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Hi Mark I started playing with the schedule files in the way you described to me. I tried to allow for only one degree of freedom e.g. scaling in the y-direction. However, the resulting omat was: 1 0 0 0 0 0.952213 0 3.0586 0 0 1 0 0 0 0 1 In my understanding of the matrix described in technical report about FLIRT, scaling as well as translation in y was performed in this case. I guess I was not able to modify the schedule file appropriately which is attatched it to this email. I hope, you can help me! Thanks, Markus Mark Jenkinson wrote: >Dear Markus, > >I'm happy for people to try out their own schedule files. >The documentation is in $FSLDIR/doc/flirt/schedule.html > >It doesn't really cover the paramsubset option (as it is >the newest) but you have probably worked it out anyway. >Basically the first number, N, represents the number of degrees >of freedom you want, and then the other numbers are an Nx12 >matrix which specificies how these new degrees of freedom >relate to the fixed 12 DOF. Typically you just put a one >in the appropriate slot, although things like global scaling >involve several of the scaling parameters being set by one >of the "new" degrees of freedom. > >The order of the fixed 12 DOF are: >rotation x, y, z, translation x, y, z, scaling x, y, z, >skew xy, xz, yz. > >As for the optimise command - you shouldn't need to play with >that too much. This is documented in the schedule.html file >and the numbers simply represent offsets from the given point. >Just use the schedule files I sent, but modify the paramsubset >lines. That should give you what you want. > >Also note that the schedule files I sent do not include an >initial search phase, since this cannot, at present, be >adapted to different degrees of freedom. Hence the optimisation >is essentially local (although multi-scale) - much like that done >in other packages. You can add perturbations easily enough >though, like those in the standard FLIRT schedule, contained in the >documentation. > >Best of luck, > Mark > > >