I've only done this once and I did it with the assistance of a sysadmin. The sysadmin set up FreeTDS and then created a sort of handle, basically an ODBC data source. Once he had that created, I use this command:
$connect = odbc_connect("data_source_name", "my_userid", "my_password");
Sorry, I wish I could tell you more than that. The first thing I'd check is to see if the data source was created correctly. (I'm sure you have FreeTDS installed but that doesn't mean that you created the data source and gave it a name).
For troubleshooting purposes, just to check to see if FreeTDS and your data source are working correctly, you can use this command from the Linux command line:
isql -v data_source_name userid 'password'
That will bring you to a MSSQL command line just as if you'd typed "mysql -u username -p databasename" on the command line.
If you can't use the isql command above, then certainly nothing you do from PHP is going to work either.