Fully automated rodent brain MR image processing pipeline on a Midas server: from acquired images to region-based statistics

被引：21
作者：
Budin, Francois [1 ]
Hoogstoel, Marion [1 ]
Reynolds, Patrick [2 ]
Grauer, Michael [2 ]
O'Leary-Moore, Shonagh K. [3 ]
Oguz, Ipek [1 ]
机构：
[1] Univ N Carolina, Dept Psychiat, Neuro Image Res & Anal Labs, Chapel Hill, NC 27599 USA
[2] Kitware Inc, Carrboro, NC USA
[3] Univ N Carolina, Dept Psychiat, Bowles Ctr Alcohol Studies, Fetal Toxicol Lab, Chapel Hill, NC 27599 USA
来源：
FRONTIERS IN NEUROINFORMATICS | 2013年 / 7卷
关键词：
rodent; magnetic resonance imaging; automatic processing; server; MOUSE-BRAIN; RAT MODEL; DIFFUSION; ATLAS; SEGMENTATION; INJURY; REGISTRATION; CONTRAST; DISEASE;
D O I：
10.3389/fninf.2013.00015
中图分类号：
Q [生物科学];
学科分类号：
07 ; 0710 ; 09 ;
摘要：
Magnetic resonance imaging (MRI) of rodent brains enables study of the development and the integrity of the brain under certain conditions (alcohol, drugs etc.). However, these images are difficult to analyze for biomedical researchers with limited image processing experience. In this paper we present an image processing pipeline running on a Midas server, a web-based data storage system. It is composed of the following steps: rigid registration, skull-stripping, average computation, average parcellation, parcellation propagation to individual subjects, and computation of region-based statistics on each image. The pipeline is easy to configure and requires very little image processing knowledge. We present results obtained by processing a data set using this pipeline and demonstrate how this pipeline can be used to find differences between populations.
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页数：12
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