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Hi, You should be able to use a command like: flirt -in inputvol -ref refvol -init mymatrix -schedule measurecost1.sch -cost normcorr If you don't have a matrix relating the images, then you can leave out the "-init mymatrix" part as it will go with the identity matrix as the default. As for the schedule files, they control how the optimisation works, and can also do things like print out the cost values. All the best, Mark On 10 Nov 2008, at 17:02, Siamak Yousefi wrote: > Hi Mark, > > Thank you very much for your previous nice comments. I applied -flirt > command with -measurecost1.sch that you sent me. I got 1.000000 as the > result of registration cost function. I think it is not true. > However, I didn't use > the -init matrix option. I think I should generate a unit matrix for > this reason > and also apply it to get the correct result. Am I right? Besides, > could you > please say me what the schedule files exactly do? > > Best, > Siamak >