[MINC-users] more minctracc questions!

[mojdeh.zamyadi@utoronto.ca]

Hi Andrew,

Thanks a lot for the hints! I just have some more questions:

I probably don't know that much about the Simplex optimization method!  
But, my initial understanding was that these weights scale the axis in  
the search space (so that the search space looks more like concentric  
circles rather than ellipses that are elongated in one direction! ...  
because in case of ellipses the algorithm may never find the min/max  
or may converge very slowly), does what I say make any sense?!! But  
after doing some experiments with different param values, I thought I  
have to set the rotation weight higher and the translation weight much  
lower in case I have embryos in completely different orientations (in  
this way the algorithm searches for a transformation with more  
rotation and not that much translation!!) again! does it make ANY  
sense?! ... So, for example one set of params that I used and got some  
result was :
-w_rotation 0.5 0.5 0.5  -w_translation 0.01 0.01 0.01 !!!!!
(I am saying SOME result, bc/ in some cases  all I was getting after  
finding the tform by minctracc and resampling the source volume, was  
either a zero volume, half of an embryo or one that was in totally  
different orientation with the target volume! ... although not  
properly registered using these params either, at least the source and  
target embryos look to be in same coordinate sys and in almost same  
orientation!)

Also, do you know if the optimization method used optimized one  
parameter (tx, ty, tz, rx, ry, rz) at a time?

I really appreciate any help and advice :)
Thanks again,

Mojdeh