I’m not sure what happened. I see you have three mri_convert runs. Each time it
behaves differently.
Can you try the following without invoking your makefile?
1. install Freesurfer 7.4.1
2. register and get a license file, put it in your home directory. set
FS_LICENSE environment variable to point to the license file.
3. source Freesurfer 7.4.1
4. set SUBJECTS_DIR
5. run mri_convert command (use ‘which mri_convert’ to see where the command
is located)
Yujing
From: Noah Reardon <nrear...@umich.edu>
Sent: Monday, November 11, 2024 3:09 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: Jeffrey Neal <jsn...@umich.edu>; Huang, Yujing <yhuan...@mgh.harvard.edu>;
fsbu...@contbay.com
Subject: Re: [Freesurfer] mri_convert: Command terminated by signal 9
External Email - Use Caution
Hi all,
Please see the attached screenshot demonstrating how mri convert is getting
deleted when we try to use it. This doesn't seem to be specific to recon-all,
nor does it appear to be a result of running it through our makefile.
Please advise.
Noah Reardon, B.S.
Lab Coordinator
Computational & Cognitive Neuroscience (Polk)
Lab<https://secure-web.cisco.com/1YSpoF1iNpG-t18N08xQdJiRvrxCzf5E1BckhEUnIlGeb5Acr9LffkS29mAlErtB_yPSU16dylSATp5jrdqwn55hLqYyeZbXTaLzV3-oRsM_2CqRqZGo2GQmoDAbZsXJ1Y8lOnxX5s_Nuc6TajxphJwbhIXGWHV1AK3zF9SqsRErNDirK9wl0s-Xgzi3ctQCV44BbH7iSlQiM8WnzaqwBxiShAGRl4oWS1kWEURVK-YXTCAdGm85RZAVLWatUNgnyX2Mf4isUkAY6zt1r8OwiZEDAYpFZGu_BxbNRi27JVUKyXR8wxvyjaVjvE_1loyxC/https%3A%2F%2Fpolklab.psych.lsa.umich.edu%2F>
Department of Psychology
University of Michigan
Email: nrear...@umich.edu<mailto:nrear...@umich.edu>
Phone: (734) 763-0343
[https://secure-web.cisco.com/1oT06BBuGYg3930ay1U8bnqF-wkVnvsRkTBIfI5URS5t1ntffKRrPMfsWz0fYVIGsg50dcFBnlx-xARL9MzlBfrVQV8OdmffkiYfMBJpaKg0rEbUCAk7MF62FKUCfNj0YTb2650lWrmO7c1xxNSuFQTEhkRtJXJgcwJrDfZSv34EDjMCCEvWYaHFiRqZ79O1MqBFCgUpUKOx99ezFiaFRmNXCoJtO4AfWq-EBQr50YDChYnoJ10rqn9l0AZh4_2vdd6H4UuVZzQG1tTMNtR-DYJf5LVi8lgB4m4CQbIrVkVeqUTqWwr7DMy2QV6UPm99i/https%3A%2F%2Fci3.googleusercontent.com%2Fmail-sig%2FAIorK4wMo2fv-bJ_klBEg8oY2BU9WFkonpQ2Ewor5yRWkcj2Ooy_hTbKZECvqZ91Lql4rbHifVEuDro]
On Mon, Nov 11, 2024 at 2:50 PM Jeffrey Neal
<jsn...@umich.edu<mailto:jsn...@umich.edu>> wrote:
Thanks for the insight on that. The lab is going to be working through a run of
it manually to see what they come across. I am still hung up a bit on the fact
that during the runs, commands from freesurfer/bin are being deleted - I guess
It could be from the makefile issue but seems unlikely since it runs fine on
7.1.1 and version 6. If you think of anything else let us know, otherwise we’ll
report our findings from doing it manually.
Best Regards,
Jeffrey Neal
jsn...@umich.edu<mailto:jsn...@umich.edu>
LSA EHTS Desktop Support Specialist Senior
University of Michigan
On Nov 11, 2024, at 1:56 PM, fsbuild
<fsbu...@contbay.com<mailto:fsbu...@contbay.com>> wrote:
External Email - Use Caution
The signal 9 error can mean the OS killed the process running the command
because it was using too much of some system resource, e.g., memory. You
might want to bring up your activity monitor before running the command and
look at memory usage, especially if it you get the signal 9 error each time it
is run.
