Hmmm, not sure what's going on. Can you try this:

cd /mnt/Local_Data/Reliability/Matt/5514syxa_110502_3Tnu_HFBd_wmseg/scripts setenv DIAG 0x04048 mris_sphere -w 0 -seed 1234 ../surf/lh.inflated ../surf/lh.sphere

and send us the output?

On Thu, 19 Jan 2017, Sanjana Shellikeri wrote:

Hi Freesurfer Developers,

We are attempting to regenerate the pial surfaces from an edited brainmask.mgz. We deleted dura voxels (precentral and postcentral gyri both hemispheres) on the original brainmask.mgz on Freeview. The command we ran is:

recon-all -autorecon-pial -subjid [subjectID]

There was no error output, however, the process hangs indefinitely (>36 hours) after 'randomSeed 1234'  and the pial surfaces have not been regenerated.

Please see the attached text file which contains the terminal output of the command.

We are using xUbuntu 12.04 and freesurfer-Linux-centos4-stable-pub-v5.3.0.

Regards,   Sanjana Shellikeri, PhD Student

Department of Speech-Language Pathology Faculty of Medicine, University of Toronto 160-500 University Ave. Toronto, ON M5G 1V7 sanjana.shellikeri@mail.utoronto.ca