Hi,
I'm trying to set up a rat brain template for analysis using the freesurfer tool. Before setting up the complete template I have to process a representable rat dataset with the available human template.
With some much appreciated help I managed to get to the skull strip procedure . But the application ceases its operations at this point with the message:
"White matter intensity 0 is lower than CSF intensity 21. Please examine input images. Will terminate ..."
Evaluation using tkmedit does not show something a proper segmentation of the rat brain, however it does show a proper outline of the brain. Since a rat brain and a human brain are very dissimilar I'm not surprised by the fact that the segmentation is incorrect. However the brain is outlined ok. It is also known that the WM intensity values in the rat dataset is somewhat reduced to the GM structure. Which is not expected by the freesurfer tool, which expects WM to be highest intensity value.
My question is: is there a way of circumventing this problem. For instance by defining the mean intensity values of each tissue class or..
Hope someone can help me?
Thanks!
Mark