Hi Mark,
So, to simplify things, I created a schedule with only X translation (see below). The resulting matrix was:
Final result:
0.987688 0.156434 0.000000 -67.100123
-0.156434 0.987688 0.000000 12.894380
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 0.000000 1.000000
You can see the rotation in the output files (https://www.dropbox.com/sh/dlffiglvyd1jwgh/AABFpH1Gwe3W2aj4PRxfbdSTa?dl=0). Btw, I created an arbitrary qform and sform for my two files, though I made them the same for the input and reference images. Could that cause problems for FLIRT?
thanks!
jack
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# 8mm scale
setscale 8
setoption smoothing 8
setoption paramsubset 1 0 0 0 1 0 0 0 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 1 0 0 0 1 0 0 0 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 1 0 0 0 1 0 0 0 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 1 0 0 0 1 0 0 0 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
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