For the registration of embryo data, we use slightly different s= ettings for MICe-build-model compared to the registration of brain data. So= far we have not been able to determine a workable set of parameters for mi= ncANTS, and so we use minctracc. To allow for larger deformations (embryo d= ata tends to be more dissimilar) a non-linear stage with a larger blurring = kernel is added at the start of the non-linear stage, and the stiffness set= tings for the elastic grid for minctracc are set more loosely.

For input data at a resolution of 15micron, the following is a sample in= cantation of the MICe-build-model.pl script :

Assumptions:

- the embryo data is either OPT or CT (because we use the -no-nuc option,= meaning that we do not do non-uniformity correction caused by the MR)
- the data is already roughly aligned, i.e., they overlap in space and fa= ce the same direction. If this is not the case,the -lsq6-identity flag shou= ld be changed

=20

> MI= Ce-build-model.pl -pipeline-name some_embryo_pipeline -init-model /some/initial/model/prefix -no-inormalize -no-resample-atlas -no-registration-accuracy -no-nuc -lsq6-initial-step 0.1 -lsq6-identity -no-lsq6-large-rotations -lsq6-kernels 1.0_blur,0.8_blur,0.5_blur=20 -lsq12 -lsq12-initial-step 0.1 -lsq12-kernels 2.0_blur,1.0_blur -lsq12-max-pairs 0 -nlin -nlin-stats -nlin-registration-method minctracc -nlin-protocol embryo_smasher.pl -stiffness 0.5=20 -similarity 0.5=20 -weight 0.3 [ input embryo MINC files ]=20

where the file embryo_smasher.pl contains:

=20

> cat embryo_smasher.pl ( { memory =3D> 4, generation =3D> 1, kernel =3D> 0.6, iterations =3D> 40, simplex =3D> 3, ncpus =3D> 1, use_gradient =3D> 0, optimization =3D> "-use_simplex", step =3D> 0.3,=20 }, { memory =3D> 4, generation =3D> 2, kernel =3D> 0.4, iterations =3D> 40, simplex =3D> 3, ncpus =3D> 1, use_gradient =3D> 0, optimization =3D> "-use_simplex", step =3D> 0.3, }, { memory =3D> 4, generation =3D> 3, kernel =3D> 0.2, iterations =3D> 20, simplex =3D> 3, ncpus =3D> 1, use_gradient =3D> 0, optimization =3D> "-use_simplex", step =3D> 0.2, }, { memory =3D> 4, generation =3D> 4, kernel =3D> 0.15, iterations =3D> 20, simplex =3D> 3, ncpus =3D> 1, use_gradient =3D> 0, optimization =3D> "-use_simplex", step =3D> 0.15, }, { memory =3D> 4, generation =3D> 5, kernel =3D> 0.09, iterations =3D> 10, simplex =3D> 3, ncpus =3D> 1, use_gradient =3D> 0, optimization =3D> "-use_simplex", step =3D> 0.09, }, { memory =3D> 4, generation =3D> 6, kernel =3D> 0.05, iterations =3D> 10, simplex =3D> 3, ncpus =3D> 1, use_gradient =3D> 0, optimization =3D> "-use_simplex", step =3D> 0.05, }, { memory =3D> 4, generation =3D> 7, kernel =3D> 0.03, iterations =3D> 10, simplex =3D> 3, ncpus =3D> 1, use_gradient =3D> 0, optimization =3D> "-use_simplex", step =3D> 0.03, }, =20 =20 );=20