Projects:RegistrationLibrary:RegLib C14 - Revision history

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

2017-07-10T17:38:55Z

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

Meier: /* Modules */

2010-10-13T15:13:48Z

Modules

Meier at 15:12, 13 October 2010

2010-10-13T15:12:58Z

Meier: /* Discussion: Key Strategies */

2010-10-13T15:11:18Z

Discussion: Key Strategies

Meier: /* Methods */

2010-10-13T15:09:58Z

Methods

Meier: /* Methods */

2010-10-13T15:08:56Z

Methods

Meier at 14:50, 13 October 2010

2010-10-13T14:50:18Z

Meier: /* Input Data */

2010-10-13T14:49:47Z

Input Data

Meier at 14:46, 13 October 2010

2010-10-13T14:46:52Z

Meier at 14:29, 13 October 2010

2010-10-13T14:29:54Z

@@ Line 23: / Line 23: @@
 === Modules ===
-*'''Slicer 3.6.1 recommended modules:  [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BrainsFit], [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 Expert Automated Registration]'''
+*'''Slicer 3.6.1 recommended modules:  [https://www.slicer.org/wiki/Modules:BRAINSFit BrainsFit], [https://www.slicer.org/wiki/Modules:RegisterImages-Documentation-3.6 Expert Automated Registration]'''
 ===Download ===

@@ Line 23: / Line 23: @@
 === Modules ===
-*'''Slicer 3.6.1 recommended modules:  [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BrainsFit], [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImagesMultiRes-Documentation-3.6 Robust Multiresolution Affine]'''
+*'''Slicer 3.6.1 recommended modules:  [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BrainsFit], [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImages-Documentation-3.6 Expert Automated Registration]'''
 ===Download ===

@@ Line 21: / Line 21: @@
 *reference/fixed : baseline MRI:coronal T1w , 256 x 256 x 79, 0.86 x 0.86 x 2.5 mm
 *moving: PET: axial, fluorodeoxyglucose, 128 x 128 x 35,    4.29  x 4.29 x 4.25 mm
 ===Download ===

@@ Line 79: / Line 79: @@
 **the "Transforms" module is used to correct orientation. We enter manual rotations of 90 and 180 degrees around the LR (left-right) and IS (inferior-superior) axes, respectively
 **the corrected MRI volume is resampled in the Data module via "harden transforms"
-*Register Images is used to automatically align the PET with the MRI. We choose mutual information ("MI") as the criterion and a 5% sampling rate. We request an affine transform to correct for small distortion differences between the PET and the MRI
+*The ''BRAINSfit'' or ''Expert Automated Registration'' modules are recommended to automatically align the PET with the MRI. We choose mutual information ("MI") as the criterion and a 5% sampling rate. We request an affine transform to correct for small distortion differences between the PET and the MRI
 === Acknowledgments ===
 Our thanks to the [http://www.uwo.ca '''University of Western Ontario''']  for providing this example case.

@@ Line 54: / Line 54: @@
 ##Click: ''Apply'' ;  Registration should complete within ~ 30 seconds
 ##Go back to the ''Data'' module: you should see the RegLib_C14_PET image moved under the newly created transform
-#'''Harden/Export results:''''
+#Apply Transform
-#To apply the registration transform to the PET image, select it in the ''Data'' module, and from right-click menu select ''Harden Transform''. Note that this will overwrite the original unregistered image (in memory) and replace it with the resampled one. Not also that the resolution will not change. If you wish the registered PET to be in the same resolution as the reference MRI, use the resample module below:
+##To apply the registration transform to the PET image, select it in the ''Data'' module, and from right-click menu select ''Harden Transform''. Note that this will overwrite the original unregistered image (in memory) and replace it with the resampled one. Not also that the resolution will not change. If you wish the registered PET to be in the same resolution as the reference MRI, use the resample module below:
-#Go to ''Filtering / Resample Scalar/Vector/DWI Volume'''
+##Go to ''Filtering / Resample Scalar/Vector/DWI Volume'''
-##Input: RegLib_C14_PET, Reference: RegLib_C14_MRI_fixed
+###Input: RegLib_C14_PET, Reference: RegLib_C14_MRI_fixed
-##Output: "create new Volume", rename to "RegLib_C14_PET_reg" or similar
+###Output: "create new Volume", rename to "RegLib_C14_PET_reg" or similar
-##Transform Parameters: Transform Node: 'Xf2_BFit''
+###Transform Parameters: Transform Node: 'Xf2_BFit''
-##Leave all other settings at default and click: ''Apply''
+###Leave all other settings at default and click: ''Apply''
-##Choose ''File/Save'' to save results.
+#Choose ''File/Save'' to save results.
 <br>

@@ Line 41: / Line 41: @@
 === Methods ===
+*'''Phase I: fix distortion from incorrect header info'''
 <!--

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 |}
 === Keywords ===
 PET-MRI, brain, intra-subject, image fusion

@@ Line 21: / Line 21: @@
 ===Input Data===
-*reference/fixed : baseline MRI: 0.97  x 0.97 x 3.27 mm ,  PET: 4.7 x 4.7 x 3.3 mm
+*reference/fixed : baseline MRI:coronal T1w , 256 x 256 x 79, 0.86 x 0.86 x 2.5 mm
-*moving: PET: 4.1 x 4.1 x 5 mm
+*moving: PET: axial, fluorodeoxyglucose<br>128 x 128 x 35,    4.29  x 4.29 x 4.25 mm
 ===Download ===
@@ Line 34: / Line 32: @@
 **[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]
 *Documentation
-**'''[[Media:RegLib_C14_Tutorial_BrainPET-MRI.ppt|download step-by-step tutorial  <small> (PowerPoint 1.2 MB) </small>]]'''
+**'''[[Media:RegLib_C14_Tutorial.ppt|download step-by-step tutorial  <small> (PowerPoint 1.2 MB) </small>]]'''
-**'''[[Media:RegLib_C14_Tutorial_BrainPET-MRI.pdf|download step-by-step tutorial  <small> (PDF  MB) </small>]]'''
+**'''[[Media:RegLib_C14_Tutorial.pdf|download step-by-step tutorial  <small> (PDF  MB) </small>]]'''
 === Registration Results===

@@ Line 7: / Line 7: @@
 {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
 |[[Image:RegLib_C14_Thumb_MRI.png|100px|lleft|this is the fixed reference image. All images are aligned into this space]]
-|[[Image:Arrow_left_gray.jpg|100px|lleft]]
+|[[Image:RegArrow_Affine.png|100px|lleft]]
 |[[Image:RegLib_C14_Thumb_PET.png|100px|lleft|   this indicates the moving image that determines the registration transform]]
 |-
@@ Line 25: / Line 25: @@
 **axial, fluorodeoxyglucose<br>128 x 128 x 35<br>      4.29  x 4.29 x 4.25 mm  </small>
 **coronal T1w <br>256 x 256 x 79<br>0.86 x 0.86 x 2.5 mm
 ===Download ===
@@ Line 43: / Line 36: @@
 **'''[[Media:RegLib_C14_Tutorial_BrainPET-MRI.ppt|download step-by-step tutorial  <small> (PowerPoint 1.2 MB) </small>]]'''
 **'''[[Media:RegLib_C14_Tutorial_BrainPET-MRI.pdf|download step-by-step tutorial  <small> (PDF  MB) </small>]]'''