imx

Below is a demonstration of the features of the imx function

Contents

clear; close all; clc;

Syntax

hf=imx(varargin);

Description

The imx function provides a figure window based GUI for 3D image segmentation

Examples

Example: Segmenting MRI data

Get a 3D image (see also dcmFolder2MATobject to import DICOM data)

testCase=2;
switch testCase
    case 1 %MATLAB brain data
        load mri;
        M=squeeze(D); %example image data set
        v=2./[1,1,.4]; %example voxel size
    case 2 %MRI imported from DICOM files, see also HELP_dcmFolder2MATobject
        defaultFolder = fileparts(fileparts(mfilename('fullpath'))); %Set main folder
        pathName=fullfile(defaultFolder,'data','DICOM','0001_human_calf');
        loadName=fullfile(pathName,'IMDAT','IMDAT.mat');

        IMDAT_struct=load(loadName); %The image data structure
        G = IMDAT_struct.G; %Geometric/spatial information
        v=G.v; %The voxel size
        M= IMDAT_struct.type_1; %The image data
end

Start segmentation using imx

hf=imx(M,v);

Viewing

Sketching a contour

Accepting a contour

Finalizing segmentation - After the slice is complete, press space to go to the next slice and continue segmentation for all MRI slices. Periodically check the view of all slices using the showHide tool to verify continuity along the length of an element until completion.

GIBBON www.gibboncode.org

Kevin Mattheus Moerman, gibbon.toolbox@gmail.com

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License: https://github.com/gibbonCode/GIBBON/blob/master/LICENSE

GIBBON: The Geometry and Image-based Bioengineering add-On. A toolbox for image segmentation, image-based modeling, meshing, and finite element analysis.

Copyright (C) 2019 Kevin Mattheus Moerman

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.