Hi there, 
I am trying to generate some tumor-free FLAIR images using TumorSim.
(The goal is to generate some ground truth healthy MRI data to compare with the corresponding
images with tumors.)  Look like the program expects a "correct" tumor seed to work
(I try to cheat the program with an empty seed, but without luck. It gave the warning about the
bad seed and crashed after running for a little while ). 

I am wondering is there a simple way that I could skip the step of "planting" tumors into the image?
Thanks a lot!

-best,
Xiaoxiao

Hey,

Maybe you can have a look at Marcel Prastawa's answer from January 13th, 2014:
http://www.nitrc.org/forum/forum.php?thread_id=4249&forum_id=2386
In this post, it is suggested to create a 'healthy' MR-image by making a linear combination of the input probabilities and the input textures that you use for generating the tumor image.

Good luck,

Tom

Hi Tom, 
Thanks for the quick reply.
Did you try the recipe yourself using TumorSim? or some other programs you wrote?

In order to match up with the tumor-containing images (generated from the default parameters provided in the xml file), I need to know the tissue probabilities that were used? Where I should look for those numbers?
Thank you.

-Best,
Xiaoxiao

Hey Xiaoxiao,

sorry for my late reply!
The tissue probabilities are part of the input that is provided to the simulator, i.e. p_csf.mha, p_white.mha, p_grey, ...
You need to multiply each one of these probabilities with the corresponding texture image and add the results of the multiplications.
Multiplication and addition of images can easily be done with any program where you have straight access to the image values, e.g. Matlab.

Greetings,

Tom