Re: [Freesurfer] mri_convert: Command terminated by signal 9 - Freesurfer

14 Nov 2024


      External Email - Use Caution
With the .deb and .rpm installers on Linux, you can optionally apt/yum remove freesurfer to delete the old release prior to installing a new release.&nbsp; A new release will be installed in a subdirectory named after the (different) release version so there will be no overlap of files.&nbsp; Or 7.4.1 is installed as /usr/local/freesurfer/7.4.1 and 8.0.0-beta is installed as /usr/local/freesurfer/8.0.0-beta.&nbsp; You may get run time errors if you don't use those installers.
- R.
On Nov 14, 2024, at 14:13, Jeffrey Neal &lt;jsneal@umich.edu&gt; wrote:For what it’s worth, we moved to Beta version 8 and after setting&nbsp;export FS_ALLOW_DEEP=1&nbsp;it seems to be running fine now. Noah is running it now and it will take several hours to finish before we know if it works 100% for what they want. I installed it the exact same way I did 7.4.1; short of a bug in 7.4.1 or a configuration issue either in the OS or something possibly being cached from a prior install I’m not sure what else to look into.
Best Regards,
Jeffrey Neal
jsneal@umich.edu
LSA EHTS Desktop Support Specialist&nbsp;Senior
University of Michigan
On Nov 14, 2024, at 12:06 PM, Noah Reardon &lt;nreardon@umich.edu&gt; wrote:Hi Yujing,
We did as you suggested and this was the result (see attached).&nbsp;
For step 5, the output was:lrwxrwxrwx&nbsp; 1 root root&nbsp; &nbsp; 27 Nov&nbsp; 6 10:15 freesurfer -&gt; /usr/local/freesurfer-7.4.1
Best,
Noah Reardon, B.S.&nbsp;Lab CoordinatorComputational &amp; Cognitive Neuroscience (Polk) LabDepartment of Psychology&nbsp;University of MichiganEmail:&nbsp;nreardon@umich.eduPhone: (734) 763-0343
On Mon, Nov 11, 2024 at 5:56 PM Huang, Yujing &lt;YHUANG43@mgh.harvard.edu&gt; wrote:
I’m not sure what happened. I see you have three mri_convert runs. Each time it behaves differently.&nbsp;Can you try the following without invoking your makefile?install Freesurfer 7.4.1register and get a license file, put it in your home directory. set FS_LICENSE environment variable to point to the license file.source Freesurfer 7.4.1set SUBJECTS_DIRrun mri_convert command (use ‘which mri_convert’ to see where the command is located)&nbsp;Yujing&nbsp;From:&nbsp;Noah Reardon &lt;nreardon@umich.edu&gt;&nbsp;
Sent:&nbsp;Monday, November 11, 2024 3:09 PM
To:&nbsp;Freesurfer support list &lt;freesurfer@nmr.mgh.harvard.edu&gt;
Cc:&nbsp;Jeffrey Neal &lt;jsneal@umich.edu&gt;; Huang, Yujing &lt;YHUANG43@mgh.harvard.edu&gt;;&nbsp;fsbuild@contbay.com
Subject:&nbsp;Re: [Freesurfer] mri_convert: Command terminated by signal 9&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hi all,&nbsp;Please see the attached&nbsp;screenshot&nbsp;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.&nbsp;Please advise.&nbsp;Noah Reardon, B.S.&nbsp;Lab CoordinatorComputational &amp; Cognitive Neuroscience (Polk) LabDepartment of Psychology&nbsp;University of MichiganEmail:&nbsp;nreardon@umich.eduPhone: (734) 763-0343&nbsp;&nbsp;On Mon, Nov 11, 2024 at 2:50 PM Jeffrey Neal &lt;jsneal@umich.edu&gt; 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.&nbsp;Best Regards,
Jeffrey Neal
jsneal@umich.edu
LSA EHTS Desktop Support Specialist&nbsp;Senior
University of Michigan
On Nov 11, 2024, at 1:56 PM, fsbuild &lt;fsbuild@contbay.com&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;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.&nbsp;&nbsp; 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 &lt;YHUANG43@mgh.harvard.edu&gt; wrote:&nbsp;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.&nbsp;From:&nbsp;Noah Reardon &lt;nreardon@umich.edu&gt;&nbsp;
Sent:&nbsp;Monday, November 11, 2024 1:43 PM
To:&nbsp;Huang, Yujing &lt;YHUANG43@mgh.harvard.edu&gt;
Cc:&nbsp;Freesurfer support list &lt;freesurfer@nmr.mgh.harvard.edu&gt;; Jeffrey Neal &lt;jsneal@umich.edu&gt;
Subject:&nbsp;Re: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]Re: mri_convert: Command terminated by signal 9&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hi Yujing,&nbsp;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:&nbsp;.PHONY: recon-all cleanfreesurfer&nbsp;recon-all: /nfs/tpolk/mind/freesurfer/$(subject)/scripts/recon-all.done&nbsp;/nfs/tpolk/mind/freesurfer/$(subject)/scripts/recon-all.done: $(mrsstruct) $(placstruct)&nbsp; &nbsp; export SUBJECTS_DIR=/nfs/tpolk/mind/freesurfer ;&nbsp; &nbsp; recon-all -all -s $(subject) -i $(mrsdicom) -i $(placdicom)&nbsp;#/nfs/tpolk/mind/freesurfer/$(subject)/scripts/recon-all.done: $(drugstruct) $(mrsstruct) $(placstruct)# &nbsp; &nbsp;export SUBJECTS_DIR=/nfs/tpolk/mind/freesurfer ;# &nbsp; &nbsp;recon-all -all -s $(subject) -i $(drugdicom) -i $(mrsdicom) -i $(placdicom)&nbsp;cleanfreesurfer:&nbsp; &nbsp; rm -r /nfs/tpolk/mind/freesurfer/$(subject)&nbsp;We have never encountered&nbsp;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.&nbsp;Please advise.&nbsp;Noah Reardon, B.S.&nbsp;Lab CoordinatorComputational &amp; Cognitive Neuroscience (Polk) LabDepartment of Psychology&nbsp;University of MichiganEmail:&nbsp;nreardon@umich.eduPhone: (734) 763-0343&nbsp;&nbsp;On Mon, Nov 11, 2024 at 1:08 PM Huang, Yujing &lt;YHUANG43@mgh.harvard.edu&gt; wrote:‘recon-all’ is a shell script that is ready to be run.&nbsp;I don’t understand why they need to have makefile to make recon-all.&nbsp;Here are the steps to setup Freesurfer environment and run ‘recon-all’:Source the correct Freesurfer environment needs to be sourced before running recon-all -&nbsp;MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be&nbsp;https://secure-web.cisco.com/1VL27ZGOezvqIVIBck6JA1nRicpHO91ZHaO-JPqhyD7ZpWP... ‘SUBJECTS_DIR’ to point to directory outside the Freesurfer installation tree, and make sure you have write permissionRun recon-all&nbsp;MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/recon-all(ex. recon-all -all -s &lt;&gt; -i &lt;&gt;)&nbsp;Yujing&nbsp;&nbsp;&nbsp;From:&nbsp;freesurfer-bounces@nmr.mgh.harvard.edu&nbsp;&lt;freesurfer-bounces@nmr.mgh.harvard.edu&gt;&nbsp;On Behalf Of&nbsp;Jeffrey Neal
Sent:&nbsp;Monday, November 11, 2024 10:47 AM
To:&nbsp;Freesurfer support list &lt;freesurfer@nmr.mgh.harvard.edu&gt;
Cc:&nbsp;Noah Reardon &lt;nreardon@umich.edu&gt;
Subject:&nbsp;Re: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]Re: mri_convert: Command terminated by signal 9&nbsp;Hello,&nbsp;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..&nbsp;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.&nbsp;&lt;image001.jpg&gt;&lt;image002.png&gt;Best Regards,
Jeffrey Neal
jsneal@umich.edu
LSA EHTS Desktop Support Specialist&nbsp;Senior
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