|'''FAQ''' here]]
-##To obtain displacements at arbitrary coordinates, interpolate the transform into a deformation field, e.g. using this module (details  [http://www.slicer.org/slicerWiki/index.php/Slicer-3-6-FAQ#How_can_I_convert_a_BSpline_transform_into_a_deformation_field.3F FAQ here]):
+##To obtain displacements at arbitrary coordinates, interpolate the transform into a deformation field, e.g. using this module (details  [[Slicer-3-6-FAQ#How_can_I_convert_a_BSpline_transform_into_a_deformation_field.3F|FAQ here]]):
 === Registration Results===

@@ Line 74: / Line 74: @@
 |[[Image:RegLib_C46_Thumb2.gif|300px|lleft|moving input]]
 |[[Image:RegLib_C46_registered.gif|300px|lleft|moving input after registration (only frames 1-27 shown)]]
 |[[Image:RegLib_C46_DisplacementField.gif|300px|lleft|deformation shown as displacement vectors (only frames 35-60 shown)]]
 |[[Image:RegLib_C46_Displacements.png|300px|lleft|displacements]]
 |-
-|unregistered moving series
+|deformation shown as displacement vectors (only frames 35-60 shown)
 |[[Media:RegLib_C46_Displacements.pdf|displacements (PDF)]]
 |}

@@ Line 74: / Line 74: @@
 |[[Image:RegLib_C46_Thumb2.gif|300px|lleft|moving input]]
 |[[Image:RegLib_C46_registered.gif|300px|lleft|moving input after registration (only frames 1-27 shown)]]
 |[[Image:RegLib_C46_Displacements.png|300px|lleft|displacements]]
 |-

@@ Line 31: / Line 31: @@
 *'''Phase I: run a pilot registration to determine optimal registration parameters'''
 #load reference image and one moving image from the series
-#open the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]##Registration Phases:
+#open the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
 ##set "ref_lung" as fixed and "moving_??" as moving image
 ###''Slicer BSpline Transform'' (create new transform, rename to: "Xf1_BSpline" or similar

@@ Line 22: / Line 22: @@
 == Download (from NAMIC MIDAS) ==
 <small>Note that the main registration processing for this case is done in batch mode via a shell script, and not in the main GUI. The mrb file below therefore includes only 2 out of the 200 frames of the whole series to illustrate the concept. To get the full dataset including solutions and script, download the zip file.</small>
-*[http://slicer.kitware.com/midas3/download/?items=119459 '''RegLib_C46.mrb'''] <br><small>(input data only (incl. example fiducials) , Slicer mrb file. 0.6 MB) </small><br>
+*[http://slicer.kitware.com/midas3/download/?items=119459 '''RegLib_C46.mrb'''] <br><small>(input data, reference + 1 slice only, Slicer mrb file. 0.6 MB) </small><br>
 *[http://slicer.kitware.com/midas3/download/?items=119460 '''RegLib_C46_Data.zip''']<br><small>(input data + results, zip file with original DICOM + registration script. 65 MB). </small>

@@ Line 62: / Line 62: @@
 #call the script via (assuming directories are called "Reference" and "Moving_001" etc. :
    cd PATH/TO/DIRECTORY/WITH/DATA/AND/SCRIPT
-   ./RegLib_C46_BatchReg.sh Reference Moving_*
+   ./RegLib_C46_BatchReg.sh Reference/refLung_001.dcm Moving/*/*.dcm
 #the script will write result transforms and images into the same moving directories
 *'''Phase III:  Evaluate Transform files'''
@@ Line 81: / Line 81: @@
 |[[Media:RegLib_C46_Displacements.pdf|displacements (PDF)]]
 |}
 == Discussion / Overall Strategy ==
 *because the torso is already well registered and does not move across the sequence, a global affine/rigid registration is of no use. Instead we seek to assess the internal displacements caused across the breathing cycle. We therefore choose a low-DOF BSpline model.

@@ Line 23: / Line 23: @@
 MRI,  lung, 2D, time-series,  deformation
-===Download ===
+== Download (from NAMIC MIDAS) ==
-*Data
+<small>Note that the main registration processing for this case is done in batch mode via a shell script, and not in the main GUI. The mrb file below therefore includes only 2 out of the 200 frames of the whole series to illustrate the concept. To get the full dataset including solutions and script, download the zip file.</small>
-**[[Media:RegLib_C46_Data.zip‎ ‎|'''RegLib_C46_Data''' : DICOM 2D series  <small> (DICOM files, zip file 18 MB) </small>]]'''
+*[http://slicer.kitware.com/midas3/download/?items=103749 '''RegLib_12.mrb''': input data only, use this to run the tutorial from the start <small>(Slicer mrb file. 35 MB). </small>]
-*Results
+*[http://slicer.kitware.com/midas3/download/?items=103748 '''RegLib_C12_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify <small>(Slicer mrb file. 68 MB). </small>]

@@ Line 82: / Line 82: @@
 {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
 |[[Image:RegLib_C46_Thumb2.gif|300px|lleft|moving input]]
-|[[Image:RegLib_C46_Moving_animReg.gif|300px|lleft|moving input after registration (only frames 1-27 shown)]]
+|[[Image:RegLib_C46_registered.gif|300px|lleft|moving input after registration (only frames 1-27 shown)]]
 |[[Image:RegLib_C46_Displacements.png|300px|lleft|displacements]]
 |-
@@ Line 89: / Line 89: @@
 |[[Media:RegLib_C46_Displacements.pdf|displacements (PDF)]]
 |}
 === Acknowledgments ===
 Thanks to Amir Owrangi and [http://www.imaging.robarts.ca/~gep Dr.Grace Parraga] from the [http://www.robarts.ca Robarts Institute] for sharing the registration problem and data.