Joel Jaramillo Biomedical engineering undergraduate

This is my brain's cortical surface, reconstructed from a research MRI with FreeSurfer 7.4.1. It's an anatomical visualization, not a medical image or a diagnosis. The backdrop can show a live 3D model of the cortex, slices of the T1 MRI (brain only, resampled to 1.5 mm), or a still image. The Explore page adds deep structures and a movable MRI slice plane. Every cortical region is also listed as text on the About page.

Notes / how-to ·

Running FreeSurfer's TensorFlow tools on Apple silicon

The x86 build of FreeSurfer 7.4.1 runs under Rosetta, but its TensorFlow-based tools needed AVX exposed first.

FreeSurfer 7.4.1 ships an x86 build, which runs on an Apple-silicon Mac under Rosetta. Most of recon-all worked as is. The TensorFlow-based tools, such as SynthSeg and SynthStrip, did not run until I exposed AVX to Rosetta:

export ROSETTA_ADVERTISE_AVX=1