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Message-ID:  <[log in to unmask]>
Date:         Fri, 3 May 2002 19:44:48 +1000
Reply-To:     ImageJ Interest Group <[log in to unmask]>
Sender:       ImageJ Interest Group <[log in to unmask]>
From:         Greg Joss <[log in to unmask]>
Subject:      Re: Is there a way to define an anulus?
Comments: To: [log in to unmask]

/*There are a number of approaches that can be taken to this problem.
The following is intended to take a flexible macro approach minimising
the java necessary and allowing non-java users to follow procedure.
Essentially, the use of a binary mask
(which lies behind the implementation of any non rectangulsr roi)
allows very flexible design of measured area with (multiple) holes.
The combination of the "limit to threshold" and "setThreshold(1,255);"
limits measurements to densitySliced regions, avoids a minimum of 0
which would otherwise result and gives a correct area.*/
import ij.*;
import ij.process.*;
import ij.gui.*;
import java.awt.*;
import ij.plugin.*;
import ij.measure.*;      // ResultsTable
import ij.gui.*;          // Plotwindow
import ij.plugin.filter.*;// Analyzer
public class LimitMeasureMacro_ implements PlugIn {
        public void run(String arg) {
                IJ.run("Colors...");
                IJ.setForegroundColor(255, 255, 255);
                IJ.setBackgroundColor(0, 0, 0);
                IJ.run("Set Measurements...", "area modal min limit decimal=0");
                IJ.run("Clear Results");
                IJ.run("MRI Stack (528K)");

                IJ.run("Duplicate...", "title=binaryMask");
                IJ.run("Select All");
                IJ.run("Clear");
                IJ.setTool(1);
                IJ.makeOval(50, 125, 84, 76);
                IJ.run("Fill");
                IJ.makeOval(79, 139, 35, 29);
                IJ.run("Clear");
                IJ.run("Select None");

                IJ.run("Image Calculator..."
                , "image1=mri-stack.tif operation=AND image2=binaryMask create stack");
//all the above would probably be tailored manually to suit image
// and code commented out except for demonstration purpose.
                IJ.setThreshold(1,255);
                int n=WindowManager.getCurrentImage().getStackSize();
                for(int i=1;i<=n;i++){
                        IJ.run("Measure");
                        IJ.run("Next Slice [>]");
                }
                ResultsTable rt=Analyzer.getResultsTable();
                float[]max=rt.getColumn(ResultsTable.MAX);
                float[]min=rt.getColumn(ResultsTable.MIN);
                float[]contrast=new float[max.length];
                float[]time=new float[max.length];
                for(int i=0;i<max.length;i++)time[i]=(float)i;
                for(int i=0;i<max.length;i++)contrast[i]=max[i]-min[i];
                PlotWindow pw =new PlotWindow("Tumor constrast vs time"
                        ,"time","contrast",time,contrast);
                pw.draw();
        }
}


Greg Joss,
Department of Biological Sciences, Phone: (61)(2) 9850 8212 Fax: 9850 8245
Macquarie University,              Email: [log in to unmask]
North Ryde, (Sydney,) NSW 2109, Australia


>>> "Prof. Walter Wolf" <[log in to unmask]> 05/03/02 10:43AM >>>
Wayne and others:

Is there a way to define an annulus? We are studying the ability of
contrast agents to detect changes in the contrast enhancement of tumors
(DEMRI or DCE-MRI) and because many solid tumors develop a necrotic core,
it there any way to define the ring (annulus) so as to generate a kinetic
plot of that ring from a temporal stack of MRI images?

Any suggestions would be appreciated. Thank you.

--
Professor Walter Wolf, Ph.D.
Distinguished Professor of Pharmaceutical Sciences
Director, Pharmacokinetic Imaging Program
Department of Pharmaceutical Sciences, School of Pharmacy
University of Southern California
1985 Zonal Ave., Los Angeles, CA 90089-9121
E-Mail: [log in to unmask]
Telephone: 323-442-1405
Fax: 323-442-9804

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