EMSegmenter-Tasks:MRI-Human-Brain-HIPR - Revision history

Grundlett: Text replacement - "\[http:\/\/www\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

2019-11-27T02:27:17Z

Text replacement - "\[http:\/\/www\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

Belhachemi: /* Description */

2011-03-29T17:55:09Z

Description

Belhachemi: /* Result */

2011-03-29T17:53:40Z

Result

Belhachemi: /* Description */

2011-03-29T17:50:43Z

Description

Belhachemi: /* Result */

2011-03-29T17:47:36Z

Result

Belhachemi: /* Input data */

2011-03-29T14:21:57Z

Input data

Belhachemi: /* Description */

2011-03-16T23:26:04Z

Description

Belhachemi: /* Collaborators */

2011-03-16T22:49:01Z

Collaborators

Belhachemi: /* Acknowledgment */

2011-03-16T15:52:22Z

Acknowledgment

Belhachemi at 15:14, 16 March 2011

2011-03-16T15:14:50Z

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 '''High In-Plane Resolution (HIPR)''' <br>
 Single channel automatic segmentation of T1 and T2 MRI brain scans into the major tissue classes (gray matter, white matter, csf). The task can be applied to T1 and T2 brain scan showing parts of the skull and neck. The pipeline consist of the following steps:
-* Step 1: Perform image inhomogeneity correction of the MRI scan via [http://www.slicer.org/slicerWiki/index.php/Modules:N4ITKBiasFieldCorrection-Documentation-3.6 N4ITKBiasFieldCorrection] (Tustison et al 2010)
+* Step 1: Perform image inhomogeneity correction of the MRI scan via [[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4ITKBiasFieldCorrection]] (Tustison et al 2010)
 * Step 2: Register the atlas to the MRI scan via [[Modules:BRAINSFit| BRAINSFit]] (Johnson et al 2007)
 * Step 3: Compute the intensity distributions for each structure <BR>

@@ Line 7: / Line 7: @@
 * Step 2: Register the atlas to the MRI scan via [[Modules:BRAINSFit| BRAINSFit]] (Johnson et al 2007)
 * Step 3: Compute the intensity distributions for each structure <BR>
-Compute intensity distribution (mean and variance) for each label by automatically sampling from the MR scan. The sampling for a specific label is constrained to the region that consists of voxels with high probability (top 95%) of being assigned to the label according to the aligned atlas. The alpha parameter for the EMSegmenter has been set to 0.01 to handle the high in-plane resolution of the scans.
+Compute intensity distribution (mean and variance) for each label by automatically sampling from the MR scan. The sampling for a specific label is constrained to the region that consists of voxels with high probability (top 95%) of being assigned to the label according to the aligned atlas. '''The alpha parameter for the EMSegmenter has been set to 0.01 to handle the high in-plane resolution of the scans.'''
 * Step 4: Automatically segment the MRI scan into the structures of interest using [[Modules:EMSegmenter-3.6|EM Algorithm]]  (Pohl et al 2007)

@@ Line 52: / Line 52: @@
 <gallery perrow=1: widths=1100px : heights=350px>
-Image:MRI-Human-Brain-HIPR-T1Flair_map.png
+Image:MRI-Human-Brain-HIPR-T1Flair_map.png|T1FLAIR
-Image:MRI-Human-Brain-HIPR-T2Flair_map.png
+Image:MRI-Human-Brain-HIPR-T2Flair_map.png|T2FLAIR
-Image:MRI-Human-Brain-HIPR-T2FSE_map.png
+Image:MRI-Human-Brain-HIPR-T2FSE_map.png|T2FSE
 </gallery>

@@ Line 3: / Line 3: @@
 =Description=
 '''High In-Plane Resolution (HIPR)''' <br>
-Single channel automatic segmentation of t1w-MRI brain scans into the major tissue classes (gray matter, white matter, csf). The task can only be applied to t1w brain scan showing parts of the skull and neck. The pipeline consist of the following steps:
+Single channel automatic segmentation of T1 and T2 MRI brain scans into the major tissue classes (gray matter, white matter, csf). The task can be applied to T1 and T2 brain scan showing parts of the skull and neck. The pipeline consist of the following steps:
 * Step 1: Perform image inhomogeneity correction of the MRI scan via [http://www.slicer.org/slicerWiki/index.php/Modules:N4ITKBiasFieldCorrection-Documentation-3.6 N4ITKBiasFieldCorrection] (Tustison et al 2010)
 * Step 2: Register the atlas to the MRI scan via [[Modules:BRAINSFit| BRAINSFit]] (Johnson et al 2007)
 * Step 3: Compute the intensity distributions for each structure <BR>
-Compute intensity distribution (mean and variance) for each label by automatically sampling from the MR scan. The sampling for a specific label is constrained to the region that consists of voxels with high probability (top 95%) of being assigned to the label according to the aligned atlas.
+Compute intensity distribution (mean and variance) for each label by automatically sampling from the MR scan. The sampling for a specific label is constrained to the region that consists of voxels with high probability (top 95%) of being assigned to the label according to the aligned atlas. The alpha parameter for the EMSegmenter has been set to 0.01 to handle the high in-plane resolution of the scans.
 * Step 4: Automatically segment the MRI scan into the structures of interest using [[Modules:EMSegmenter-3.6|EM Algorithm]]  (Pohl et al 2007)

← Older revision		Revision as of 17:47, 29 March 2011
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	=Result=		=Result=
		+
		+	<gallery perrow=1: widths=1100px : heights=350px>
		+	Image:MRI-Human-Brain-HIPR-T1Flair_map.png
		+	Image:MRI-Human-Brain-HIPR-T2Flair_map.png
		+	Image:MRI-Human-Brain-HIPR-T2FSE_map.png
		+	</gallery>

	=Acknowledgment=		=Acknowledgment=

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 Image Dimension = 512 x 512 x 26 <br>
 Image Spacing   = 0.4688 x 0.4688 x 6 <br>
 =Anatomical Tree=

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 The construction of the pipeline was supported by funding from NIH NCRR 2P41RR013218 Supplement.
 =Collaborators=
 =Citations=

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 =Input data=
-.4688 0.4688 6
+Image Dimension = 512 x 512 x 26 <br>
 =Anatomical Tree=