Re: [Freesurfer] mris_smooth error: can't allocate region

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Hi Bruce,

This is the FS version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c I reinstalled the MATLAB. Do you think this will result in the issue?

Thanks,

PH

On Wed, Aug 22, 2018 at 4:12 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

what version of FS are you using? I think this is a bug that we had years ago for only a few weeks. One workaround would be to load each .mgz volume into matlab and write them back out (which will strip all the tags from them). I'm not sure why you are having the problem though Bruce

On Wed, 22 Aug 2018, Paysing Wu wrote:

...

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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 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%3E

...

  > 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
  >
  >
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