Re: [Freesurfer] Spiky Brains

ase_participant" ]; then # Run command $freesurfer_bin/recon-all \ -long "${cross_file}" "${base_file}" \ -sd "${output_dir}" \ -all fi done done Best wishes, Marieke & Mano

Re: [Freesurfer] Spiky Brains

This sometimes happens with noisy data. The difference in SNR between those two scans is a factor of 2. What is your recon-all command line? Can you send pics of the brain image with the surface overlaid on a slice with one of the spikes? What does the white surface look like in those regions?