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Introduction

The output file names used in Pydpiper are similar to the ones used in our original version of MICe-build-model. Nevertheless, there are some differences. Key ones are listed here.

Jacobian Determinants

We use the terms "absolute jacobians" and "relative jacobians" to describe the final determinants calculated from the deformation fields. For users of our previous version of MICe-build-model, absolute jacobians correspond to what we previously called scaled jacobians, and relative jacobians correspond to what we previously called jacobians.

Absolute Jacobians: Jacobian determinant that measures the true volumetric difference at each voxel between input and target. These differences include uniform scales and shears as well as non-linear deformations.

Relative Jacobians: Jacobian determinant that measures the volume differences at each voxel between input and target, but after removing scaling and shearing differences. That is, once the overall differences in brain volume have been accounted for (i.e. normalized), we can look at the remaining differences between input and target.

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