Wyatt: /* Methods */

2009-01-08T14:36:35Z

Methods

Wyatt: New page: Back to AHM 2009 Agenda NOTOC ==External Collaboration: Measuring Alcohol and Stress Interactions with Structural and Perfusion MRI== [[media:NAMIC_External-Wyatt...

2009-01-08T14:34:50Z

New page: Back to AHM 2009 Agenda __NOTOC__ ==External Collaboration: Measuring Alcohol and Stress Interactions with Structural and Perfusion MRI== [[media:NAMIC_External-Wyatt...

New page

[[AHM_2009#Agenda|Back to AHM 2009 Agenda]]

__NOTOC__
==External Collaboration: Measuring Alcohol and Stress Interactions with Structural and Perfusion MRI==

[[media:NAMIC_External-Wyatt09.ppt|Wake Forest Collaboration Update (ppt)]]

{|
|[[Image:MonkeyProject09Slicer.png|thumb|170px|Segmentation of Vervet Subcortical Structures]]
|}

==Introduction==
Our goal is to use MRI to examine the effects of chronic alcohol self-administration on brain structure and function in a group of monkeys that have been mother-reared or nursery-reared.

[[NA-MIC_NCBC_Collaboration:Measuring_Alcohol_and_Stress_Interaction|Main Project Page]]

[[Image:MonkeyProjectOverview.png‎|thumb|170px|Project Overview]]

==Team==
* Jim Daunais (WFUHS PI)
* Bob Kraft (WFUHS MR Physicist)
* Chris Wyatt (VT Engineering)
* Vidya Rajagopalan (VT Engineering)
* Killian Pohl (NA-MIC Core 1)

==Goals for 2008==
* Acquisition of baseline vervet images for atlas development (completed)
* Vervet atlas completed (completed)
* Animal Training and Induction 3-4 months (completed)

==Methods==
The first stage of atlas construction was based on a method by
Styner et al [1]. A template image was chosen randomly from the
training images. This image was manually skull-stripped and a
skull-strip mask determined. All other training images were histogram
matched and then affinely registered to this template using FSL FLIRT
[2] and skull-stripped using the skull-strip mask after dilation by
one voxel. The images of only the Extra Cranial Content (ECC) are
averaged to form the ECC template.

The Intra Cranial Content (ICC) images of the various subjects are
again affinely registered to the ICC image of the chosen template
using FSL FLIRT [2]. The affinely registered images were deformably
registered to the same target using the diffeomorphic demons
registration method. The registered images were then averaged. The ICC
average was now combined with the ECC template to form the template
image for the whole head.

This high-CNR template image was then segmented into gray matter,
white matter, and CSF tissue classes using initial k-means clustering
and manual correction. Subcortical structures were then manually
traced on the high-CNR template. The tissue and structure
segmentations were smoothed using a Gaussian kernel to obtain the
initial spatial probability maps.

The second stage of the construction used the initial spatial
probability maps from stage 1 with the expectation-maximization
segmentation (EMS) method by Pohl et al. [4]. Using the initial
spatial probabilities the EMS algorithm, the initial spatial
probability maps were combined with manually estimated structure
intensity distributions for each structure to produce the final
segmentation for the template image. This segmentation was then
manually corrected for errors and then was smoothed using a guassian
kernel of variance 1.

[1] M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. Proc SPIE Medical Imaging Conference, Proc SPIE Vol 6512 Medical Imaging 2007, pp 65122L-1 - 65122L-8.

[2] M. Jenkinson and S.M. Smith. A global optimisation method for robust affine registration of brain images. Medical Image Analysis, 5(2):143-156, June 2001.

[3] Balci, Serdar K.; Golland, Polina; Wells, William M. Non-rigid Groupwise Registration using B-Spline Deformation Model, ISC/NA-MIC Workshop on Open Science at MICCAI 2007.

[4] Pohl KM, Fisher J, Levitt JJ, Shenton ME, Kikinis R, Grimson WEL, Wells WM. A unifying approach to registration, segmentation, and intensity correction. Medical Image Computing And Computer-Assisted Intervention - MICCAI 2005; PT 1 Lecture Notes In Computer Science 3749: 310-318.

==Products==
* [http://www.bsl.ece.vt.edu/data/vervet_atlas/vervet.php Vervet template, tissue, and subcortical atlas]
* [http://www.bsl.ece.vt.edu/tutorials.php Tutorial: Using Slicer3 to segment vervet images]

==Future Work==
* Animal ad-lib access to alcohol for 12 months
* Final structural scans ~August 2009

@@ Line 56: / Line 56: @@
 The second stage of the construction used the initial spatial
 probability maps from stage 1 with the expectation-maximization
-segmentation (EMS) method by Pohl et al. [4]. Using the initial
+segmentation (EMSegmenter) method by Pohl et al. [3]. Using the initial
 spatial probabilities the EMS algorithm, the initial spatial
 probability maps were combined with manually estimated structure
@@ Line 68: / Line 68: @@
 [2] M. Jenkinson and S.M. Smith. A global optimisation method for robust affine registration of brain images. Medical Image Analysis, 5(2):143-156, June 2001.
-[3] Balci, Serdar K.; Golland, Polina; Wells, William M. Non-rigid Groupwise Registration using B-Spline Deformation Model, ISC/NA-MIC Workshop on Open Science at MICCAI 2007.
+[3] Pohl KM, Fisher J, Levitt JJ, Shenton ME, Kikinis R, Grimson WEL, Wells WM. A unifying approach to registration, segmentation, and intensity correction. Medical Image Computing And Computer-Assisted Intervention - MICCAI 2005; PT 1 Lecture Notes In Computer Science 3749: 310-318.
 ==Products==

AHM2009:ExternalWFU - Revision history

Wyatt: /* Methods */

Wyatt: New page: Back to AHM 2009 Agenda __NOTOC__ ==External Collaboration: Measuring Alcohol and Stress Interactions with Structural and Perfusion MRI== [[media:NAMIC_External-Wyatt...

Wyatt: New page: Back to AHM 2009 Agenda NOTOC ==External Collaboration: Measuring Alcohol and Stress Interactions with Structural and Perfusion MRI== [[media:NAMIC_External-Wyatt...