For the registration of embryo data, we use slightly different settings 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 mincANTS, and so we use minctracc. To allow for larger deformations (embryo data 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 settings for the elastic grid for minctracc are set more loosely.
For input data at a resolution of 15micron, the following is a sample incantation of the MICe-build-model.pl script :
- 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 face the same direction. If this is not the case,the -lsq6-identity flag should be changed
where the file embryo_smasher.pl contains: