New subject: mri_convert: Command terminated by signal 9

11 Nov 2024


      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.&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: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/1agV-jwNd1GbPnnrgr4furznVqz4vIxGIprFSNQkaYonMu-... ‘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
University of Michigan&nbsp;On Nov 6, 2024, at 4:27 PM, Huang, Yujing &lt;YHUANG43@mgh..harvard.edu&gt; wrote:&nbsp;&nbsp;&nbsp;The information in this e-mail is intended only for the person to whom it is addressed.&nbsp; If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at&nbsp;MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://http://secure-web.cisco.com/1zxH6hlquJaNw2I0t1oAIPgGYuxnkGkdj-_1CpW7... note that this e-mail is not secure (encrypted).&nbsp; If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.&nbsp; Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.&nbsp;_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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