Viewing CT scans

[ChrisP]

I'm a new user who is having trouble differentiating brain
structures in CT scans. I am trying to segment the entire brain and a
hemorrhage within it. When I open the scans using ImageJ I have no
trouble differentiating. However, once the scans are opened in ITKSnap
most of the structures disappear in a gray homogenous region. I've
tried messing with the image contrast but that hasn't seemed to help.
Is there some way to make segmenting in these CT scans easier?

[hui Zhang]

Hi Chris,

Is it possible for you to provide an example image like that for us?  If you are willing, please go here

http://sourceforge.net/tracker/?group_id=154886&atid=793595

and file a bug report with your example image.

Gary

[Lo, Warren]

Hi Dr. Zhang,

I'm replying for Chris (we work with each other). We've attached the header file as you've requested below. We're running into another problem. When we save segmentation images after we're done, we can see the files on our desktop, but when we try to open them, we get an Error Loading Image message, "Could not create IO object for file_____ " and "The File doesn't exist."

Has anyone else reported this? We're using

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[Gary Hui Zhang]

Thanks for the header file. You're right. The right contrast is
difficult to determine. We'll look into improving this situation.

As to your 2nd problem, what filename did you give to the segmentation
file? When I use hdr or nii as suffix, the sgmentation can be saved
correctly.

Gary

On Jun 24, 2009, at 3:11 PM, "Lo, Warren" <Warr...@nationwidechildrens.org

> <winmail.dat>

[Lo, Warren]

We found that when the file is stored on a desktop, the program can't
find it. We have to store it in the c:\ without a subdirectory. Would
you consider this a glitch or just the way it is.

-----Original Message-----
From: itksna...@googlegroups.com
[mailto:itksna...@googlegroups.com] On Behalf Of Gary Hui Zhang
Sent: Wednesday, June 24, 2009 6:00 PM
To: itksna...@googlegroups.com
Subject: [itksnap-users:438] Re: Viewing CT scans


Thanks for the header file. You're right. The right contrast is
difficult to determine. We'll look into improving this situation.

As to your 2nd problem, what filename did you give to the segmentation
file? When I use hdr or nii as suffix, the sgmentation can be saved
correctly.

Gary

[Hui Zhang]

It seems like some preprocessing steps of your CT scans introduced
negative intensity values. Do those values make sense? Their
existence makes the image intensity range unusually large, which makes
finding the right contrast for your intensity range of interest
(between 20 and 200) difficult to adjust (although you can). If it is
part of the data, you can use c3d to remove those values by
thresholding. c3d is available for download from the itksnap homepage.