Ok thanks. From the BrainSuite GUI, goto Cortex->Select SVReg directory.
Then from the dialog box, goto BrainSuite installation folder and select directory named svreg.
After this, try running the whole sequence for your subject data and it should work.
The next error is something else. It is due to some errors in surface extraction. Please make sure that the cortical surface you get look reasonable, as shown on brainsuite website.