Running the commands separately, I see the following log for some of the defects. Is the weblink my cue?
CORRECTING DEFECT 0 (vertices=4912, convex hull=886, v0=0) 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://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview -Tashrif . ________________________________ From: Billah, Tashrif Sent: Sunday, May 10, 2020 2:11 PM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Cc: Bouix, Sylvain,Ph.D. <sylv...@bwh.harvard.edu>; Knyazhanskaya, Evdokiya <eknyazhansk...@bwh.harvard.edu> Subject: mris_fix_topology command does not finish Hi there, The following commands part of `recon-alll -i some_T1w.nii.gz -autorecon2` does not finish for some of our data: #@# Fix Topology lh Sat May 9 14:17:52 EDT 2020 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 sub-7049_ses-01_desc-XcMaN4_T1w lh #@# Fix Topology rh Sat May 9 14:17:52 EDT 2020 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 sub-7049_ses-01_desc-XcMaN4_T1w rh Waiting for PID 57296 of (57296 57299) to complete... Waiting for PID 57299 of (57296 57299) to complete... We kept them running for about 48 hours in multiple attempts, yet no luck. Moreover, mris_fix_topology​ is a binary file so I am unable to debug through. Any suggestion on where to look at? Best, Tashrif
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