EMSegmenter-Tasks:LesionExp - Revision history

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

Belhachemi: /* Result */

2011-06-18T23:23:28Z

Result

Belhachemi: /* Result */

2011-06-18T23:20:50Z

Result

Belhachemi: /* Anatomical Tree */

2011-06-18T22:49:51Z

Anatomical Tree

Belhachemi: Created page with 'Return to EMSegmenter Task Overview Page =Description= Two channel automatic segmentation of T1 and FLAIR MRI brain scans into the major tissue classes (gr…'

2011-06-18T22:49:33Z

Created page with 'Return to EMSegmenter Task Overview Page =Description= Two channel automatic segmentation of T1 and FLAIR MRI brain scans into the major tissue classes (gr…'

New page

[[EMSegmenter-Tasks|Return to EMSegmenter Task Overview Page]]

=Description=
Two channel automatic segmentation of T1 and FLAIR MRI brain scans into the major tissue classes (gray matter, white matter, csf). 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 T1 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.
* Step 4: Assign T1 GM intensity distribution to T1 Lesion intensity distribution
* Step 5: Automatically segment the MRI scan into the structures of interest using [[Modules:EMSegmenter-3.6|EM Algorithm]] (Pohl et al 2007)

=Anatomical Tree=

* root
** background (BG)
** intracranial cavity (ICC)
*** white matter (WM)
*** grey matter (GM)
*** cerebrospinal fluid (CSF)

=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>
Image Spacing = 0.9375 x 0.9375 x 1.5 <BR>

{| class="wikitable"
|-
| [[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]]
|-
| Template (T1)
| CSF
| GM
| WM
|}

=Result=
<gallery perrow=1: widths=630px : heights=210px>
Image:MRI-Human-Brain-T1.png
Image:MRI-Human-Brain-Labelmap.png
</gallery>

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

=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

@@ Line 39: / Line 39: @@
 =Result=
-<gallery perrow=1: widths=630px : heights=210px>
+<gallery perrow=1: widths=1000px : heights=300px>
 Image:EMS LesionExp T1.png
 Image:EMS LesionExp FLAIR.png

@@ Line 3: / Line 3: @@
 =Description=
 Two channel automatic segmentation of T1 and FLAIR MRI brain scans into the major tissue classes (gray matter, white matter, csf). 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 T1 MRI scan via [[Modules:BRAINSFit| BRAINSFit]] (Johnson et al 2007)
 * Step 3: Compute the intensity distributions for each structure <BR>

@@ Line 18: / Line 18: @@
 *** grey matter (GM)
 *** cerebrospinal fluid (CSF)
 =Atlas=