View source for EMSegmenter-Tasks:Template

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

=This wiki template can be used for new tasks=

=Description=
-- Data Assumption
-- description of pipeline with citations to algorithms used

=Anatomical Tree=

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

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

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=
[[Image:MRI-Human-Brain-T1.png|630px]]<br>
[[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.