The initial running of recon-all autorecon-1 autorecon-2 for a sample scan
resulted in a bad skull strip. I am attempting to troubleshoot the issue
through running just the skull strip portion of the recon-all pipeline again,
followed by adjusting the watershed parameters.
During re-running -skullstrip, I am given a
mri_watershed Error: read failed
(the em_register portion of the -skullstrip flag ran without interruption). I
have attached the corresponding log.
Is there a way to fix this watershed error (when I have tried to run the
watershed command by itself, the command is not recognized)?
https://share.polymail.io/v1/z/f/NThkMzUzYTU4ODA4/Vp21pl8rsUD4Tvw7tgnoOONDLHvyqODHm-JuJ2CuYvbpNRv74VHiIXFW2sq1hbb-_IVq_gsswxsr7C_ze5rXaYdUNPgZe62f-6Nkfl5OYuq3oGTdw0D4lWWL-eF5CxE20aCbJXC_5RQpmTiuFb46yJ13lSZ5Dvo3xeSo4ogTr6_M5umIcZTfK7sFK3yjPIXu2Cc=/recon-all.log
https://share.polymail.io/v1/z/f/NThkMzUzYTU4ODA4/Vp21pl8rsUD4Tvw7tgnoOONDLHvyqODHm-JuJ2CuYvbpNRv74VHiIXFW2sq1hbb-_IVq_gsswxsr7C_ze5rXaYdUNPgZe62f-6Nkfl5OYuq3oGTdw0D4lWWL-eF5CxE20aCbJXC_5RQpmTiuFb46yJ13lSZ5Dvo3xeSo4ogTr6_M5umIcZTfK7sFK3yjPIXu2Cc=/recon-all.log
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
