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Mark, Thanks for the clarification. In FSL 4.1.5, -P or --Prior is able to run by itself without the -a option. Maybe an error message would be helpful to avoid the confusion. Gordon On 06/26/2010 03:49 AM, Mark Jenkinson wrote: > Hi, > > This isn't quite right. > The -P and --Prior option are the same option. > In both cases they use the prior supplied with > FSL, and they *must* be used with the -a option > to specify a transformation to standard space. > > The -A option allows you to specify your own > prior images instead of using the ones supplied > with FSL. If these are in standard space then > you still need to use the -a option. > > I hope this is clear. > All the best, > Mark > > > On 26 Jun 2010, at 08:39, Junqian Gordon Xu wrote: > >> I want to make sure I understand the fast prior probability map >> switchs correctly: >> >> fast -P needs a user supplied prior probability map while --Prior uses >> the probability map supplied by FSL in the standard space (I assume). >> If that's the case, I'm a little surprised that --Prior does not >> require <standard2input.mat> as in the case of -a. Does that mean >> ---Prior performs a FLIRT transform to standard space under the hood >> by itself or am I misinterpreting the similarity between --Prior and >> -a? >> >> Thanks >> Gordon >> >