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 nreardon@umich.edu Sent: Monday, November 11, 2024 1:43 PM To: Huang, Yujing YHUANG43@mgh.harvard.edu Cc: Freesurfer support list freesurfer@nmr.mgh.harvard.edu; Jeffrey Neal jsneal@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) Labhttps://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: nreardon@umich.edumailto:nreardon@umich.edu Phone: (734) 763-0343 [https://secure-web.cisco.com/1u1kow1uMmO0OxsrydIOQ0YlsZ9Tf72p3-7SXCTOa1wdhzC...]

On Mon, Nov 11, 2024 at 1:08 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@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 - https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Linuxhttps://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 https://surfer.nmr.mgh.harvard.edu/fswiki/recon-allhttps://secure-web.cisco.com/1JcLCMRYRR-5oiIi2UX0csBNjOLI5fQLI1lJkAlQOiyaCyFMBdf60KCnhXNWGjuzCe-xTlLMkCWYAu4nmkvypUSOpAXPDv4I0U1vv7RLQ3PHu2Rh2-ensSgo1iUTD2sb1TG85l-IjZOBxDSd-PZctkBJ2LYOMsgFfYdcwiLYEje8_HN3C6OMZAW-GH_X0W2HmE8Chzho2SEkaF8lBiFHVHsM4pxhFYDRt3KymF5jttZGoIJXykn2RH8Mg5Qo3enSvMjsEc0M7mH6W1NxC2PLcxsKYr0EBejOhBoh0S1BnoVqqkeBCOCy-S2sU1Bu9LtyL/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all

(ex. recon-all -all -s <> -i <>)

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc: Noah Reardon <nreardon@umich.edumailto:nreardon@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.

[cid:image001.jpg@01DB3440.4F83A360] [cid:image002.png@01DB3440.4F83A360] Best Regards, Jeffrey Neal jsneal@umich.edumailto:jsneal@umich.edu LSA EHTS Desktop Support Specialist Senior University of Michigan

On Nov 6, 2024, at 4:27 PM, Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote:

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