We noticed AutoEACSF's default skullstrips were bad, so we'd like to provide a brainmask on the command line.  (We don't have T2 images, only T1, so that may be a factor).     Unfortunately, it looks like default skullstripping is occurring anyway, even when we provide a brainmask.     Any idea what I'm doing wrong?


I'm running: 

(Config file is attached.)  


In the Output/SkullStripping  directory, I get all same files with names taken from the skullstripping atlases (IBIS, Colin).  
I also tried setting the "skullStrippingAtlasesDirectory" to "" in the parameters file, but that produced its own error. 

Any idea what I'm doing wrong?

You need to turn off the skull stripping in the parameter file. Auto_EACSF allows for automatic + user specified skull stripping and will thus run the skull stripping if a brain mask is provided (unless the skull stripping step is turned off in the parameters).

Martin