External Email - Use Caution

Hello Vittal,

Your output resembles the error from a previous post about running the old Freesurfer 5.3 release on Ubuntu 16,
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2016-May/045393.html

You can try running that command listed at the end of your log directly from the terminal to see if it gives more detailed info about the error,

 $ mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz

In that post the user saw a perl error,

  Can't use 'defined(@array)' (Maybe you should just omit the defined()?)

If you get a perl error, then following thru the "next in thread" links, one resolution was to install a pre 5.22 version of perl on the machine, https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2016-May/045402.html

Another option is to download and try the Freesurfer 6.0 release (which was not available at the time of that posting in 2016); the 6.0 Freesurfer release can be downloaded from, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall

- R.

vittal korann

January 8, 2019 at 02:17

External Email - Use Caution
Hello FreeSurfer Developers,

I'm attempting to run recon-all on schizophrenia patients and controls. For some reason freesurfer is crashing.
I wanted to know the reason for frequent crashing.
I'm using Ubuntu 16.04 LTS and freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.
Below I have attached the recon-all.log file for your reference.
Kindly help me to sort this out.

Thank you

Regards
Vittal

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