- R.
On Nov 11, 2024, at 13:49, Huang, Yujing
<yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>> wrote:
I would suggest running 7.4.1 ‘recon-all’ with those manual setup to first make
sure 7.4.1 works for your system. If that works, the issue is in the makefile.
From: Noah Reardon <nrear...@umich.edu<mailto:nrear...@umich.edu>>
Sent: Monday, November 11, 2024 1:43 PM
To: Huang, Yujing <yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>>
Cc: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>;
Jeffrey Neal <jsn...@umich.edu<mailto:jsn...@umich.edu>>
Subject: Re: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]Re: mri_convert:
Command terminated by signal 9
External Email - Use Caution
Hi Yujing,
I'm the lab manager for this lab. I appreciate your help and wanted to provide
some background information. We use a makefile that helps us run all of our
preprocessing steps for a large number of subjects. Here is the code we use in
the makefile:
.PHONY: recon-all cleanfreesurfer
recon-all: /nfs/tpolk/mind/freesurfer/$(subject)/scripts/recon-all.done
/nfs/tpolk/mind/freesurfer/$(subject)/scripts/recon-all.done: $(mrsstruct)
$(placstruct)
export SUBJECTS_DIR=/nfs/tpolk/mind/freesurfer ;\
recon-all -all -s $(subject) -i $(mrsdicom) -i $(placdicom)
#/nfs/tpolk/mind/freesurfer/$(subject)/scripts/recon-all.done: $(drugstruct)
$(mrsstruct) $(placstruct)
# export SUBJECTS_DIR=/nfs/tpolk/mind/freesurfer ;\
# recon-all -all -s $(subject) -i $(drugdicom) -i $(mrsdicom) -i $(placdicom)
cleanfreesurfer:
rm -r /nfs/tpolk/mind/freesurfer/$(subject)
We have never encountered this issue with freesurfer, but now that we're trying
to use the updated version (7.4.1), it is giving us the errors Jeffrey attached.
Please advise.
Noah Reardon, B.S.
Lab Coordinator
Computational & Cognitive Neuroscience (Polk)
Lab<https://secure-web.cisco.com/14MCND2-sMUEYhcfeSe6r9vcyncEvDu280Il-6kGz1PSTySsclCLt9bAGaspYyfM-ybR1iArM41n_kfFeqnyv_Cc-1JWxvceg5X_aY8B5oojei31lBq8PzUMfIFc-44AKmy5p3C_DLQ3HZHctE7VBN8eylNnbHx--CEhcDp6vZnSmas140jEg5WSabAl9jNGtJp-luMDMyOYpqVCooZ_QFN0cmOtCyaGeHcdIBsZErHUouLNv3vSEMsv2BEXTjFO5gotoOq7QksNXf99de3uJkU0fUcKa19rbyhJWVmmU2Covx4FtWSYl711gINkNDU65/https%3A%2F%2Fpolklab.psych.lsa.umich.edu%2F>
Department of Psychology
University of Michigan
Email: nrear...@umich.edu<mailto:nrear...@umich.edu>
Phone: (734) 763-0343
[https://secure-web.cisco.com/1u1kow1uMmO0OxsrydIOQ0YlsZ9Tf72p3-7SXCTOa1wdhzCgtaRioM8KM0RfHw_6R9nXcDuBizJJFtrNnm40zuQSBiVH5ss4Xrh8EtH1ZrtHzzCLdfwiD5NhH8HUhCKyThgiljamGzHtE3AM66nXp56umS8z7eXeC02mVQG3EsVfWTZMOYHqwIc7fuZ68jbVWbG1QavmTbqpELY7hFJcXa5wb9ap2RjC4faIJORFJzOTi-LIBIOzrpi2FHrrzie34vJjbFbAT7bdXL_2CdQ48KwpinrG80u3bRFruWWW7I8SU8sKzWC8Drz-e2Xqh5Nqo/https%3A%2F%2Fci3.googleusercontent.com%2Fmail-sig%2FAIorK4wMo2fv-bJ_klBEg8oY2BU9WFkonpQ2Ewor5yRWkcj2Ooy_hTbKZECvqZ91Lql4rbHifVEuDro]
On Mon, Nov 11, 2024 at 1:08 PM Huang, Yujing
<yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard..edu>> wrote:
‘recon-all’ is a shell script that is ready to be run. I don’t understand why
they need to have makefile to make recon-all.
