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Hello Freesurfer experts,
I am trying to run recon-all to assess cortical thickness on a 3D FSPGR+C scan. The run keeps timing out during the fix topology lh step. I have looked at the resulting images and I am not sure whether I need to fix the white matter, add control points, or do something else entirely to fix the problem. The lh.inflated.nofix does not seem to have anything unwanted still attached and the lh.defect_label will not load. The lh.inflated.nofix does show some areas that have strands/spikes, which I think might be due to the gadolinium contrast. I wanted to ask for opinions on how to proceed. I have attached the recon-all.log.
This is also a link to the output folder: https://drive.google.com/drive/folders/14fj1JAGAvuB-DpgLCxQwOXQ08u6-Vfvj?usp...
Thank you! Ricky