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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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
Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-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
________________________________ Disclaimer:
The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
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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-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 ------------------------------------------------------------------------ Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwMD-g&c=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA&r=Ej6I9f50Syd-eFwAKeesOPRE0P9n7bIMdmFlrQs00s8&m=qUBQUfe6VhochMLPNBRHqwc7DRgmKXx0o6_lBEk6SbU&s=Iwhj1Bf6_0f-DcFTZZCZ7V_9pt5FkeVvjzU9Gp-odLE&e=>
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-
Douglas Greve -
Song, Da-Yea