DBP3:Utah:RegSegPipeline - Revision history

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

2017-07-10T16:59:43Z

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

Sbengali at 17:37, 16 November 2012

2012-11-16T17:37:08Z

Ggardner at 04:10, 30 August 2011

2011-08-30T04:10:01Z

Ggardner at 04:00, 30 August 2011

2011-08-30T04:00:30Z

Dillonl: /* Current Progress */

2011-08-29T19:23:03Z

Current Progress

Dillonl: /* Current Progress */

2011-08-29T19:21:35Z

Current Progress

Dillonl: /* Current Progress */

2011-08-29T19:21:13Z

Current Progress

Dillonl at 19:20, 29 August 2011

2011-08-29T19:20:17Z

Dillonl: /* Current Progress */

2011-08-29T19:15:57Z

Current Progress

Dillonl at 19:13, 29 August 2011

2011-08-29T19:13:28Z

@@ Line 23: / Line 23: @@
 . N4 bias field correction for the MRI (surface coils):
 ::*'''Input''': MRI_pre and MRI_post, each run separately with the same parameters below; '''Output:''' MRI_pre_n4 and MRI_post_n4
-::*'''Module used:''' [http://www.slicer.org/slicerWiki/index.php/Modules:N4ITKBiasFieldCorrection-Documentation-3.6 N4 ITK]; '''Parameters:''' convergence: 1e-5, iterations: 50,40,30,20, shrink factor: 3
+::*'''Module used:''' [https://www.slicer.org/wiki/Modules:N4ITKBiasFieldCorrection-Documentation-3.6 N4 ITK]; '''Parameters:''' convergence: 1e-5, iterations: 50,40,30,20, shrink factor: 3
 ::*''Comments:'' a run  on entire image gives some benefit that '''may''' be improved with masking: again the dominant intensity dropoff from the surface coil occurs along the chest wall and ribcage. Even if that is not the structure of interest, it is the low-freq. variation the bias correction algorithm is searching for, and masking that out can be counter-productive: via masking we may end up with a smoother image, but the intensity variations removed were not caused by the coil but are actually true signal.
 . affine registration MRA ->MRI (both pre and post)
 ::*'''Input''': MRI_pre_n4 (fixed) and MRA_pre ; '''Output:''' Xf1_pre_MRA-MRI.tfm"
 ::*'''Input''': MRI_post_n4 (fixed) and MRA_post ; '''Output:''' Xf2_post_MRA-MRI.tfm"
-::*'''Module used:'''  [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit]
+::*'''Module used:'''  [https://www.slicer.org/wiki/Modules:BRAINSFit BRAINSfit]
 ::*'''Parameters:''' no initialization; samples: 200k, convergence: 1e-5, iterations:
 ::*''Comments:'' from the example dataset (P1) we infer that the two scans tend to have little initial alignment, hence initialization steps are not recommended. We choose registration parameters such that the chance of the registration making the alignment worse is minimized.  Decide in a subsequent review/QC step if we keep the transform or the original pose. The MRA contains the same FOV and has surrounding structures (liver, chest, spine etc) visible also, despite lower intensities. A global affine is thus not necessarily going to benefit from masking the heart, unless the relative motion of the heart becomes the dominant reason for misalignment. We tried masking with both BrainsFit and RobustMultires modules. Both failed to provide better alignment with masking.
 . registration post -> pre: phase 1: AFFINE
 ::*'''Input''': MRI_pre_n4 (fixed) and MRI_post_n4 (moving) ; '''Output:''' Xf3_pre-post_affine.tfm
-::*'''Module used:'''  [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit]
+::*'''Module used:'''  [https://www.slicer.org/wiki/Modules:BRAINSFit BRAINSfit]
 ::*'''Parameters:''' DOF: rigid+similarity+affine (possibly rigid only);  initialization: Moments align ; samples: 200k, convergence: 1e-5, iterations:
 ::*''Comments:'' done on the entire image. The surrounding structures are useful in constraining the solution transform and should provide a more robust behavior. Cropping down to the cardiac only ROI is deferred to the nonrigid registration in phase 2. The inferior-superior FOV can differ, e.g. how much of the liver is included. If the two exams differ significantly (>30%) in that content, the above affine could fail and a prior cropping step is then suggested to better match image content before registration. Resampling to isotropic voxel size at this stage is also advantageous but will generate very large files > 100MB due to the full FOV.
 . Cropping to VOI:
 ::*'''Input''': MRI_pre_n4 (fixed) and MRI_post_n4 (moving) ; '''Output:''' MRI_pre_n4_cropped,  MRI_post_n4_cropped
-::*'''Module used:''' [http://www.slicer.org/slicerWiki/index.php/Modules:CropVolume-Documentation-3.6 Crop Volume]
+::*'''Module used:''' [https://www.slicer.org/wiki/Modules:CropVolume-Documentation-3.6 Crop Volume]
