loading Head CT's in itk-snap

[Alana Feiler]

Hi,

Whenever I try to load Head CT's (from raw dicom files) in itk-snap the contrast is off, and I find myself having to futz with the contrast for a while before I am able to to clearly see brain tissue, ventricles, and the hematomas that I am looking for.  Is there anyway to preset itk-snap to avoid this problem of the contrast being terribly off?  I don't tend to encounter the same problem when I analyze T2's. 

Thanks!
Alana

--
Alana Feiler
Research Technician
Department of Neurology
Children's Hospital of Philadelphia
office: 267.426.7332
mobile: 201-491-6381
fax: 267.426.5166
fei...@sas.upenn.edu

[Paul Yushkevich]

Alana,

In the latest version on itksnap.org, there is an Auto button on the
intensity adjustment window. Try using that to see if it sets the
contrast properly.

Paul.

--
Paul A. Yushkevich, Ph.D.
Research Assistant Professor
Penn Image Computing and Science Laboratory
Department of Radiology
University of Pennsylvania

[Antonios Konstantinos Thanellas]

Dear Paul, 

I am using  v3.8.0-alpha (git commit 6fa07ca9a90e32b24e257eba093fc454e4293c1c) and I still encounter the same issue that Alana mentioned in the past. Even if through the preferences I click for the "Automatically adjust contrast when loading images", the head CT image is loaded with a very wide contrast range that does not correspond to neither the brain window nor the bone window. So for every new head CT image loaded quite some time is spent on adjusting manually the window and level of the contrast. If there would be an option where the user can preset the window and level of itksnap it would be very helpful and save a lot of time. 

Even better, if the user could save such different presets with itksnap ( i.e headCT_bone, headCT_brain) and pick later whichever preset fits for his study images. More generally presets that could also include other options (i.e showing an axial plane only for the brain window of a head CT)

Would you consider such an option in the upcoming releases?

Thank you

Antonios Konstantinos