You'll probably have to manually edit the wm.mgz to remove big defects.
On 1/8/2021 3:44 AM, Stephan Wunderlich wrote:
External Email - Use CautionDear all,
I want to process brains with tumor lesions with the recon-all -all command. Recon-all (freesurfer version 6) gets always stucked when calling the function mris_fix_topology. It used to work with freesurfer version 4.5, but I still want to use the version 6.
It does work when I first run recon-all -all until it gets stucked and calculates for several days mris_fix_topology, then cancel the command and rerun with recon-all -all -nofix.
Is there a more smooth way to run recon-all for tumor lesion brains? (When I add -nofix to the recon-all command from the beginning, recon-all exits with errors, since it cannot find rh/lh.orig).
Best, Steph
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