Hi everyone,
I’m upgrading from FreeSurfer v7.4.1 to v8.0.0 and I’m a bit lost on how SynthMorph is now supposed to be invoked inside the recon-all pipeline. In v7.4.1 I would:
bash
after recon-all, manually apply the warp to get a MNI152‐aligned volume
mri_synthmorph apply
$SUBJECTS_DIR/subj001/mri/transforms/synthmorph.mgz
$SUBJECTS_DIR/subj001/mri/T1.mgz
$SUBJECTS_DIR/subj001/mri/T1_mni152.nii.gz
—but in the v8.0.0 release notes it says:
“Now uses SynthSeg, SynthStrip, and SynthMorph (deep learning algorithms)… Technically, SynthMorph is not needed for recon-all to run, but the nonlinear registration can be used in multimodal analysis to map to the MNI152.”
and:
“you can just add -synthmorph to recon-all without extra steps.”
Could someone help clarify:
• How is SynthMorph integrated into recon-all in 8.0.0?
• Which flags or environment variables actually enable it?
• Does recon-all ever automatically output a MNI152‐aligned volume, or must I still do a manual apply step?
Thanks in advance!
Tags: freesurfer recon-all synthmorph mni152 deep-learning