Hi Mike, Did you check the talairach. And how do nu.mgz and T1.mgz look. Also you could probably try running the following command to see if the skull strip step finishes without errors.
recon-all -skullstrip -no-wsgcaatlas -s <subjid> Sita. On Thu, 18 Mar 2010, Michael Waskom wrote: > Hi Bruce, Nick, > > I'm getting a segmentation fault that's crashing recon-all at the start of > the watershed during skull-stripping. I've tried this three times, once > starting the unpacking stream fresh from the raw dicoms, and it keeps > happening at exactly the same place. I've been reconstructing brains of > other subjects in the same directory all the while, so I don't think it's a > permissions issue of any sort. > > Full recon-all log is atatched, but here's the section where it crashes: > > *************************WATERSHED************************** > Sorting... > first estimation of the COG coord: x=116 y=166 z=95 r=51 > first estimation of the main basin volume: 585576 voxelsSegmentation > fault > Linux ba2 2.6.31-20-generic #57-Ubuntu SMP Mon Feb 8 09:02:26 UTC 2010 > x86_64 GNU/Linux > > recon-all exited with ERRORS at Wed Mar 17 14:22:26 EDT 2010 > > > And here's the OS data from the bugr script: > > FREESURFER_HOME: /software/Freesurfer/4.4.0 > > Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.4.0 > > Debian version: squeeze/sid > > Kernel info: Linux 2.6.31-20-generic x86_64 > > > Do you have any idea what might be going wrong? > > Thanks! > Mike > _______________________________________________ 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.
