Hello, 

I’m just contacting to ask for advice with the use of recon-all on a participant that has an abnormally structured brain, specifically a compressed Anterior temporal lobe. Recon-all finished without error, but didn’t completely encapsulate the anatomy properly. 

I ran recon-all using this code:

recon-all -s omni07 -i /mnt/sml_share/OMNI/derivatives/fpp/sub-omni0
7/anat/sub-omni07_space-individual_res-1_desc-preproc_Tlw.nii.gz -all -deface -T2 /mnt/sml.
share/OMNI/derivatives/fpp/sub-omni07/anat/sub-omni07_space-individual_res-1_desc-preproc_7
2w.nii.gz -T2pial

The final recon-all brain mask.mgz file came out like this: 

Questions:

1. Are there flags to or steps to manually adjust surface place for such cases?
2. Would you recommend disabling certain steps/running in stages to improve the outcome?

Thank you for your help, and let me know if there is anything else I can provide to clarify the issue