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Hi Mark, On Wed, 15 Dec 2004, Mark Jenkinson wrote: > Hi Martin, > > I hadn't forgotten your email, I just needed time to make a schedule > file to do what you wanted. I am very sorry if I have urged you, which certainly didn't mean to. I understand that with FSL gaining more and more popularity you guys are getting exceedingly busy with support. I am aware that my last question was a bit unusual (and few last emails to the list too) and I am glad that you found a time to answer. FSL is a fantastic tool and I count myself lucky that I can use it. > > There are three things you need in the schedule file: > measurecost (which you had) , printparams and setscale commands > > Flirt (at present) requires all the scales to be stepped through > sequentially in order to generate the appropriate reference and input > images internally. Hence you need setscale for 8 then 4 then 2 then 1. > > I'm attaching my schedule file (showcost) which printed the correct cost > function measurement for me. You need to use it in registration > mode, rather than applyxfm mode. For example: > flirt -in epi -ref highres -schedule showcost -init epi2out.mat -omat > /dev/null > where epi2out.mat is the previously generated registration matrix, > and -omat /dev/null is just used to junk the printing out of the final > matrix (which of course is just the same as the -init in this case). > Thanks for the schedule file I will try it later today and let you know how it works. I am sure it will work just fine. > Let me know if you have any trouble with this. > All the best, > Mark Thanks again. Regards, Martin