External Email - Use Caution Hi Freesurfer team,
I have gotten this error message on a successful run before: An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://secure-web.cisco.com/1kY22AwBCARfSQUY7cjfeplC3gw9EQSf1L_ErLh8Y6XncMttzSfui32YtKdC8yzeSGA6EvSJzqGrvVh45T_FOBdeGPtikP-NnKxpiuzQAOS5tZARwjSTPVZYPUvsVpk7ehOFT9Oj2jScxguAwyxvMsa5Ge1SkwNewJ8RW1choweXRNZRr6STkkSqSWWzUqE0t0gDEEsfue7cWQx1jxNHhXK1KtH3yVAn-tF2IrM-QJwqj3kgXKSC5pm4YF366jYShQnEX3r_BOFvobrwUavi11j2F_tlUUuEXVH0AwpDgFHpiX1UuTurUiRpLYHEKioSDNXUeFWxrtz_Kl_oCjrfr3Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTopologicalDefect_freeview Try following those instructions while running recon-all on a T1.nii.gz structural scan. I read the link and it seems I have to use the wm.mgz file I get from the freesurfer run, but I was wondering if there is any preprocessing I can do to the T1 scan to prevent it? Thanks, Abeoseh Flemister
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