I'm attempting to compare the pre-operative (pre-op) and post-operative (post-op) anatomical images for a group of patients who underwent brain tumor resection. During the operation, part of the brain tissue and the skull were removed, and I would like to mark
or label the removed/changed region (both cortical and subcortical) in the pre-op intact reconstructed brain.
For one sample subject (tumor on the left side), I have completed the recon-all for the pre-op T1 images without any error reported. However, for the post-op images, the key volumes such as T1/brainmask/wm.mgz were generated from recon-all steps but failed
in getting almost all surfaces. The related recon-all log and T1.mgz can be found in
the attachment.
I wonder whether (and how to) a detailed quality check or troubleshooting could solve such recon-all errors? Could I reconstruct the post-op brain when part of the structure is missing and reach my original goal?
I used FreeSurfer 7.4.1 on MacOS Ventra 13.0.
Thank you for your kind assistance.
