Hi Ricky

how did you try to load the defect_labels? The end of the recon-all.log file lists a defect with 26K vertices, which is probably too big to fix (it's about 1/5 of a normal surface). You should be able to visualize it by loading the lh.defect_labels file as an overlay on the lh.inflated.nofix and lh.orig.nofix surfaces. Make sure to change the threshold for the overlay to 0, then finde defect #116, which is the one it is stuck on. I think we actually add 1 to the index in the labels file so that non-defective vertices show as 0, so it may be 117. It should be clear though as it will be a lot bigger than others

cheers
Bruce


On Sat, 14 Mar 2020, Hoang, Ricky wrote:

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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?us
p=sharing

Thank you!
Ricky

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