Projects:RegistrationLibrary:RegLib C04 - Revision history

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

2017-07-10T18:07:16Z

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

Meier at 20:14, 12 June 2012

2012-06-12T20:14:00Z

Meier: /* Slicer 4.1 recommended Modules */

2012-06-12T20:13:28Z

Slicer 4.1 recommended Modules

Meier: /* Procedure */

2012-06-12T20:12:55Z

Procedure

Meier: /* Download */

2012-06-12T20:07:22Z

Download

Meier: /* Download */

2012-06-12T20:06:30Z

Download

Meier: /* Download */

2012-06-12T20:06:04Z

Download

Meier at 19:46, 12 June 2012

2012-06-12T19:46:41Z

Meier at 19:42, 12 June 2012

2012-06-12T19:42:06Z

Meier: /* Objective / Background */

2012-06-05T15:37:26Z

Objective / Background

@@ Line 33: / Line 33: @@
 === Slicer 4.1 recommended Modules ===
-*[http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit BrainsFit]
+*[https://www.slicer.org/wiki/Documentation/4.1/Modules/BRAINSFit BrainsFit]
 *tutorials here are for the above module, but you may also use the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/AffineRegistration Affine Registration] or [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ExpertAutomatedRegistration Expert Automated Registration] modules.

@@ Line 3: / Line 3: @@
 [[Projects:RegistrationDocumentation:UseCaseInventory|Back to Registration Use-case Inventory]] <br>
-= <small>v3.6.3</small> [[Image:Slicer_cvers_banner.png|150px]]  Slicer Registration Library Case 04:   Multi-contrast brain MRI of Multiple Sclerosis  =
+= <small>updated for '''v4.1'''</small> [[Image:Slicer4_RegLibLogo.png|150px]] <br> Slicer Registration Library Case 04:   Multi-contrast brain MRI of Multiple Sclerosis  =
 === Input ===
 {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"

@@ Line 34: / Line 34: @@
 === Slicer 4.1 recommended Modules ===
 *[http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit BrainsFit]
 ===Objective / Background ===

@@ Line 71: / Line 71: @@
 *because of the contrast differences and anisotropic resolution we use Mutual Information as cost function for better robustness
 === Procedure ===
-*there is a brief movie in the download section that shows this procedure step by step. Guides below use the  [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit General Registration (BRAINS)] module, but you may also use the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/AffineRegistration Affine Registration or [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ExpertAutomatedRegistration Expert Automated Registration] modules.
+*there is a brief movie in the download section that shows this procedure step by step. Guides below use the  [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit General Registration (BRAINS)] module, but you may also use the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/AffineRegistration Affine Registration] or [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ExpertAutomatedRegistration Expert Automated Registration] modules.
 *'''Phase 1''': register inter-exam exam 2 -> exam 1
 #open the [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSFit General Registration (BRAINS) module]

@@ Line 43: / Line 43: @@
 **[[Media:RegLib_C04_Data.zip‎|'''Registration Library Case 04: MS Multi-contrast series (PD,T2, T1-GdDTPA): Lesion change assessment''' <small> (Data & Solution Xforms, zip file 18 MB) </small>]]
 *Documentation
-**[[Media:RegLib_C04_Register_interExam.mov‎|ScreenCast Video: inter-exam registration: aligning exam 2 to exam 1 <small> (quicktime movie, 8 MB) </small>]]
+**[[Media:RegLib_C04_Register_interExam.mov‎|ScreenCast Video: loading data & inter-exam registration: aligning exam 2 to exam 1 <small> (quicktime movie, 8 MB) </small>]]
-**[[Media:RegLib_C04_Register_interExam.mov‎|ScreenCast Video: intra-exam registration: aligning T1Gd of exam 2 to PD of exam 2 <small> (quicktime movie, 8 MB) </small>]]
+**[[Media:RegLib_C04_Register_intraExam.mov‎|ScreenCast Video: intra-exam registration: aligning T1Gd of exam 2 to PD of exam 2 <small> (quicktime movie, 8 MB) </small>]]
-**[[Media:RegLib_C04_Register_interExam.mov‎|ScreenCast Video: transform hierarchy: how to arrange the MRML data tree to properly reflect the mutual dependencies of transforms <small> (quicktime movie, 2 MB) </small>]]
+**[[Media:RegLib_C04_Register_XformHierarchy.mov‎|ScreenCast Video: transform hierarchy: how to arrange the MRML data tree to properly reflect the mutual dependencies of transforms <small> (quicktime movie, 2 MB) </small>]]
 === Keywords ===

@@ Line 110: / Line 110: @@
 #to apply the transform and lock in the new position, right click on the volume and select ''Harden Transform'' from the popup menu. The node will move back out to the main level. Note that this applies the transform to the physical orientation info in the image header and does not actually perform a resampling. It is recommended to not apply resampling until the very end of an analysis pipeline, to avoid interpolation-related data loss. To perform a resampling follow steps below:
 *'''Phase 4''': Resampling (optional)
+#go to [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSResample ''Resample Image (BRAINS)'' module] (in the Registration menu)
+##''Image To Warp'': e2_PD
+##''Reference Image'': e1_PD
+##''Output Image'': create new & rename: e2_PD_Xf1
+##''Pixel Type'': ushort
-#Go to the ''Data'' module. You should see 6 images (e1_PD, e1_T2 etc.) and 3 solution transforms (Xform_...)
+##''Warp By Transform'': Xf1_e21_Affine  created in Phase I above
-#Set background view to e1_PD and foreground to e2_PD. Toggle to see misalignment
+##''Interpolation Mode'': '''linear'''
-#'''Align Exam 1:'''
+#note to avoid multiple resampling, combine the two nested transforms for the two volumes before performing the resampling step above. Alternatively you can execute the ''Harden Transform'' step above first and then resample the volume after, by giving no transform (i.e. resampling in place) but listing the fixed image (e.g. e1_PD) as reference. This will resample the moving image into the same representation as the reference.
 before registration: [[Image:RegLib_C04_DataTree.png|200px|Orig. MRML Data tree]]
 after registration: [[Image:RegLib_C04_DataTree2.png|200px|Registered. MRML Data tree: exam 2 is within nested affine transforms]]

@@ Line 37: / Line 37: @@
 ===Objective / Background ===
 This scenario occurs in many forms whenever we wish to assess change in a series of multi-contrast MRI. The follow-up scan(s) are to be aligned with the baseline, but also the different series within each exam need to be co-registered, since the subject may have moved between acquisitions. Hence we have a set of nested registrations. This particular exam features a dual echo scan (PD/T2), where the two structural scans are aligned by default. The post-contrast T1-GdDTPA scan however is not necessarily aligned with the dual echo. Also the post-contrast scan is taken with a clipped field of view (FOV) and a lower axial resolution, with 4mm slices and a 1mm gap (which we treat here as a de facto 5mm slice).
 === Download ===
 *Data: