Login  Register

Re: ROI Thresholding

Posted by Fabrice Cordelières on Sep 11, 2008; 2:03pm
URL: http://imagej.273.s1.nabble.com/ROI-Thresholding-tp3695022p3695026.html

Hi Brandee,

Try first to make a threshold (Image/Adjust/Threshold), then use the  
magic wand tool: click on the "red" zone on the image, and the ROI  
will be drawn around the thresholded area.

Alternatively, you may use this macro to automate the measurement over  
all slices: simply copy the following lines, go to plugins/macro/new  
and paste the text:

8<------------------------------------------
roiManager("Reset");
x=getWidth/2;
y=getHeight/2;
setThreshold(1, pow(2,bitDepth()));
for (i=1; i<=nSlices; i++){
        setSlice(i);
        doWand(x, y);
        roiManager("Add");
        roiManager("Select", i-1);
        roiManager("Rename", "ROI on slice n°"+i);
}
roiManager("Deselect");
run("Set Measurements...", "area redirect=None decimal=3");
roiManager("Multi Measure");
8<------------------------------------------

Open your image then go to the macro window: macro/run macro. In the  
result table, the value indicate the area for each ROI.

NB: in this example, the threshold is set to 1 (change the value if  
necessary). I tried it on the sample MRI stack it worked well except  
on some slices such as n°12... I can't figure out why the doWand  
fails: any idea ?


Fabrice


Le 10 sept. 08 à 17:10, Brandee Winstead a écrit :

> I'm new to ImageJ, having only done simple ROI measurements  
> successfully. Now I am needing to get total intracranial volume from  
> an MRI and I am hoping to find an easier way to do this than  
> manually tracing the brain on each slice. I thought that if I had a  
> tool similar to the wand select tool in Photoshop that I could  
> adjust thresholds and automatically have an ROI of the brain, since  
> everything but the brain is black. Are there any suggestions as how  
> to go about doing this? Thank you.
>
> Brandee Winstead
> Emory University
>


Fabrice Cordelières, PhD

Institut Curie - Section de recherche/ CNRS UMR 146
Plateforme d'Imagerie Cellulaire et Tissulaire
Bâtiment 112 - Centre universitaire
91405 Orsay Cedex
FRANCE

Tél. : +33 1 69 86 31 30
Fax. : +33 1 69 86 17 03

Consultez mes disponibilités sur http://www.google.com/calendar/embed?src=fabrice.cordelieres%40gmail.com