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CSE: Usage

BrainSuite’s Cortical Surface Extraction Sequence can be run via both the program GUI and the command-line as a series of modules. As the GUI calls these same modules, there is no difference in output between using the GUI vs using the command-line. For large batch jobs, it is usually helpful to run a few scans through BrainSuite using the GUI, to see how the parameters change the output and to determine settings that produce the best results. The rest of the scans can then be run using the command-line modules with those custom parameters.

For information on both the GUI and command-line versions of each stage of surface extraction, click the corresponding link in the following list.

Stages of CSE:

  1. Skull Stripping
  2. Skull and Scalp
  3. Nonuniformity Correction
  4. Tissue Classification
  5. Cerebrum Labeling
  6. Identify Inner Cortical Mask
  7. Scrub Mask
  8. Topology Correction
  9. Wisp Removal
  10. Inner Cortical Surface
  11. Pial Surface
  12. Split Hemispheres