Dear FSL users,
I have normalized a fractional anisotropy map, called "FA", on the FA atlas
"JHU-ICBM-FA-2mm". I used a double transformation obtained applying first an
affine transformation (flirt: input FA --> output FA_affine_trasformed),
followed by a non-linear one (fnirt: input FA_affine_trasformed --> output
FA_warped).
Now, I'm interested in computing the jacobian of the total transformation,
excluding the roto-translational component of the affine transformation, to
obtain a quantitative parameter of deformation (shrinking, enlargement) that
each voxel of the original FA map underwent to match the FA atlas.
I used the following FSL commands:
flirt -ref JHU-ICBM-FA-2mm -in FA -out FA_affine_trasformed -dof 12 -omat
affine.mat
I used the following 3 instructions to compute the roto-translation (6 dof)
component of affine.mat, that I called D6.mat, and D12.mat that represent
the affine transformations without the D6.mat component:
avscale affine.mat | sed -n 2,5\p > D6.mat
convert_xfm -omat invD6.mat -inverse D6.mat
convert_xfm -omat D12.mat -concat invD6.mat affine.mat
Then I ran the command:
fnirt --ref=JHU-ICBM-FA-2mm --in=FA_affine_trasformed --config=conf.cnf
--cout=nonLinear
Then, to compute the "merged" transformation "D12_nonLinear", I used this
instruction:
convertwarp --ref=nonLinear --warp1=nonLinear --premat=D12.mat
--out=D12_nonLinear --relout
After that, to obtain the jacobian of the "total" transformation:
fnirtfileutils --in=D12_nonLinear --ref=JHU-ICBM-FA-2mm
--jac=jac_D12_nonLinear --withaff
I'd like to know if it makes sense to compute the jacobian of this double
transformation (D12+nonLinear), and if so, if this was the right way to proceed.
Thanks for the help
Giovanni
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