Dear Freesurfers,

I am attempting to run the full reconstruction in Freesurfer on several hundred patient images with diseased areas of the brain.

Without skipping any steps of the analysis chain, I am able to complete the full reconstruction for about 50% of said patients. When the analysis is able to complete, the disease sites are generally not included in the white or gray segmentation labels, which is ideal for my use case. However, when the disease is far from the cortical surface, it generally results in a large topological defect. (In other cases, the Talairach check fails.) I would like to know, does it really make sense to try to analyze the images with a "real" topological defect, and if so, how to accomplish it?

I have tried to run the reconstruction with flags "-nofix" and "-notal-check" to accept an imperfect Talairach transform and avoid crashes trying to fix these unfixable topological defects. Unfortunately, the step "mris_autodet_gwstats" which comes after "mris_sphere", seems to look for a file "surf/lh.orig.premesh" which is not found, causing a crash. From what I can understand, that file is produced by the so-called old topology fix [1], so it would imply that a full analysis chain is not supported if you eschew topology-fixing. Is this a feature, or do you recommend modifying the logic of the script to work around it? This is as far as I got, but I suppose there may be steps later in the analysis chain that will also look for files only produced if the topology fix runs.

For your information, I am currently using the nightly build from February 12 for CentOS7, and I am amenable to switching to an older or newer build. Thank you for taking the time to help me.

Best regards,

Dylan Hsu, Ph.D

Memorial Sloan-Kettering Cancer Center

[1] https://github.com/freesurfer/freesurfer/blob/6044b3df08de93c15e4b44807349f21d9e4bc794/scripts/recon-all#L3128-L3139