-::*''Comments:'' the [http://www.slicer.org/slicerWiki/index.php/Modules:VolumeRendering-Documentation-3.6 volume rendering module] may help in obtaining a good cropping ROI. Because of the high contrast, the MRA provides a good source for volume rendering.
+::*''Comments:'' the [https://www.slicer.org/wiki/Modules:VolumeRendering-Documentation-3.6 volume rendering module] may help in obtaining a good cropping ROI. Because of the high contrast, the MRA provides a good source for volume rendering.
 . registration post -> pre: phase 2: nonrigid / BSPLINE
 ::*'''Input''': MRI_pre_n4_cropped (fixed) and MRI_post_n4_cropped (moving) ; '''Output:''' Xf4_pre-post_BSpline.tfm"
-::*'''Module used:'''  [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit] or  [http://www.slicer.org/slicerWiki/index.php/Modules:CMTK CMTK]
+::*'''Module used:'''  [https://www.slicer.org/wiki/Modules:BRAINSFit BRAINSfit] or  [https://www.slicer.org/wiki/Modules:CMTK CMTK]
 ::*'''Parameters:''' DOF: BSpline only;  initialization: Xf3_pre-post_affine.tfm ; samples: 200k, convergence: 1e-5, iterations:
-::*''Comments:'' crop to volume of interest: [http://www.slicer.org/slicerWiki/index.php/Modules:CropVolume-Documentation-3.6 CropVolume module], use ''Resample to isotropic voxelsize'' option.
+::*''Comments:'' crop to volume of interest: [https://www.slicer.org/wiki/Modules:CropVolume-Documentation-3.6 CropVolume module], use ''Resample to isotropic voxelsize'' option.
 . resample MRA: apply above BSpline to the pre MRA
 ::*'''Input Volume''': MRA_post_n4_cropped
 ::*'''Input Transform''': above Xf4_pre-post_BSpline.tfm; '''Output Volume''': MRA_post_n4_cropped_Xf4
-::*'''Module used:'''  [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleScalarVectorDWIVolume-Documentation-3.6 ResampleScalarVectorDWIVolume]
+::*'''Module used:'''  [https://www.slicer.org/wiki/Modules:ResampleScalarVectorDWIVolume-Documentation-3.6 ResampleScalarVectorDWIVolume]
 ::*'''Parameters:''' output-to-input box checked, interpolation: linear
 . ROI definition (manual box ROI or automated via atlas)
-::*'''Module used:'''  [http://www.slicer.org/slicerWiki/index.php/Modules:BRAINSFit BRAINSfit] or  [http://www.slicer.org/slicerWiki/index.php/Modules:CMTK CMTK]
+::*'''Module used:'''  [https://www.slicer.org/wiki/Modules:BRAINSFit BRAINSfit] or  [https://www.slicer.org/wiki/Modules:CMTK CMTK]
 . segmentation of LA from MRA -> inner wall
-::*'''Module used:'''  [http://www.slicer.org/slicerWiki/index.php/Modules:RobustStatisticsSeg-Documentation-3.6 Robust Statistics module] or     [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 Editor: thresholding]  for thresholding within [http://www.slicer.org/slicerWiki/index.php/Modules:CMTK CMTK]
+::*'''Module used:'''  [https://www.slicer.org/wiki/Modules:RobustStatisticsSeg-Documentation-3.6 Robust Statistics module] or     [https://www.slicer.org/wiki/Modules:Editor-Documentation-3.6 Editor: thresholding]  for thresholding within [https://www.slicer.org/wiki/Modules:CMTK CMTK]
-::*''Comments:'' as a dynamic image the MRA contains significant spread and likely requires interactive segmentation/thresholding to yield a satisfactory LA volume. For validation/visualization, use the :[http://www.slicer.org/slicerWiki/index.php/Modules:Volumes-Documentation-3.6 Volumes] thresholding option within ''Display'' tab, use ''iron'' colormap & low alpha setting to check for ventricular wall borders. (see figures below)
+::*''Comments:'' as a dynamic image the MRA contains significant spread and likely requires interactive segmentation/thresholding to yield a satisfactory LA volume. For validation/visualization, use the :[https://www.slicer.org/wiki/Modules:Volumes-Documentation-3.6 Volumes] thresholding option within ''Display'' tab, use ''iron'' colormap & low alpha setting to check for ventricular wall borders. (see figures below)
 . LA wall segmentation
 ::*'''Module used:'''  ''Atrium Cardiac Wall Segmentation'' (Extension Module, no documentation yet, authors: Yi Gao, Behnood Gholami, Allen Tannenbaum)
 . segmentation of enhancement
-::*'''Module:'''  [http://www.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6 Editor: thresholding]
+::*'''Module:'''  [https://www.slicer.org/wiki/Modules:Editor-Documentation-3.6 Editor: thresholding]
 ::*'''alternative Module:''' [http://wiki.na-mic.org/Wiki/index.php/Projects:AblationScarSegmentation AblationScarSegmentation]
 ::*''Comments:'; operate only on ROI within LA wall. Based on proper intensity statistics. An atlas-based set of intensity distributions may be more meaningful here than a simple Otsu, because both amount and location of enhancement is unknown and can in theory be 0.

