EMSegmenter-Tasks:Template - Revision history

Pohl: /* Result */

2010-12-08T21:53:05Z

Result

Pohl: /* Result */

2010-12-08T21:52:56Z

Result

Pohl: /* Atlas */

2010-12-08T21:52:31Z

Atlas

Pohl: /* Atlas */

2010-12-08T21:52:08Z

Atlas

Pohl: /* Anatomical Tree */

2010-12-08T21:51:48Z

Anatomical Tree

Pohl: /* Description */

2010-12-08T21:50:50Z

Description

Pohl: /* Description */

2010-12-08T21:50:28Z

Description

Belhachemi: Created page with 'Return to EMSegmenter Task Overview Page =This wiki template can be used for new tasks= =Description= Single channel automatic segmentation of t1w-MRI bra…'

2010-12-08T21:29:01Z

Created page with 'Return to EMSegmenter Task Overview Page =This wiki template can be used for new tasks= =Description= Single channel automatic segmentation of t1w-MRI bra…'

New page

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

=This wiki template can be used for new tasks=

=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)

=Anatomical Tree=

* root
** background (BG)
*** air (AIR)
** intracranial cavity (ICC)
*** white matter (WM)

=Atlas=
- how did you construct the atlas ? 
-- what did you do for skull stripping or any other preprocessing 
-- What did you do for group registration 
-- how did you generate the segmentations 
-- how many set of images did you use 
-- where did you get the data from 
 

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. 
Image Dimension = 256 x 256 x 124 
Image Spacing = 0.9375 x 0.9375 x 1.5 

{| 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=
[[Image:MRI-Human-Brain-T1.png|630px]] 
[[Image:MRI-Human-Brain-Labelmap.png|630px]]

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

=Citations=
* 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.

@@ Line 35: / Line 35: @@
 =Result=
-show original scans with segmentation as in the example below
+show original scans with segmentation as in the example below <BR>
 [[Image:MRI-Human-Brain-T1.png|630px]]<br>
 [[Image:MRI-Human-Brain-Labelmap.png|630px]]

@@ Line 20: / Line 20: @@
 -- how many set of images did you use <br>
 -- where did you get the data from <br>
--- example images of atlas
+-- example images of atlas such as
 {| class="wikitable"
 |-

@@ Line 20: / Line 20: @@
 -- how many set of images did you use <br>
 -- where did you get the data from <br>
 <br>

@@ Line 4: / Line 4: @@
 =Description=
--- Data Assumption
+-- Data Assumption <BR>
 -- description of pipeline with citations to algorithms used

@@ Line 8: / Line 8: @@
 =Anatomical Tree=
+-- Define Anatomical Tree used in mrml file - first list the complete name and then the abbreviating used in the mrml file
 * root
 ** background (BG)
 *** air (AIR)
 =Atlas=