It looks like a corrupted file. Try renaming/deleting lh.orig.nofix, regenerating it, then seeing if mris_smooth works.
On 08/22/2018 10:44 AM, Paysing Wu wrote: > > External Email - Use Caution > > Hi FreeSurfer Developers, > > I was running recon-all and it stoped at smooth1. The command is: > recon-all -i T1image.nii.gz -s subject_name -all > > Below is error message on the screen: > #@# Smooth1 lh Mon Aug 20 23:51:55 EDT 2018 > /Volumes/AERS_BACKUP/Data/OSA/FREESURFER/OSA_048/scripts > \n mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix > ../surf/lh.smoothwm.nofix \n > setting seed for random number generator to 1234 > mris_smooth(27701,0x7fffec01b3c0) malloc: *** > mach_vm_map(size=13835344293369151488) failed (error code=3) > *** error: can't allocate region > *** set a breakpoint in malloc_error_break to debug > TAGskip: tag=-8454144, failed to calloc 4286513152 bytes! > > Cannot allocate memory > Darwin lspfis-imac.uphs.upenn.edu <http://lspfis-imac.uphs.upenn.edu> > 16.7.0 Darwin Kernel Version 16.7.0: Fri Apr 27 17:59:46 PDT 2018; > root:xnu-3789.73.13~1/RELEASE_X86_64 x86_64 > > recon-all -s OSA_048 exited with ERRORS at Mon Aug 20 23:51:55 EDT 2018 > Although the message looks like the shortage of memory, it could run a > few weeks ago. So, I really doubt memory is the main reason (the > physical memory is 40GB)...The only difference before and after I can > run is I reinstall the same version of Matlab 2016b by accident. Do > you think I have to change some setting to run it? > > Also, I've looked for solutions and couldn't find a one which really > fits my problem. Would you please help me trouble-shoot this issue? > Thank you so much. > > 1) FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c > 2) Platform: macOS Sierra version 10.12.6, with physical memory 40GB > 3) uname -a: Darwin lspfis-imac.uphs.upenn.edu > <http://lspfis-imac.uphs.upenn.edu> 16.7.0 Darwin Kernel Version > 16.7.0: Fri Apr 27 17:59:46 PDT 2018; > root:xnu-3789.73.13~1/RELEASE_X86_64 x86_64 > 4) recon-all.log: see attached > > > Best, > > PH > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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.
