Labelmap warping for mesh creation

Workflow example for warping & meshing arbitrary geometry, including

• example surface mesh
• image creation from surface mesh
• creation of example displacement field
• warping by displacement field using ANTs
• meshing of final warped image

Functionality depends on

• python vtk
• simpleITK
• ANTs installation
• installation of MeshTool

All dependencies are included in this docker image. Functionality has been tested with singularity image created from above docker, using the ipython3 executable.

Get & Use Singularity Image with dependencies

A singularity image containing all dependencies is available at singularity hub.

It can be downloaded from the shell using:

singularity pull shub://danielabler/dockerfiles:libadjoint-2017-2_ants_meshtool

To start an interactive session:

singularity shell -e <path_to_singularity_image>

To leave an interactive singularity session:

exit

Usage Example

• Go to folder where git repository was downloaded .

• start singularity session

  singularity shell -e <path_to_singularity_image>

• adapt script in analysis folder, eg. analysis/pptT_prePTA.py, for one of three steps:

  1. Downsample original OCT image & produce Matlab output:
     • From this output we compute displacement.
  2. Resize original OCT image based on displacement field: This requires the disps.mat file to be present in the respective folder.
     • Uses coarse displacement field to identify approximate dimensions of image after warping.
     • Creates image and matlab output for resized image
  3. Warp image based on displacement field: This requires disps.mat as well as centerlines OCTCenterLine.mat and XrayCenterLine.mat to be present in respective folder.
     • create high-res warped image using high-res displacement field

  These steps are outlined in any of the example files in <repository/analysis/*.py> . The procedure can be followed by un/commenting the respective lines of code for each step.

• run script from analysis folder, e.g.

  python3 analysis/pptT_prePTA.py

  When running the code with the singularity image mentioned above, make sure to use python3, not python.

• leave an interactive singularity session:

  exit