The terminal output is evrything that gets printed to the screen. The
analysis in the recon-all.log file looks like it did not finish right
away (and there is no error msg in it)
On 9/7/18 11:51 AM, Song, Da-Yea wrote:
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@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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