Projects:RegistrationLibrary:RegLib C09 - Revision history

Grundlett: Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

2017-07-10T18:07:21Z

Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

Meier: /* Methods */

2011-08-29T14:30:26Z

Methods

Meier: /* Registration Results */

2011-08-29T14:16:19Z

Registration Results

Meier: /* Registration Results */

2011-08-29T14:16:03Z

Registration Results

Meier: /* Registration Results */

2011-08-29T14:13:12Z

Registration Results

Meier at 20:00, 26 August 2011

2011-08-26T20:00:59Z

Meier at 17:53, 1 June 2010

2010-06-01T17:53:51Z

Meier at 17:53, 1 June 2010

2010-06-01T17:53:33Z

Meier: moved Projects:RegistrationDocumentation:RegLib 09 fMRI to Projects:RegistrationLibrary:RegLib C09

2010-05-28T15:25:28Z

moved Projects:RegistrationDocumentation:RegLib 09 fMRI to Projects:RegistrationLibrary:RegLib C09

Meier: /* Download */

2010-02-18T18:35:48Z

Download

@@ Line 16: / Line 16: @@
 === Modules ===
-*'''Slicer 3.6.1 recommended modules:  [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BrainsFit]'''
+*'''Slicer 3.6.1 recommended modules:  [https://www.slicer.org/wiki/Modules:BRAINSFit BrainsFit]'''
 ===Objective / Background ===
@@ Line 46: / Line 46: @@
 === Methods ===
 *place SPGR in background and fMRI in foreground. Review initial misalignment.
-*if there is little or no initial overlap, go to the [http://www.slicer.org/slicerWiki/index.php/Modules:Volumes-Documentation-3.6 Volumes module], select the ''Info'' tab and click the ''Center Volume'' button. Repeat for both images. This should roughly center the volumes in the same physical space. Alternatively, when loading the data, consider checking the box for "Centered'' in the "Open File" dialog
+*if there is little or no initial overlap, go to the [https://www.slicer.org/wiki/Modules:Volumes-Documentation-3.6 Volumes module], select the ''Info'' tab and click the ''Center Volume'' button. Repeat for both images. This should roughly center the volumes in the same physical space. Alternatively, when loading the data, consider checking the box for "Centered'' in the "Open File" dialog
 *'''Phase 1: BRAINSfit rigid w/o masking'''
-#open the Registration / [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit module]
+#open the Registration / [https://www.slicer.org/wiki/Modules:BRAINSFit BRAINSfit module]
 ##Select Preset "Xf0_Rigid" or set the parameters as shown below:
 ##fixed image: SPGR;  moving image: fMRI
@@ Line 57: / Line 57: @@
 ##click: ''Apply''
 *'''Phase 2: Nonrigid BSpline'''
-#open the Registration / [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit module]
+#open the Registration / [https://www.slicer.org/wiki/Modules:BRAINSFit BRAINSfit module]
 ##Select Preset "Xf1_BSpline" or set the parameters as shown below:
 ##fixed image: SPGR;  moving image: fMRI

@@ Line 46: / Line 46: @@
 === Methods ===
 *place SPGR in background and fMRI in foreground. Review initial misalignment.
-*if there is little or no initial overlap, go to the [http://www.slicer.org/slicerWiki/index.php/Modules:Volumes-Documentation-3.6 Volumes module], select the ''Info'' tab and click the ''Volume'' button. Repeat for both images. This should roughly center the volumes in the same physical space. Alternatively, when loading the data, consider checking the box for "Centered'' in the "Open File" dialog
+*if there is little or no initial overlap, go to the [http://www.slicer.org/slicerWiki/index.php/Modules:Volumes-Documentation-3.6 Volumes module], select the ''Info'' tab and click the ''Center Volume'' button. Repeat for both images. This should roughly center the volumes in the same physical space. Alternatively, when loading the data, consider checking the box for "Centered'' in the "Open File" dialog
 *'''Phase 1: BRAINSfit rigid w/o masking'''
 #open the Registration / [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit module]
@@ Line 52: / Line 52: @@
 ##fixed image: SPGR;  moving image: fMRI
 ##Registration phases:
-###Initialize check: useGeometryAlign;  check: Rigid
+###Initialize check: ''useGeometryAlign'';  check: ''Rigid''
-##Output: under ''Slicer BSpline Transform'', select "create new" and rename to "Xf3_BFit_unmasked"
+##Output: under ''Slicer Linear Transform'', select "create new" and rename to "Xf0_Rigid" or similar
 ##leave rest at defaults
 ##click: ''Apply''
-*'''Version 2: Expert Automated + Fast BSpline Modules incl. masking'''
+*'''Phase 2: Nonrigid BSpline'''
-#build brain mask for the fixed image only:
+#open the Registration / [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit module]
-##open '''Skull Stripping''' module.
+##Select Preset "Xf1_BSpline" or set the parameters as shown below:
-##Settings:  100 iterations, 20 subdivisions.
+##fixed image: SPGR;  moving image: fMRI
-##Ouput: create new volum, rename to  "fixed_mask"
+##Initialize with previous transform: select the above "Xf0_Rigid"
 ##Click: ''Apply''
-##manually edit brain mask with '''Editor''' module. required manual fix at frontal and occipital lobe
+#Return to ''Data'' module. To compare the different alignments, move the fMRI volume back under the rigid transform. BRAINSfit automatically places the moving volume into the result transform, but since nonrigid transformations cannot be visualized directly the orientation does not seem to change. For Nonrigid deformations a resampled volume must be produced to see the effect.
 === Registration Results===

