your best option is to include the flag -no-gcut at the end of recon-all, which will bypass usage of mri_gcut. you should inspect your brainmask.mgz upon completing the -atuorecon1 stage though.
n.
On Wed, 2011-03-23 at 11:26 -0500, Paige Scalf wrote:
Hello,
I'm getting the memory allocation error that is causing autorecon1 to abort. I've also attached the log file. Please help!
\n mri_gcut -110 -mult brainmask.auto.mgz T1.mgz brainmask.auto.mgz \n mri_gcut(6855) malloc: *** vm_allocate(size=8421376) failed (error code=3) mri_gcut(6855) malloc: *** error: can't allocate region mri_gcut(6855) malloc: *** set a breakpoint in szone_error to debug terminate called after throwing an instance of 'std::bad_alloc' what(): St9bad_alloc reading mask... use voxels with intensity 110 as WM mask threshold set to: 110.000000*0.360000=39.600000 calculating weights... doing mincut... Abort
Thanks, Paige _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer