Difference between revisions of "Documentation:Nightly:Registration:RegistrationLibrary:RegLib C42"

From Slicer Wiki
Jump to: navigation, search
 
(One intermediate revision by the same user not shown)
Line 12: Line 12:
 
|}
 
|}
  
−
== Modules Used ==
+
== Modules used ==
 +
*[[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']]
 +
 
 +
== Download (from NAMIC MIDAS) ==
 +
<small>''Why 2 sets of files?  The "input data" mrb includes only the unregistered data to try the method yourself from start to finish. The full dataset includes intermediate files and results (transforms, resampled images etc.). If you use the full dataset we recommend to choose different names for the images/results you create yourself to distinguish the old data from the new one you generated yourself. ''</small>
 +
*[http://slicer.kitware.com/midas3/download/?items=119557 '''RegLib_C42.mrb'''] <br><small>(input data only, Slicer mrb file. 12 MB) </small><br>
 +
*[http://slicer.kitware.com/midas3/download/?items=119556 '''RegLib_C42_full.mrb''']<br><small>(input data + results, Slicer mrb file. 36 MB). </small>
  
 
== Description ==
 
== Description ==
 
This is a typical case of change assessment.  
 
This is a typical case of change assessment.  
−
 
−
*[http://slicer.kitware.com/midas3/download/?items=119557 '''RegLib_C42.mrb'''] <br><small>(input data only, Slicer mrb file. 12 MB) </small><br>
 
−
*[http://slicer.kitware.com/midas3/download/?items=119556 '''RegLib_C42_full.mrb''']<br><small>(input data + results, Slicer mrb file. 36 MB). </small>
 
  
 
=== Keywords ===
 
=== Keywords ===
 
MRI, brain, head, intra-subject, T1, autism, change assessment, pediatric MRI
 
MRI, brain, head, intra-subject, T1, autism, change assessment, pediatric MRI
  
−
 
+
== Procedure ==
−
=== Procedures ===
+
#'''Affine Registration''': open the [[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']] module.
−
*'''Phase I:  Register Rigid/Affine'''
+
##''Fixed Image Volume'': "Autism_T1_4yrs"
−
#open Registration : ''BrainsFit'' module (presets: BRAINSfit_Xf1 or _Xf2
+
##''Moving Volume'': "Autism_T1_2yrs"
−
##Input Parameters:
+
##Registration phases: check boxes for ''Rigid" ,"Scale", "Affine"  
−
###Fixed: "Autism_T1_2yrs"
+
##''Slicer Linear Transform'': select "create new transform", rename to "Xf1_Affine" or similar
−
###Moving: "Autism_T1_4yrs"
+
##leave rest at defaults. Click ''Apply''
−
##Registration Phases:
+
##registration should take ~ 10 secs.
−
###select/check ''Include Rigid registration phase'' , ''Include Scale Versor 3D'' , ''Include Affine'', ''Include BSpline''  
+
##use fade slider to verify alignment; compare with result snapshots shown below. Alignment will not be perfect but should be better than before.
−
##Output Settings
+
##note: you can also change the colormaps for the fixed and moving volumes to better judge the alignment: go to the  [[Documentation/Nightly/Modules/Volumes| ''Volumes'']] module and in the ''Display'' tab, select "green" and "magenta" as the respective colormaps for the two volumes (vhf, vhm)
−
###select a new "Slicer BSpline Transform", rename to "Xf3_Affine+BSpline" or similar "
+
#'''Nonrigid Registration''': open the  [[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']].
−
###select a new volume "Output Image Volume'', rename to "Autism_T1_4yrs_Xf3", indicating that this is the result volume after being resampled with the Xf3 transform.
+
##''Fixed/Moving Image Volume'': as above
−
###Output Image Pixel Type: check "ushort". As a general rule, match the datatype of the input image, unless specific reason demands otherwise (e.g. you wish to avoid rounding of interpolation effects). The "float" datatype is 4-bytes per pixel and can produce unnecessary large files.
+
##Registration phases: uncheck boxes for rigid, scale and affine and check box for  ''BSpline''
−
##Registration Parameters:
+
##Output: Slicer Linear transform: set to None
−
###increase ''Number Of Samples'' to 300,000
+
##Output: Slicer BSpline transform: create new, rename to "Xf2_BSpline" or similar
−
##Registration Parameters: set  ''Number Of Grid Subdivisions'' to 5,5,5
+
##Output Image Volume:  create new, rename to "Autism_T1_2yrs_Xf2"; ''Pixel Type'': "short"
 +
##Registration Parameters: increase ''Number Of Samples'' to 300,000; ''Number of Grid Subdivisions'': 5,5,5
 
