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