Share Email Print
cover

Proceedings Paper • new

Automatic rat brain segmentation from MRI using statistical shape models and random forest
Format Member Price Non-Member Price
PDF $14.40 $18.00
cover GOOD NEWS! Your organization subscribes to the SPIE Digital Library. You may be able to download this paper for free. Check Access

Paper Abstract

In MRI neuroimaging, the shimming procedure is used before image acquisition to correct for inhomogeneity of the static magnetic field within the brain. To correctly adjust the field, the brain’s location and edges must first be identified from quickly-acquired low resolution data. This process is currently carried out manually by an operator, which can be time-consuming and not always accurate. In this work, we implement a quick and automatic technique for brain segmentation to be potentially used during the shimming. Our method is based on two main steps. First, a random forest classifier is used to get a preliminary segmentation from an input MRI image. Subsequently, a statistical shape model of the brain, which was previously generated from ground-truth segmentations, is fitted to the output of the classifier to obtain a model-based segmentation mask. In this way, a-priori knowledge on the brain’s shape is included in the segmentation pipeline. The proposed methodology was tested on low resolution images of rat brains and further validated on rabbit brain images of higher resolution. Our results suggest that the present method is promising for the desired purpose in terms of time efficiency, segmentation accuracy and repeatability. Moreover, the use of shape modeling was shown to be particularly useful when handling low-resolution data, which could lead to erroneous classifications when using only machine learning-based methods.

Paper Details

Date Published: 15 March 2019
PDF: 7 pages
Proc. SPIE 10949, Medical Imaging 2019: Image Processing, 109492O (15 March 2019); doi: 10.1117/12.2512409
Show Author Affiliations
Simone Bendazzoli, KTH Royal Institute of Technology (Sweden)
Irene Brusini, KTH Royal Institute of Technology (Sweden)
Karolinska Institute (Sweden)
Peter Damberg, Karolinska Institute (Sweden)
Örjan Smedby, KTH Royal Institute of Technology (Sweden)
Leif Andersson, Uppsala Univ. (Sweden)
Chunliang Wang, KTH Royal Institute of Technology (Sweden)


Published in SPIE Proceedings Vol. 10949:
Medical Imaging 2019: Image Processing
Elsa D. Angelini; Bennett A. Landman, Editor(s)

© SPIE. Terms of Use
Back to Top