I have just posted a similar question.
Have you had any resolution of your question?
I’m wondering if we need to download the “BrainSuite GUI and command line tools [ 5.5 MB]” and build the command-line tools ourselves. Either that, or someone forgot to package the command line tools in the latest release!
-Tod
The MAC and Linux versions of BrainSuite17a have all the binaries included. Would you be able to use them by any chance? In the meantime we will check about the Windows build.
I did it with the gui now. Took me some time but you know instantly if it worked and can adjust the mask. Would still be nice to have the files in the new version. Thanks!