##Leave all other settings at default
 
##Leave all other settings at default
−
##click Apply
+
##click apply
−
=== Registration Results===
 
  
 +
== Registration Results==
 
[[Image:RegLib_C42_unregistered.gif|300px]] baseline and follow-up before registration (click to enlarge) <br>
 
[[Image:RegLib_C42_unregistered.gif|300px]] baseline and follow-up before registration (click to enlarge) <br>
 
[[Image:RegLib_C42_affine.gif|300px]] after affine alignment. Note the residual shape differences (click to enlarge) <br>
 
[[Image:RegLib_C42_affine.gif|300px]] after affine alignment. Note the residual shape differences (click to enlarge) <br>

Latest revision as of 19:02, 1 October 2013

Home < Documentation:Nightly:Registration:RegistrationLibrary:RegLib C42

Back to Registration Library

Slicer Registration Library Case #42:
Intra-subject Brain MRI: serial assessment of brain development in autism

Input

this is the fixed reference image. All images are aligned into this space lleft this is the moving image. The transform is calculated by matching this to the reference image
fixed image/target moving image

Modules used

Download (from NAMIC MIDAS)

Why 2 sets of files? The "input data" mrb includes only the unregistered data to try the method yourself from start to finish. The full dataset includes intermediate files and results (transforms, resampled images etc.). If you use the full dataset we recommend to choose different names for the images/results you create yourself to distinguish the old data from the new one you generated yourself.

Description

This is a typical case of change assessment.

Keywords

MRI, brain, head, intra-subject, T1, autism, change assessment, pediatric MRI

Procedure

  1. Affine Registration: open the General Registration (BRAINS) module.
    1. Fixed Image Volume: "Autism_T1_4yrs"
    2. Moving Volume: "Autism_T1_2yrs"
    3. Registration phases: check boxes for Rigid" ,"Scale", "Affine"
    4. Slicer Linear Transform: select "create new transform", rename to "Xf1_Affine" or similar
    5. leave rest at defaults. Click Apply
    6. registration should take ~ 10 secs.
    7. use fade slider to verify alignment; compare with result snapshots shown below. Alignment will not be perfect but should be better than before.
    8. note: you can also change the colormaps for the fixed and moving volumes to better judge the alignment: go to the Volumes module and in the Display tab, select "green" and "magenta" as the respective colormaps for the two volumes (vhf, vhm)
  2. Nonrigid Registration: open the General Registration (BRAINS).
    1. Fixed/Moving Image Volume: as above
    2. Registration phases: uncheck boxes for rigid, scale and affine and check box for BSpline
    3. Output: Slicer Linear transform: set to None
    4. Output: Slicer BSpline transform: create new, rename to "Xf2_BSpline" or similar
    5. Output Image Volume: create new, rename to "Autism_T1_2yrs_Xf2"; Pixel Type: "short"
    6. Registration Parameters: increase Number Of Samples to 300,000; Number of Grid Subdivisions: 5,5,5
    7. Leave all other settings at default
    8. click apply

Registration Results

RegLib C42 unregistered.gif baseline and follow-up before registration (click to enlarge)
RegLib C42 affine.gif after affine alignment. Note the residual shape differences (click to enlarge)
RegLib C42 Xf2 registered.gif after nonrigid BSpline registration (click to enlarge)
RegLib C42 Xf2a DeformOnly.gif| visualization of the nonrigid deformation component only


Retrieved from "https://www.slicer.org/w/index.php?title=Documentation:Nightly:Registration:RegistrationLibrary:RegLib_C42&oldid=36054"