ROIs and analyze

[Douglas Benn-2]

Hi everybody,

I would be grateful for some help with regard to ROIs and Analyze. I have written the following code:

run("Image Sequence...", "open=[C:\\CBCT research\\04\\ID001122032.dcm] number=513 starting=1 increment=1 scale=100 file=[] or=[] sort");
setAutoThreshold("Default");
//run("Threshold...");
setAutoThreshold("Default dark");
run("Convert to Mask", "calculate black");
run("Outline", "stack");
//run("Image Sequence...", "open=[C:\\CBCT research\\04\\ID001122032.dcm] number=513 starting=1 increment=1 scale=100 file=[] or=[] sort");
run("Set Measurements...", "area mean centroid center perimeter bounding shape area_fraction display redirect=None decimal=3");
run("Analyze Particles...", "size=10-Infinity pixel circularity=0.00-1.00 show=Outlines display clear record add stack");

This successfully outlines my ROIs and extracts measurements to the Results table. However, I would like to measure the Mean Gray Value, Centroid and Center of Mass. Currently my Mean Gray value is 255 and the Centroid x,y coords = the Center of Mass. I assume this is because the measurements are being made from my outline stack which has only black and white pixels. How do I select a ROI which contains gray values to measure Mean Gray Value, Centroid and Center of Mass?

Thank you.

Douglas

Dr Douglas K Benn, BDS,DDS, M.Phil., Ph.D., Dipl. Dental Radiology (Royal College of Radiologists, England).
Professor and Director of Oral & Maxillofacial Radiology
Dept of General Dentistry
Creighton University Dental School
2802 Webster St, Boyne 210
Omaha
Nebraska 68178

Tel: [phone]
Fax: [phone]

[Michael Schmid]

Hi Douglas,

you can use 'redirect to' in 'Set Measurements' to do the measurements on
an image different from the one used to define the ROI(s).

Michael
________________________________________________________________

On Sat, April 17, 2010 17:21, Benn, Douglas K. wrote:

> Hi everybody,
>
> I would be grateful for some help with regard to ROIs and Analyze. I have
> written the following code:
>
> run("Image Sequence...", "open=[C:\\CBCT research\\04\\ID001122032.dcm]
> number=513 starting=1 increment=1 scale=100 file=[] or=[] sort");
> setAutoThreshold("Default");
> //run("Threshold...");
> setAutoThreshold("Default dark");
> run("Convert to Mask", "calculate black");
> run("Outline", "stack");
> //run("Image Sequence...", "open=[C:\\CBCT research\\04\\ID001122032.dcm]
> number=513 starting=1 increment=1 scale=100 file=[] or=[] sort");
> run("Set Measurements...", "area mean centroid center perimeter bounding
> shape area_fraction display redirect=None decimal=3");
> run("Analyze Particles...", "size=10-Infinity pixel circularity=0.00-1.00
> show=Outlines display clear record add stack");
>
> This successfully outlines my ROIs and extracts measurements to the
> Results table. However, I would like to measure the Mean Gray Value,
> Centroid and Center of Mass. Currently my Mean Gray value is 255 and the
> Centroid x,y coords = the Center of Mass. I assume this is because the
> measurements are being made from my outline stack which has only black and
> white pixels. How do I select a ROI which contains gray values to measure
> Mean Gray Value, Centroid and Center of Mass?
>
> Thank you.
>
> Douglas
>
> Dr Douglas K Benn, BDS,DDS, M.Phil., Ph.D., Dipl. Dental Radiology (Royal
> College of Radiologists, England).
> Professor and Director of Oral & Maxillofacial Radiology
> Dept of General Dentistry
> Creighton University Dental School
> 2802 Webster St, Boyne 210
> Omaha
> Nebraska 68178
>
> Tel: [phone]
> Fax: [phone]
>