Freesurfer

Freesurfer is a tool that algorithmically segments structural T1 images.

For an automated script to run Freesurfer recon-all -all on your BIDS formatted data, see: https://github.com/ryn-thorn/Image_Analysis_Scripts/blob/main/freesurfer-reconall.sh

LogoImage_Analysis_Scripts/freesurfer-reconall.sh at main · ryn-thorn/Image_Analysis_ScriptsGitHub

The Freesurfer user guide is extensive and includes installation instructions, command documentation, and tutortials.

Whole brain Freesurfer segmentation can be done with the following command:

recon-all -all -i [path]/T1.nii -s subj1

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