Dictionary: alignment & resampling

These commands take a known transformation, usually determined by jip-align, and register data to the new space.

register <stack list>

Performs registration from one space to another. Typically, one would first read the output of jip-align to define registration variables:

    read align.com

    read original.nii


    write new-space.nii


However, it’s also possible to simply enter registration variables directly into jip. To simply change the image resolution:

    read original.nii

    set registration-matrix 80 80 60



All registration uses either a Lanczos or a Gaussian kernel, controlled by the variable “interpolation-kernel”.

inverse-register <stack list>

Perform the inverse operation relative to the example above (registered space -> original space) using the same align.com file as the forward path.

register-histology <stack list>

This command is analogous to the registration above but uses different input files (not distributed).

down-sample <volume list>

This uses the variable “target-matrix” to define the desired resolution. Data are resampled using a Gaussian convolution kernel.

Joseph B. Mandeville, Athinoula A. Martinos Center for Biomedical Imaging at MGH/MIT/Harvard