Elastic Surface Warping (Cortical Pattern Matching)

Written by Owen Phillips. Email Dr. Katherine Narr if you have any questions. For more information, see the protocols page.

Dicom to analyze.img
Warped mesh


After Sulcal Lines are combined to one file, the data is ready to be run through the warping pipeline. The purpose of the warping pipeline is to use the sulcal linemarks to drive homology between they subjects surfaces. You can find a more comprehensive overview here: http://www.loni.ucla.edu/twiki/bin/view/MAST/ElasticSurfaceWarpProtocolDataAssumptions?skin=plain. To run the pipeline you will need to the LONI Pipeline as well as the ElasticSurfaceWarp.pipe (this can be downloaded by right clicking).

It is important to decide the kind of analysis you want to do before warping. Unless you are doing an asymmetry analysis, the left and right hemispheres should be run as separate pipelines. This will preserve their original left and right orientation. If they are run together, both hemispheres will be flipped into the left hemisphere space.

Set the inputs:

  1. Curves - these are the sulcal lines that were combined into one file.
  2. Surface Meshes - The hemisphere surfaces.

Set the ouputs:

  1. Data Directories - these are the individual output directories created for each subject. They will contain all of the warping files that were created as the pipeline runs.
  2. Warped Meshes - these are the warped output surfaces (.m).
  3. Atlas - the average surface. It's a good idea to check this surface to make sure your data was run correctly.