@@ Line 85: / Line 85: @@
 === Registration Results===
-[[Image:RegLib_C09_unregistered.gif|300px|unregistered]] unregistered  <br>
+[[Image:RegLib_C09_unregistered.gif|400px|unregistered]] unregistered  <br>
-[[Image:RegLib_C09_rigid.gif|300px|after rigid registration]] after rigid registration<br>
+[[Image:RegLib_C09_rigid.gif|400px|after rigid registration]] after rigid registration<br>
 [[Image:RegLib_C09_BSpline.gif‎|400px|after non-rigid registration]] after additional BSpline non-rigid registration<br><br>

@@ Line 85: / Line 85: @@
 === Registration Results===
-[[Image:RegLib_C09_unregistered.gif|300px|unregistered]] unregistered
+[[Image:RegLib_C09_unregistered.gif|300px|unregistered]] unregistered  <br>
-[[Image:RegLib_C09_rigid.gif|300px|after rigid registration]] after rigid registration<br><br>
+[[Image:RegLib_C09_rigid.gif|300px|after rigid registration]] after rigid registration<br>
-[[Image:RegLib_C09_BSpline.gif‎|400px|after non-rigid registration]] after additional BSpline non-rigid registration<br>
+[[Image:RegLib_C09_BSpline.gif‎|400px|after non-rigid registration]] after additional BSpline non-rigid registration<br><br>

@@ Line 85: / Line 85: @@
 === Registration Results===
-[[Image:RegLib_C10_unreg_AnimGif.gif|300px|unregistered]] unregistered
+[[Image:RegLib_C09_unregistered.gif|300px|unregistered]] unregistered
-[[Image:RegLib_C10_BSpline_AnimGif.gif|300px|after BSpline non-rigid registration]] afterAffine+ fast BSpline non-rigid registration<br><br>
+[[Image:RegLib_C09_rigid.gif|300px|after rigid registration]] after rigid registration<br><br>
-[[Image:RegLib_C10_BFit_AGif.gif‎|400px|after BRAINSfit affine+ non-rigid registration]] after BRAINSfit affine+ non-rigid registration<br>
+[[Image:RegLib_C09_BSpline.gif‎|400px|after non-rigid registration]] after additional BSpline non-rigid registration<br>

@@ Line 3: / Line 3: @@
 [[Projects:RegistrationDocumentation:UseCaseInventory|Back to Registration Use-case Inventory]] <br>
-==Slicer Registration Library Exampe #9: Functional MRI aligned with structural reference MRI==
+== <small>v3.6.3</small> [[Image:Slicer3-6Announcement-v1.png‎|150px]] Slicer Registration Library Case 09: Functional MRI aligned with structural reference MRI ==
-[[Image:under-construction_icon.jpg|left|100px|this case is still under active development. Comments and priority requests welcome to the slicer-users mailing list]]
+=== Input ===
 {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
-{| style="color:#bbbbbb; background-color:#333333;" cellpadding="10" cellspacing="0" border="0"
+|[[Image:RegLib_C09_Thumb1.png|150px|lleft|this is the fixed T1 reference image.]]
-|[[Image:RegLib C09 fMRI1.png|150px|lleft|this is the fixed reference image. All images are aligned into this space]]
+|[[Image:RegArrow_NonRigid.png|100px|lleft]]
-|[[Image:Arrow_left_gray.jpg|100px|lleft]]
+|[[Image:RegLib_C09_Thumb2.png|150px|left|this is the fMRI baseline image, to be registered to the T1]]
 |-
-|0.5 x 0.5 x 1.0 mm axial <br> 512 x 512 x 176<br>RAS
+|Target Anatomical Ref.
+|
-|1.8 x 1.8 x 4 mm <br> axial oblique<br> 128 x 128 x 19 x 125 timepoints <br>RAS
+|fMRI
 |}
 ===Objective / Background ===
 This is a typical example of fMRI pre-processing. Goal is to align the fMRI image with a structural scan that provides accuracte anatomical reference. The fMRI contains acquisition-related distortion and low contrast to discern much anatomical detail. We also have pathology (stroke) with variable contrast across different MRI protocols.
 === Keywords ===
 MRI, brain, head, intra-subject, fMRI
 ===Input Data===
-*[[Image:Button_red_fixed_white.jpg|20px]]reference/fixed : T1
+*reference/fixed : T1  0.5 x 0.5 x 1 mm , 512 x 512 x 176
-*[[Image:Button_green_moving_white.jpg|20px]] moving: fMRI sequence of motor task (right hand clench)
+*moving: fMRI sequence of motor task (right hand clench)  2 x 2 x 4 mm, 128 x 128 x 19
 ===Download ===
-*'''[[Media:RegLib_09_fMRI_full.zip‎|download entire package  <small> (Data,Presets,Tutorial, Solution, zip file 39 MB) </small>]]'''
+*'''[[Media:RegLib_C09_Data.zip‎|download example data  <small> (Data,Presets, Solution, zip file 60 MB) </small>]]'''
-*Presets
+*'''[[Media:RegLib_C09_Presets.mrml‎|download parameter preset file  <small> ( MRML file 12 kB) </small>]]'''
-*Tutorial only
+:[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]
 === Discussion: Registration Challenges ===
@@ Line 54: / Line 40: @@
 === Discussion: Key Strategies ===
-*masking is likely necessary to obtain good results.
+*this example manages to lock onto the target w/o masking, despite the FOV clipping. For similar cases it is likely that masking of the brain in both images may be necessary to obtain a good match.
-*in this example the initial alignment of the two scans is not excessive.
+*a good rigid alignment is important before proceeding to non-rigid alignment to further correct for distortions. Affine is not recommended w/o masking, because the FOV differences would incur large scaling distortions.
-*because speed is not that critical, we increase the sampling rate from the default 2% to 15%.
+*The nonrigid portion should be constrained to a max. deformation, e.g. 3mm
-=== Acknowledgments ===
+=== Methods ===

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