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 LSA EHTS Desktop Support Specialist Senior University of Michigan > On Nov 11, 2024, at 1:56 PM, fsbuild <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> 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/1d9tO16ill3qXS38_lhu1PhB4_4YgoB-8Scdl3kAzdVJfCO7T5FyZTzqYxMdb8cxso2zl9p05o3OaKMKPPEdn_xnwBtD1OlsGwdMzsVJD80i3pyx_9xsNX4-tAFeCxg00lNrGTiyMtyHXijMNqD47nNRTMUKTvzX_HZcVc61K6aa4MwFdG_QcCeLiYFfkKe0KZv_mSJwCNZUwGA2hVjfhz9pLJNYmLsbzmptHIFS-12GQsFts1jTKLmB5k_zua_-lHEfAJmw7W0ygPLUX1AVNOsgIAkZvg-wkpocxM7ACD-16uqlbR-OqJihUcsT8uDLb/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. 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 MailScanner has detected a possible fraud attempt >> from "secure-web.cisco.com" claiming to >> behttps://http://secure-web.cisco.com/1pcVmoMrMOb6eaIOAvghfL21QafJHNJySvrE9tGbVVLO4ePaxtr_ke3DDVKT0ot2OJGwhrBqO_vyJi6jGfc-TAn7z68uxSyystfRkjQ2Okcm16fbiFEaQE-YXplH8v-bFKJjcTnLBzftfcc9t2q-2aFVfufRlU-P43qw5_047E43laZ20qxdBcGvgjI45aWA_SrypiHG-MhOPN8cCrvT1q9kXsskNuOM6r9bnqmumNWizVJL1kzgqkyATSF2kYDZKb3oTFRLVlLshDcuuvhpCUF1fs1cjxJqhvklmfM7PNrqkozVxnucDopezzvWiA_u9/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline >> >> <https://secure-web.cisco.com/1F-Bt79zfgXwQhzijF1Q1pkEJm7wd2KNUs7X6JwyWbdkhwaDeRlLZx-4O0RFA85k6TOrDQ0GkEM32am0UEqLcq0T_FV6YuTo8pz6695TX_XA8qin9FyzlAmKb2hjudad3Al89zEQqRrQE4iw_qi5PyLq_Lm-kwQ0jYcWzcMZLxNNs3AlfuO-iv8eZdxqBvAxAbfS8PLSQFTIZ5T6VqxFlzJ4XbEm7yYwCIqfa7DDumxic23OJ4UFv2S737_TWz8nrNBNVT4YhfvGqjfE_YPSuAQlJxp_w84Lt-WXLbXmKHgX5cTTT2x3ARIVsMGInUU2V/https%3A%2F%2Fwww..massgeneralbrigham.org%2Fcomplianceline> >> . >> >> 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. >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be >> https://secure-web.cisco.com/1PC0sAP_Eks4UiYyelOqDJ5rpYtEKzXL7ueTlQ-FvTJtKVnJpD-MCp-xzC1i7q0aP42tHjkayojfA7i3Y8vmoZaNuGmqyEX-oQahdnGEDJi0CnKe6ZXL1Qsqm8pUXIWYLjaHlL95YgesOOJY3JmKn6WFCyQPDmUGj_r0iXBn3sOwbRHmivcTcxTc2IR44OQjZUJ0pRwDbrzXZYGRsWYeGdVr1KUwS9WGZnh29lWCWIPKp0JevXZOHL3qJG_fuFvHwDlVtzENyA3AhTPbnf7OGfT9xRgQBwKzKsSOVvDESJTaHtwA2AIhujlyOIrzbxIA8/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> >> <https://secure-web.cisco.com/1o5Hf5mqXhN1EePwqfWdjIZipXkLoBej_mRklubyt4oAV6QOMlynvEvffykdF1YvJDiCV3PUV9G74snvPi7KZwI-EQwn94jYZRAqZp_HaEZ2B5enxu2p_qDM5awRPs8bhZLvhm6S5JuPwzxJkVYW6jeHvrCfY-oWh1Yp3_Dr70jww989YCuLGBM8HL_JBgpWSjCAbqTxBzQkMylnG8ubaMKX2vAhOxorTvNOpwHI_aZv70rDoSGjLaAKKpbIUkPhbqPth2TnWEyHvQjCJNlgRSUAt-CMCIevl16KGyFLsxb88jRr1vd2TrWZOYnIIZrxy/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1PC0sAP_Eks4UiYyelOqDJ5rpYtEKzXL7ueTlQ-FvTJtKVnJpD-MCp-xzC1i7q0aP42tHjkayojfA7i3Y8vmoZaNuGmqyEX-oQahdnGEDJi0CnKe6ZXL1Qsqm8pUXIWYLjaHlL95YgesOOJY3JmKn6WFCyQPDmUGj_r0iXBn3sOwbRHmivcTcxTc2IR44OQjZUJ0pRwDbrzXZYGRsWYeGdVr1KUwS9WGZnh29lWCWIPKp0JevXZOHL3qJG_fuFvHwDlVtzENyA3AhTPbnf7OGfT9xRgQBwKzKsSOVvDESJTaHtwA2AIhujlyOIrzbxIA8/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > 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://secure-web.cisco.com/1s8O_zpnfvoQctTcusRn3pd054zaLg5zeRau6O7_NXPDpidq2IOr9Vx10DHfe8xGE3vcTD8KExF9topYOQHpzfeJveX_2aSS21D2Pc4G0YD4D1p-Ku6iiJcnyBtVNItLudrkpG8leOqgr3fr6_YT7gdnraS7RxWAKeFZ_3Npj4e_rvFkrUF5k1W71XZ7dhY3RSZGtonFVNsOCl-bMoDZvK6ehVRpTWhlwtKdhXLUStSrgagLsZ4aGc3y-pBX2bmd4fdN9y1tBMsosnHAVTSf8nuOt0LCvhNbQjtwSNSVa0Jk7yJcyfuQGgRI1vky7qFwC/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > > <https://secure-web.cisco.com/1s8O_zpnfvoQctTcusRn3pd054zaLg5zeRau6O7_NXPDpidq2IOr9Vx10DHfe8xGE3vcTD8KExF9topYOQHpzfeJveX_2aSS21D2Pc4G0YD4D1p-Ku6iiJcnyBtVNItLudrkpG8leOqgr3fr6_YT7gdnraS7RxWAKeFZ_3Npj4e_rvFkrUF5k1W71XZ7dhY3RSZGtonFVNsOCl-bMoDZvK6ehVRpTWhlwtKdhXLUStSrgagLsZ4aGc3y-pBX2bmd4fdN9y1tBMsosnHAVTSf8nuOt0LCvhNbQjtwSNSVa0Jk7yJcyfuQGgRI1vky7qFwC/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . > Please note that this e-mail is not secure (encrypted). 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External Email - Use Caution
_______________________________________________ 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.
