Re: Regarding calibration in the dicom image

Posted by Thomson Neil (EAST KENT HOSPITALS UNIVERSITY NHS FOUNDATION TRUST) on Nov 25, 2010; 12:05pm
URL: http://imagej.273.s1.nabble.com/Regarding-calibration-in-the-dicom-image-tp3686356p3686357.html

Hi Joannelau

1. I assume you have these in DICOM format. In ImageJ it is simple to import a single DICOM image and the calibration is done for you (the DICOM header contains fields for slope and intercept (usually 1 and -1024)). Since you have a stack this is probably not much good. For importing tomographic studies I use the "Import Dicom sequence" plugin available here: http://www.iftm.de/telemedizin/dcmimex.htm

From what I remember it is not the most straight-forward plugin to install but will nicely import a sequence of DICOM images as a stack. It does not, however, seem to calibrate the gray levels into hounsfield units. To do this choose Analyse->Calibrate. Choose "Straight line" as the function, type -1024 in the left box and 0 in the right box. When you press OK you get a straight-line graph of the calibration and a label with straight line formula y = a + bx. a should be -1024 and b should be 1. If they are then we have a calibration to HU.

To demonstrate the HU calibration, move the cursor around the image and observe the "value" in the IJ status bar. The value is in HU and the gray level appears in brackets.

2. Images typically only contain 256 gray levels when displayed, even though the image may contain values of any number (eg CT from -1024 to ~32k). So gray levels have to be "binned" in an image, just like in a histogram. So the column labelled "level" is the gray level displayed in the image and the "bins" are demonstrated in the second column. The size of the bin is dictated by the min and max pixel levels.

I hope I pitched that at the right level. Enjoy ImageJ ;-)

Neil Thomson,
Nuclear Medicine Physics Section,
Medical Physics,
Kent and Canterbury Hospital,
UK. CT1 3NG
[phone]
________________________________________
From: ImageJ Interest Group [[hidden email]] On Behalf Of joannelau [[hidden email]]
Sent: 23 November 2010 09:33
To: [hidden email]
Subject: Regarding calibration in the dicom image

Hi everyone,

I am a new user in ImageJ and there are two questions that i would like to
ask for advice.

1. i have stacks of bone CT images (more than 100) and would like to know
the HU distribution on particular part of the bone. During the screening, i
put in 5 tubes with different density work like calibration phantom beside
my bone specimen. although the CT machine air calibrated everytime i used, i
need to know whether the readings are consistant. May i know how should i
calibrate with image J before i use the histogram to analyse the HU?

2. In the result of the histogram, i used the "list" and there are three
columns showed (level, bin width and no.). may i know is the level means
level of pixel?

Thanks for your advice. Please forgive me if i ask the wrong question.

JL
--
View this message in context: http://imagej.588099.n2.nabble.com/Regarding-calibration-in-the-dicom-image-tp5765974p5765974.html
Sent from the ImageJ mailing list archive at Nabble.com.

********************************************************************************************************************

This message may contain confidential information. If you are not the intended recipient please inform the
sender that you have received the message in error before deleting it.
Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents:
to do so is strictly prohibited and may be unlawful.

Thank you for your co-operation.

NHSmail is the secure email and directory service available for all NHS staff in England and Scotland
NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSI recipients
NHSmail provides an email address for your career in the NHS and can be accessed anywhere
For more information and to find out how you can switch, visit www.connectingforhealth.nhs.uk/nhsmail

********************************************************************************************************************