Here are the steps to setup Freesurfer environment and run ‘recon-all’:
1. Source the correct Freesurfer environment needs to be sourced before
running recon-all - MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be
https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linux<https://secure-web.cisco.com/17JDptBL3ShRumZyjQrkWqqZ4c7SSoKa2-M23XZ3f5pLnCs23uJyPnWz06zu_xXCKOLw1Wi6Z2cVXWzok1tZm2nAPWkt9g5lU0b_7FguyIakb2kqnC3wdCnvCYXRVaoa-W52szzSUXxOfjZsi7a7bNCc9anBhA6OCqzMFv8xa7stdn8u2XtP15yebEsn7VnBUsUK1fROn6HeqQfk99qPNLyUKWilZ3-4S-ooaDW4aBGgmJYSr7HXnfZPD-1x3wrEC7ettbQBOcNIkvX8oCxSz7BApuRj-U9yMSACNsUTpjXOZWmkarK6sG6BMrgAdk_SE/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSetupConfiguration_Linux>
2. Set ‘SUBJECTS_DIR’ to point to directory outside the Freesurfer
installation tree, and make sure you have write permission
3. Run recon-all MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to
behttps://surfer.nmr.mgh.harvard.edu/fswiki/recon-all<https://secure-web.cisco.com/1KLranqrwBMrXLl-9j31CWX0lWN-KSAFSBZhNhLpbF9-yq92qL8JmpXGBeG4vkq4xIdfSkxnJjybEh9-a9T5eb5Rm9Xq44wnVkmeO7iUUtX9cvIwDAlAVO19fc8Ds7ToN-r1Jm6RLJnWInardAyjHMpc12DNT4sxmikMktei1j-VNgEmsTjmLia-KPLJCgxD_8z8Qtyg-A0tmwcZfbm9Z0eOG4zG_Uic6u9oXqoKaav29Xw-aK7F0VoX-gqX3dqAR_cRV1oyFbcsgdzZ3tA1nj1lgfUu-ol2KdXPx0dmrKZmWRuejTLU3rT-gb-2yiq9b/https%3A%2F%2Fsecure-web.cisco..com%2F1JcLCMRYRR-5oiIi2UX0csBNjOLI5fQLI1lJkAlQOiyaCyFMBdf60KCnhXNWGjuzCe-xTlLMkCWYAu4nmkvypUSOpAXPDv4I0U1vv7RLQ3PHu2Rh2-ensSgo1iUTD2sb1TG85l-IjZOBxDSd-PZctkBJ2LYOMsgFfYdcwiLYEje8_HN3C6OMZAW-GH_X0W2HmE8Chzho2SEkaF8lBiFHVHsM4pxhFYDRt3KymF5jttZGoIJXykn2RH8Mg5Qo3enSvMjsEc0M7mH6W1NxC2PLcxsKYr0EBejOhBoh0S1BnoVqqkeBCOCy-S2sU1Bu9LtyL%2Fhttps%253A%252F%252Fsurfer.nmr.mgh.harvard.edu%252Ffswiki%252Frecon-all>
(ex. recon-all -all -s <> -i <>)
Yujing
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Jeffrey Neal
Sent: Monday, November 11, 2024 10:47 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: Noah Reardon <nrear...@umich.edu<mailto:nrear...@umich.edu>>
Subject: Re: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]Re: mri_convert:
Command terminated by signal 9
Hello,
Thanks for the helpful links. I did double check through everything and it all
looks correct; Sorry about the log file I needed to change permissions on it.
Here is the log file from the first email and here is an additional one from
today as well as some screenshots:
After running it once and getting the “terminated by signal 9” error when I try
to run it again packages have disappeared out of the freesurfer/bin causing
more issues..
The command they are running is make recon-all -k. If you need to see the
makefile or other things let me know and I will get them for you.
<image001.jpg>
<image002.png>
Best Regards,
Jeffrey Neal
jsn...@umich.edu<mailto:jsn...@umich.edu>
LSA EHTS Desktop Support Specialist Senior
University of Michigan
On Nov 6, 2024, at 4:27 PM, Huang, Yujing
<yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>> wrote:
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