@@ Line 17: / Line 17: @@
 C. Mahnkopf, T.J. Badger, N.S. Burgon, M. Daccarett, T.S. Haslam, C.T. Badger, C.J. McGann, N. Akoum, E. Kholmovski, R.S. Macleod, N.F. Marrouche. “Evaluation of the left atrial substrate in patients with lone atrial fibrillation using delayed-enhanced MRI: implications for disease progression and response to catheter ablation,” In Heart Rhythm, Vol. 7, No. 10, pp. 1475--1481. 2010.   http://www.sci.utah.edu/publications/mahnkopf10/mahnkopf2010.pdf
-We are in the process of making a small set of anonymized test data available for general use and more extensive deidentified data for exclusive use with NAMIC.  Please contact me (macleod@sci.utah.edu) for more details.
+A set of anonymized test data of sixty patients available for general use and more extensive deidentified data for exclusive use with NAMIC is available here: http://hdl.handle.net/1926/1757.  Please contact me (macleod@sci.utah.edu) for more details.
 === Main processing pipeline ===

@@ Line 81: / Line 81: @@
 </gallery>
-<gallery perrow="1" widths="1000px">
+<gallery perrow="1" widths="500px" heights="340px">
-[[File:NAMIC_Flow_Chart.pdf|Proposed processing pipeline.  This pipeline takes raw DE-MRI images pre- and post-ablation as input.  The images are registered, cropped, and corrected for MRI bias fields.  In addition to the registered output images, the transofrmation matrix of the registration steps is also included.  The red, dashed bounding box denotes the current state (8.29.11) of the completed Slicer code.]]
+Image:NAMIC_Flow_Chart.png|Proposed processing pipeline.  This pipeline takes raw DE-MRI images pre- and post-ablation as input.  The images are registered, cropped, and corrected for MRI bias fields.  In addition to the registered output images, the transofrmation matrix of the registration steps is also included.  The red, dashed bounding box denotes the current state (8.29.11) of the completed Slicer code.
 </gallery>

@@ Line 79: / Line 79: @@
 Image:PipelineStart.png|Registration Segmentation Pipeline input selection - raw images.
 Image:PipelineStep1.png|N4 ITK MRI bias correction completed.
 </gallery>

@@ Line 76: / Line 76: @@
 As we proceed and make progress with the pipeline we have simplified it by consolidating many of the steps with minimal user input. Users are now prompted to provide a pre and post set of MRI data. Once provided, a button labeled 'MRI Intensity Correction' is enabled. When the user clicks the button, Slicer begins the pipeline by using N4 ITK MRI bias correction immediately followed by a whole-image affine registration. Once completed, the user is then prompted to crop the images to the desired ROI. After the ROI is defined a non-rigid registration is performed yielding registered pre and post MRI images and the corresponding transformation matrix. The following image gallery shows the progress and current state of the GUI.
-<gallery perrow="2">
+<gallery perrow="2" widths="550px" heights="300px">
 Image:PipelineStart.png|Registration Segmentation Pipeline input selection - raw images.
 Image:PipelineStep1.png|N4 ITK MRI bias correction completed.
 </gallery>

