Freesurfer

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Usage

It's important to go through the Freesurfer documentation to first get an understanding of the recon-all command.

Freesurfer group cortical reconstructions is automated with the gofs.py script.

gofs.py assumptions

  • The command assumes subject T1 DICOMs are stored inside a subfolder, by default named as _orig_.
  • Each subject is stored under its own folder, where its folder name is the subject label.
  • Processed subjects are then located outside of _orig_, with the same label as the folder name.

Therefore if the project folder is named myproject, then it expect an initial folder structure of

  • myproject
    • _orig_
      • S1
      • S2

Where S1 and S2 are the subjects with their respective DICOMs inside. Once processed, the folder will look like:

  • my project
    • S1
    • S2
    • _orig_
      • S1
      • S2

parallel processing

By default, the command attempt to process and monitor processing using 8 threads. It's possible to use more, check the command flags. If the computer does not have 8 cores, or 4 core with Hyperthreading turned on, then it'll kill the computer.