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Infarction Core Delineator Project

Purpose

The purpose of this software is to process input DICOM images and delineate infarction core. The software is a console application and the processing can be adjusted by the used command line parameters. DICOM images are processed and the result is a serie of PNG images which are stored in an output directory. There are also provided statistical characteristics evalutated inside the infarction core.

Requirements

Licence

This software is distributed under restrictions of Creative Commons Attribution-NonCommercial-ShareAlike licence.

Installation

After downloading the software you can run it using the command line parameters which description follows.

Download

Background

The ischemic strokes are one of the leading cause of death and disability in population over 60 years old. The early admittion to hospital is essential because the ischemic strokes mean disturbance in blood supply of the brain. The brain tissue under the limited blood supply falls into penumbra which means the loss of the neuronal function and if the blood supply is not restored, the tissue dies - becomes infarction core. Possible treatment is called thrombolytical treatment but this kind of treatment can not be indicated to patients exceeding certain level of volume of the infarction core. Detection of such volume has not been solved. This software is an implementation of such method allowing automated delineating of the infarction core volume.

Input expectations

The software can handle DICOM files which are supposed to contain Cerebral Blood Volume maps (CBV) or Perfused Blood Volume maps (PBV). The method processes only images having 512x512 dimensions of one slice. If the dimensions are different the whole examination is transformed into the presumed dimension using a linear interpolation. If we consider the resolution of 512x512 the contained pixel spacing should be around 0.39 mm, but also 0.38 or 0.42 mm are satisfying. Slice thickness is supposed to be 5 mm with 3 mm of image spacing. For such settings of the input examinations you can use the recommended settings of command line parameters.

Command line parameters

The command line parameters are following:

Method overview

The method consists of several steps. First the meaning filtering is performed using the neighborhood dimension taken from the command line. Next the thresholding follows using the again the command line parameter which expresses p%-quantile of a distribution function of the image histogram. Since the thresholds are calculated for each image separately, their final form is approximated by a polynomial of the degree taken from the command line.

Recommended parameters

If the input examination conforms to the input expectations, we can recommend following parameters:

 CBV mapsPBV maps
Neighborhood dimension X710
Neighborhood dimension Y710
Neighborhood dimension Z12
Threshold value0.30.8
Polynomial degree01

Sample inputs

Here you can download sample inputs of CBV and PBV maps.

Sample results

We performed infarction core detection on a sample CBV map using the recommended command line parameters. Output statistical characteristics of the found infarction core and several output images are displayed. Red color corresponds to the detected infarction core area.

Example of CBV statistics of the found infarction core:

Statistics of infarction core:
Maximal value:           13.09 ml/l
Average value:            5.64 ml/l
Std. deviation:           0.02 ml/l
Number of voxels:     14349
One voxel dimensions:     0.39 x 0.39 x 3.00 mm
Volume:                   6.63 cm3

Example of several output images of the CBV map infarction core delineation:

User manual download

This user manual is available also in pdf form. InfarctionCoreDelinator.pdf

Acknowledgements

The research was supported by a grant of the Grant Agency of the Czech Republic - Microstructure oriented hierarchical modeling of brain perfusion for CT based cerebral blood flow evaluation, no. 106/09/0740.

This software uses Insight Segmentation and Registration Toolkit (ITK) which is distributed under BSD license:

Copyright (c) 1999-2008 Insight Software Consortium All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

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