The lesion is too severe and the data is useless. Here, we remove the problematic session from the study. Sadly, sometimes this has to be done.
Use HCP FreeSurfer, recon_all manual edits. There is a parameter in QuNex called --hcp_fs_extra_reconall which you can use to set any recon_all parameters. See hcp_freesurfer — QuNex documentation and Edits - Free Surfer Wiki for additional details. Unfortunately, no one on our team considers themselves as an expert in FreeSurfer manual edits. If the information on the page I provided is not enough, maybe you can try asking around on the HCP board or with some FreeSurfer experts. If there are any issues with passing relevant parameters from QuNex to recon_all let me know and I will help out.