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

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

2019-11-27T02:29:35Z

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

Belhachemi: /* Result */

2011-03-18T16:33:37Z

Result

Belhachemi at 21:35, 1 December 2010

2010-12-01T21:35:17Z

Belhachemi at 21:31, 1 December 2010

2010-12-01T21:31:46Z

Belhachemi: /* Description */

2010-12-01T21:21:11Z

Description

Belhachemi: /* Citations */

2010-12-01T21:19:49Z

Citations

Belhachemi at 20:54, 1 December 2010

2010-12-01T20:54:26Z

Belhachemi: /* Atlas */

2010-12-01T20:51:50Z

Atlas

Belhachemi: /* Atlas */

2010-12-01T15:36:58Z

Atlas

Pohl: /* Description */

2010-12-01T01:06:39Z

Description

@@ Line 3: / Line 3: @@
 =Description=
 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:
-* 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 39: / Line 39: @@
 =Result=
-[[Image:MRI-Human-Brain-T1.png|630px]]<br>
+<gallery perrow=1: widths=630px : heights=210px>
-[[Image:MRI-Human-Brain-Labelmap.png|630px]]
+Image:MRI-Human-Brain-T1.png
 =Acknowledgment=

@@ Line 1: / Line 1: @@
 [[EMSegmenter-Tasks|Return to EMSegmenter Task Overview Page]]
-==Description==
+=Description=
 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:
 * 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)
@@ Line 9: / Line 9: @@
 * Step 4: Automatically segment the MRI scan into the structures of interest using [[Modules:EMSegmenter-3.6|EM Algorithm]]  (Pohl et al 2007)
-==Anatomical Tree==
+=Anatomical Tree=
 * root
@@ Line 20: / Line 20: @@
 *** cerebrospinal fluid (CSF)
-==Atlas==
+=Atlas=
 Atlas was generated based on 82 scans and corresponding segmentations provided by [http://pnl.bwh.harvard.edu/ Psychiatry Neuroimaging Laboratory, BWH]. We registered the scans to a preselected template via Warfield et al. 2001. <BR>
 Image Dimension = 256 x 256 x 124 <br>
@@ Line 38: / Line 38: @@
 |}
-==Result==
+=Result=
 [[Image:MRI-Human-Brain-T1.png|630px]]<br>
 [[Image:MRI-Human-Brain-Labelmap.png|630px]]
-==Acknowledgment==
+=Acknowledgment=
 The construction of the pipeline was supported by funding from NIH NCRR 2P41RR013218 Supplement.
-==Citations==
+=Citations=
 * Tustison NJ, Avants BB, Cook PA, Zheng Y, Egan A, Yushkevich PA, Gee JC N4ITK: Improved N3 Bias Correction, IEEE Trans Med Imag, 2010
 * Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=608 A Hierarchical Algorithm for MR Brain Image Parcellation.] IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212.
 * S. Warfield, J. Rexilius, P. Huppi, T. Inder, E. Miller, W. Wells, G. Zientara, F. Jolesz, and R. Kikinis, “A binary entropy measure to assess nonrigid registration algorithms,” in MICCAI, LNCS, pp. 266–274, Springer, October 2001.
 * Johnson H.J., Harris G., Williams K. [http://hdl.handle.net/1926/1291 BRAINSFit: Mutual Information Registrations of Whole-Brain 3D Images, Using the Insight Toolkit], The Insight Journal, July 2007

← Older revision		Revision as of 21:31, 1 December 2010
Line 1:		Line 1:
−	~~MRI Human Brain~~	+	[[EMSegmenter-Tasks\|Return to EMSegmenter Task Overview Page]]

	==Description==		==Description==

@@ Line 4: / Line 4: @@
 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:
 * 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]] (ask Hans for citation)
+* 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.

← Older revision		Revision as of 21:19, 1 December 2010
Line 49:		Line 49:
	* Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=608 A Hierarchical Algorithm for MR Brain Image Parcellation.] IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212.		* Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=608 A Hierarchical Algorithm for MR Brain Image Parcellation.] IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212.
	* S. Warfield, J. Rexilius, P. Huppi, T. Inder, E. Miller, W. Wells, G. Zientara, F. Jolesz, and R. Kikinis, “A binary entropy measure to assess nonrigid registration algorithms,” in MICCAI, LNCS, pp. 266–274, Springer, October 2001.		* S. Warfield, J. Rexilius, P. Huppi, T. Inder, E. Miller, W. Wells, G. Zientara, F. Jolesz, and R. Kikinis, “A binary entropy measure to assess nonrigid registration algorithms,” in MICCAI, LNCS, pp. 266–274, Springer, October 2001.
		+	* Johnson H.J., Harris G., Williams K. [http://hdl.handle.net/1926/1291 BRAINSFit: Mutual Information Registrations of Whole-Brain 3D Images, Using the Insight Toolkit], The Insight Journal, July 2007

@@ Line 32: / Line 32: @@
 | [[Image:EMSegmenter_MRI-Human-Brain_WM_420x420.png|210px]]
 |-
-| Template
+| Template (T1)
 | CSF
 | GM
@@ Line 39: / Line 39: @@
 ==Result==
-[[Image:MRI-Human-Brain-T1.png|840px]]
+[[Image:MRI-Human-Brain-T1.png|630px]]<br>
-[[Image:MRI-Human-Brain-Labelmap.png|840px]]
+[[Image:MRI-Human-Brain-Labelmap.png|630px]]
 ==Acknowledgment==

@@ Line 29: / Line 29: @@
 | [[Image:EMSegmenter_MRI-Human-Brain_Template_420x420.png|210px]]
 | [[Image:EMSegmenter_MRI-Human-Brain_CSF_420x420.png|210px]]
 | [[Image:EMSegmenter_MRI-Human-Brain_GM_420x420.png|210px]]
 | [[Image:EMSegmenter_MRI-Human-Brain_WM_420x420.png|210px]]
 |}

@@ Line 24: / Line 24: @@
 Image Dimension = 256 x 256 x 124 <br>
 Image Spacing   = 0.9375 x 0.9375 x 1.5 <BR>
-'''Dominique show example of atlas (T1, wm , gm ,csf)'''
 ==Result==