External Email - Use Caution
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:
[cid:10e2f9c0-f6e6-4f8f-bf38-405a0b106646] 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
Abigail Gantz
PhD Student | Social Memory Lab Tulane Department of Psychology agantz1@tulane.edu
