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Hi Douglas,
Yes, I did try similar way to see if it worked. I deleted the whole folder and re-ran it. It stoped at the same place. Is there any other suggestion I could try?
Thanks,
PH
On Wed, Aug 22, 2018 at 1:23 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
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 CautionHi 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.
- FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
- Platform: macOS Sierra version 10.12.6, with physical memory 40GB
- 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
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