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Hi, That's odd. The exact same schedule file behaves correctly with some test data of mine. Can you send me (off list) the image files you are working with so I can try exactly the same thing as you? All the best, Mark > On 28 Jul 2017, at 22:15, Jack Grinband <[log in to unmask]> wrote: > > Hi Mark, > Getting back to this 2D registration problem... > >> Can you try running fslcpgeom on the input image, to copy the info from the reference image, and then see if the results are different? > > Same result. > >> It shouldn't revert to the default schedule, but if you want to be sure, just turn on the verbose output with -v and you'll see exactly what schedule lines it is using. > > So here are my commands: > > fslcpgeop ref in > flirt -in in -ref ref -out out -cost mutualinfo -2D -schedule sch2D_2dof_Xtranslation_Xscale -refweight ref -v > > It is set to use only X translation and X scale (i.e. 0 0 0 1 0 0 0 0 0 0 0 0 and 0 0 0 0 0 0 1 0 0 0 0 0), but the final matrix (see verbose output below) has values that indicate rotation (i.e. -0.153358 and 0.156434) in addition to translation and scale. Any idea why rotation is a free parameter here? > thanks! > > jack > > > Init Matrix = > 1.000000 0.000000 0.000000 0.000000 > 0.000000 1.000000 0.000000 0.000000 > 0.000000 0.000000 1.000000 0.000000 > 0.000000 0.000000 0.000000 1.000000 > >>> # 8mm scale >>> setscale 8 >>> setoption smoothing 8 >>> setoption paramsubset 2 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 >>> clear U >>> clear UA >>> setrow UA 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1 >>> optimise 12 UA:1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 rel 4 >>> >>> # 4mm scale >>> setscale 4 >>> setoption smoothing 4 >>> setoption paramsubset 2 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 >>> clear UB >>> clear UL >>> clear UM >>> # remeasure costs at this scale >>> clear U >>> measurecost 12 UA 0 0 0 0 0 0 rel >>> sort U >>> copy U UL >>> # optimise best 3 candidates >>> clear U >>> optimise 12 UL:1-3 0.0 0.0 0.0 0.0 0.0 0.0 0.0 rel 4 >>> # also try the identity transform as a starting point at this resolution >>> clear UQ >>> setrow UQ 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1 >>> optimise 7 UQ 0.0 0.0 0.0 0.0 0.0 0.0 0.0 rel 4 >>> copy U UM >>> # select best 4 optimised solutions and try perturbations of these >>> clear U >>> copy UM:1-4 U >>> optimise 12 UM:1-4 0.0 0.0 1.0 0.0 0.0 0.0 0.0 rel 4 >>> optimise 12 UM:1-4 0.0 0.0 -1.0 0.0 0.0 0.0 0.0 rel 4 >>> sort U >>> clear UB >>> copy U UB >>> >>> # 2mm scale >>> setscale 2 >>> setoption smoothing 2 >>> setoption paramsubset 2 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 >>> clear U >>> clear UC >>> clear UD >>> clear UE >>> clear UF >>> # remeasure costs at this scale >>> measurecost 12 UB 0 0 0 0 0 0 rel >>> sort U >>> copy U UC >>> clear U >>> optimise 12 UC:1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 rel 4 >>> copy U UD >>> setoption boundguess 1 >>> if MAXDOF > 7 >>> clear U >>> if MAXDOF > 7 >>> optimise 9 UD:1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 rel 1 >>> copy U UE >>> if MAXDOF > 9 >>> clear U >>> if MAXDOF > 9 >>> optimise 12 UE:1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 rel 2 >>> sort U >>> copy U UF >>> >>> # 1mm scale >>> setscale 1 >>> setoption smoothing 1 >>> setoption boundguess 1 >>> setoption paramsubset 2 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 >>> clear U >>> # also try the identity transform as a starting point at this resolution >>> setrow UF 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1 >>> optimise 12 UF:1-2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 rel 1 >>> sort U >>> > > Final result: > 0.968262 0.156434 0.000000 -12.192340 > -0.153358 0.987688 0.000000 20.952641 > 0.000000 0.000000 1.000000 0.000000 > 0.000000 0.000000 0.000000 1.000000