How do i create spatial priors of the brain using matlab

Hi All

this is my first question on here.

I am undertaking a project to segment 2d brain images into GM, WM and CSF using level sets, i know this is available in spm8 but i found this method interesting and wanted to create some code for it.

my problem is this: how do i strip the skull? how do i create spatial priors for GM, WM and CSF from the 30 images i have.

i have 10 axial, 10 coronal and 10 sagittal. i want 2d priors for each of them

thanks in advance for all the help!

[Paul]

The images are in .png format and have the following dimensions:

Type of scan Rows Columns

Axial 358 291

Coronal 457 640

Sagittal 457 640

Answer 1

[Image Analyst]

To strip the skull you threshold it so that you get the skull separated - not connected to the brain. Then you label it with bwlabel() and then use ismember() to isolate the region with label 1, which should be the skull assuming it's the outermost object (no letters or annotation present in the image). Or you can use ismember to extract out everything with labels 2 and up to get everything except the skull.

[Paul]

Thanks Image Analyst.

I will work on that.

My next question is how would i extract the separate types of tissue to create my own set of spatial priors?

would it be a similar process?

thanks

[Image Analyst]

You can search VisionBib to find algorithms. If you can find the tissue based solely on gray level, then see my File Exchange. http://www.mathworks.com/matlabcentral/fileexchange/?term=authorid%3A31862

[Paul]

thanks for everything. I gave up on the spatial priors as it was consuming too much of my time and the actual active contour implementation needs to be done. i will probably come back to it one day trying to figure it out!