← Older revision		Revision as of 19:20, 29 August 2011
Line 76:		Line 76:
	As we proceed and make progress with the pipeline we have simplified it by consolidating many of the steps with minimal user input. Users are now prompted to provide a pre and post set of MRI data. Once provided, a button labeled 'MRI Intensity Correction' is enabled. When the user clicks the button, Slicer begins the pipeline by using N4 ITK MRI bias correction immediately followed by a whole-image affine registration. Once completed, the user is then prompted to crop the images to the desired ROI. After the ROI is defined a non-rigid registration is performed yielding registered pre and post MRI images and the corresponding transformation matrix. The following image gallery shows the progress and current state of the GUI.		As we proceed and make progress with the pipeline we have simplified it by consolidating many of the steps with minimal user input. Users are now prompted to provide a pre and post set of MRI data. Once provided, a button labeled 'MRI Intensity Correction' is enabled. When the user clicks the button, Slicer begins the pipeline by using N4 ITK MRI bias correction immediately followed by a whole-image affine registration. Once completed, the user is then prompted to crop the images to the desired ROI. After the ROI is defined a non-rigid registration is performed yielding registered pre and post MRI images and the corresponding transformation matrix. The following image gallery shows the progress and current state of the GUI.

−	~~[[File~~:PipelineStart.png]]	+	<gallery perrow="4" widths="200px">
		+	Image:PipelineStart.png\|Registration Segmentation Pipeline input selection.
		+	Image:PipelineStage1.png\|N4 ITK MRI bias correction completed.
		+	</gallery>

← Older revision		Revision as of 19:15, 29 August 2011
Line 75:		Line 75:
	=== Current Progress ===		=== Current Progress ===
	As we proceed and make progress with the pipeline we have simplified it by consolidating many of the steps with minimal user input. Users are now prompted to provide a pre and post set of MRI data. Once provided, a button labeled 'MRI Intensity Correction' is enabled. When the user clicks the button, Slicer begins the pipeline by using N4 ITK MRI bias correction immediately followed by a whole-image affine registration. Once completed, the user is then prompted to crop the images to the desired ROI. After the ROI is defined a non-rigid registration is performed yielding registered pre and post MRI images and the corresponding transformation matrix. The following image gallery shows the progress and current state of the GUI.		As we proceed and make progress with the pipeline we have simplified it by consolidating many of the steps with minimal user input. Users are now prompted to provide a pre and post set of MRI data. Once provided, a button labeled 'MRI Intensity Correction' is enabled. When the user clicks the button, Slicer begins the pipeline by using N4 ITK MRI bias correction immediately followed by a whole-image affine registration. Once completed, the user is then prompted to crop the images to the desired ROI. After the ROI is defined a non-rigid registration is performed yielding registered pre and post MRI images and the corresponding transformation matrix. The following image gallery shows the progress and current state of the GUI.
		+
		+	[[File:PipelineStart.png]]

← Older revision		Revision as of 19:13, 29 August 2011
Line 72:		Line 72:
	=== Example Cases ===		=== Example Cases ===
	* [[Media:AFib_Example_P1_Data.zip\|Example Case P1 : pre-post N4 bias corregtion, registration, LA segmentation]]		* [[Media:AFib_Example_P1_Data.zip\|Example Case P1 : pre-post N4 bias corregtion, registration, LA segmentation]]
		+
		+	=== Current Progress ===
		+	As we proceed and make progress with the pipeline we have simplified it by consolidating many of the steps with minimal user input. Users are now prompted to provide a pre and post set of MRI data. Once provided, a button labeled 'MRI Intensity Correction' is enabled. When the user clicks the button, Slicer begins the pipeline by using N4 ITK MRI bias correction immediately followed by a whole-image affine registration. Once completed, the user is then prompted to crop the images to the desired ROI. After the ROI is defined a non-rigid registration is performed yielding registered pre and post MRI images and the corresponding transformation matrix. The following image gallery shows the progress and current state of the GUI.