For what it’s worth, we moved to Beta version 8 and after setting export FS_ALLOW_DEEP=1 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 jsn...@umich.edu LSA EHTS Desktop Support Specialist Senior University of Michigan > On Nov 14, 2024, at 12:06 PM, Noah Reardon <nrear...@umich.edu> wrote: > > Hi Yujing, > > We did as you suggested and this was the result (see attached). > > For step 5, the output was: > lrwxrwxrwx 1 root root 27 Nov 6 10:15 freesurfer -> > /usr/local/freesurfer-7.4.1 > > Best, > > Noah Reardon, B.S. > Lab Coordinator > Computational & Cognitive Neuroscience (Polk) Lab > <https://secure-web.cisco.com/1PYVAcfLp7aVdVIqIjqYhUOGgSG9ZhQema52xHJclk6kLJo-5N_QUDDvTW1H4VZVbwZYBBV6agBifK_OnAVWIJC8LZLptAyOyhJ-_nTLJBqTUp6Wd7ayZk7Lj9zjU08GM8j2tpkPsVylaY8BIsUqKrr6Sms4L52eKRmppKa1o6RzKlsQ-sz6AdpzLl-tNblL8uaxBDilZ8Ao779Sjp6BqSYyIMyn2JfHSci81nGJyxxMZz6BCF06fgP3NSykZoG3xEnfagQDIMY0-tZoadnopxOy6LWlSLFPsC96ZdQUMuKe2FrwM7iLrrcTxcwMnn4hr/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 > > > > On Mon, Nov 11, 2024 at 5:56 PM Huang, Yujing <yhuan...@mgh.harvard.edu > <mailto:yhuan...@mgh.harvard.edu>> wrote: >> 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? >> >> install Freesurfer 7.4.1 >> register and get a license file, put it in your home directory. set >> FS_LICENSE environment variable to point to the license file. >> source Freesurfer 7.4.1 >> set SUBJECTS_DIR >> run mri_convert command (use ‘which mri_convert’ to see where the command is >> located) >> >> >> Yujing >> >> >> >> From: Noah Reardon <nrear...@umich.edu <mailto:nrear...@umich.edu>> >> Sent: Monday, November 11, 2024 3:09 PM >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu>> >> Cc: Jeffrey Neal <jsn...@umich.edu <mailto:jsn...@umich.edu>>; Huang, Yujing >> <yhuan...@mgh.harvard.edu <mailto:yhuan...@mgh.harvard.edu>>; >> fsbu...@contbay.com <mailto: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 >> >> >> >> >> >> >> >> 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 >> >> >> >> >> >> >> >> 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’: >> >> 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://secure-web.cisco.com/1rvU_clJGa2nHGTY2XWepcaCAUjuqVpjh3EYPLXBvPDmn6bBJXAB1vbmKS5-4Jf-yFSFnFlK7vRPVAT_G1X21vvWQTUVAljWUH1oRY1X54m512ymVp9EPyQc25IQaM1FMFAuJSsxHtQY-2KvNyRUA20Y4rpzQxCo7AjalMPFv5WdT-s4YlM_fnXWGbFGnyUOPSxD4LuLR08caKAuXRUOLBxMHbqjHZB6lgK5ZXRBb1K0M04LgK0r3J7LSAc54yRE9wuGza75U4EdCRA5i8wOVNmYVDtkiHyIrm9xLphFBmQX1B9MGwLn_bm2_ZnN48GZZ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSetupConfiguration_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> >> Set ‘SUBJECTS_DIR’ to point to directory outside the Freesurfer installation >> tree, and make sure you have write permission >> 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: >> >> >> >> >> >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. 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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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 https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. 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.
