I have attached the recon-all.log on this email. I’m not so sure what you mean by the terminal output file?

Thanks,

Da-Yea

From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: Friday, September 07, 2018 11:36 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all error

can you send the terminal output and recon-all.log?
thanks

On 9/7/18 9:58 AM, Song, Da-Yea wrote:

External Email - Use Caution

Hello,

I’m running some subjects through recon-all but have noticed that some error out (terminate the job) within seconds of starting. Any suggestions would be really appreciated. Here is the recon-all.cmd error message:

#---------------------------------

# New invocation of recon-all Fri Sep 7 09:34:58 EDT 2018

mri_convert /g5/dcn/freesurfer/MPRAGE/PS070/001 /g5/dcn/freesurfer/subjects/PS070/mri/orig/001.mgz

#--------------------------------------------

#@# MotionCor Fri Sep 7 09:35:30 EDT 2018

cp /g5/dcn/freesurfer/subjects/PS070/mri/orig/001.mgz /g5/dcn/freesurfer /subjects/PS070/mri/rawavg.mgz

mri_convert /g5/dcn/freesurfer/subjects/PS070/mri/rawavg.mgz /g5/dcn/freesurfer /subjects/PS070/mri/orig.mgz --conform

mri_add_xform_to_header -c /g5/dcn/freesurfer /subjects/PS070/mri/transforms/talairach.xfm /g5/dcn/freesurfer /subjects/PS070/mri/orig.mgz /g5/dcn/freesurfer /subjects/PS070/mri/orig.mgz

#--------------------------------------------

#@# Talairach Fri Sep 7 09:35:44 EDT 2018

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

#---------------------------------

# New invocation of recon-all Fri Sep 7 09:36:58 EDT 2018

#---------------------------------

# New invocation of recon-all Fri Sep 7 09:37:03 EDT 2018

#---------------------------------

# New invocation of recon-all Fri Sep 7 09:39:43 EDT 2018

#---------------------------------

# New invocation of recon-all Fri Sep 7 09:39:47 EDT 2018

#---------------------------------

# New invocation of recon-all Fri Sep 7 09:42:58 EDT 2018

#---------------------------------

# New invocation of recon-all Fri Sep 7 09:43:02 EDT 2018

Best,

Da-yea

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