Re: [Freesurfer] Freesurfer recon-all qcache partial failure
External Email - Use Caution Dear Yujing, Thank you for your kind help (and sorry for my late reply). It worked with the added flag; - measures thickness. I appreciate your advice on adding directives at the end of the recon-all command. Best, Asuka From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Huang, Yujing Sent: 16 January 2024 13:41 To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer recon-all qcache partial failure The command should look like this ‘recon-all -s subjid -qcache -all -i input-file’ From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Asuka Toyofuku Sent: Monday, January 15, 2024 9:45 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer recon-all qcache partial failure External Email - Use Caution Dear Yujing, Thank you very much for your kind help. So, you're saying I need more directive other than -qcashe? My command was; for d in Te* te* EPK* epk* do recon-all -s $d -qcache done Do you think I should add another directive, such as -all or -autorecon-all? So, the command line looks like this? recon-all -s -subjid -qcashe - autorecon-all I ran recon-all -qcashe not on the fsaverage folder, but in the SUBJECT_DIR. In the previous post, I attached the wrong recon-all log (which was from fsaverage>scripts folder), but now I'm attaching the recon-all log file from a random subject folder. Could you please look and check this recon-all as well? Many thanks! Best, Asuka From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Huang, Yujing mailto:yhuan...@mgh.harvard.edu>> Sent: 12 January 2024 14:24 To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Freesurfer recon-all qcache partial failure Your recon-all command doesn’t have the directive to tell it what to run. You also need to specify input files for your initial run. See this wiki page for detail MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1WHtKoBRWRweL9tOk04WS_fJMQNq-6FmCk7jSMyjZxjX34yU-Dlr5b4MzSwJL0G4PCxBUEWet96Y3jjqc8Eg-MkfKhwWflyMuhk9fmnVywIMKVjjl3LCipveJDkFaKnkM_qJ3ZE4TUygho39aVC6uloeAdYv3L3E1RgcAfLZ66tZhKh6x41SPMkse4TUZNWr7qUY6z5ebLWoZYv8vnwoKlxK40EFn409Puic2n3fgLNZZOvEb99nWSNV3_rFb3lo7l29NkdLmDJzD7xafSmiEzetkbSw7Db1ENHv8B_2bVA5S5Zt2oBdDE8fBRfMMl4gs/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all<https://secure-web.cisco.com/11Bilsco5cPfi23kohUaJckmoejScJgxCVT9TueKMZWvsx7dAntYubRwWYXHtGKljKeBLeTqzQQ5UePuZUZnRFzxae5FFSuLRLH4HzelINkwLs96J8N2iaElEUM_9YKPg9etzBOD8OEAuG2UfdHxpyONcBHtLAn_f6EkrCSoSjzjNvXi_oX7KVCXXUF3o5g3Bjyz-ezPwcZ5YFtvqdbIYv52nG9qbUuOOaolTNutoq-ibvyTwQgNV48YK3yt4Hsi_B54h6NAIo1rBwTyHrWCfvL9-lF9ZVJPN9vRL5Pst33y1_GcnaQjVirIdC2QsnN3-/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all> The recon-all.log attached contains runs between 2009 and 2010 on subject ‘fsaverage’. ‘fsaverage’ is an average subject comes with Freesurfer distribution in $FREESURFER_HOME/subjects/. fsaverage is a template brain based on a combination of 40 MRI scans of real brains. It can be used as a common space for group comparison. You don’t want to run recon-all on it. Your SUBJECTS_DIR should not set to your Freesurfer download/install directory. Set it to some other directory where you have the write permission. You should see ‘fsaverage’ as a symbolic link in your SUBJECTS_DIR. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Asuka Toyofuku Sent: Friday, January 12, 2024 4:31 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Freesurfer recon-all qcache partial failure External Email - Use Caution Dear Freesurfer researchers, I have an issue with recon-all-qcashe results. (please find the recon-all.log attached.) The command created fsaverage mgh files (e.g., lh.thickness.fsaverage.mgh), but it did not create fsaverage files with different smoothing levels (e.g., lh.thickness.fwhm10.fsaverage.mgh, lh.thickness.fwhm15.fsaverage.mgh, lh.thickness.fwhm20.fsaverage.mgh...etc) in the individual subject "surf" folder. I used the command below: for d in Te* te* EPK* epk* do recon-all -s $d -qcache done (Subjects names start from either Te, te, EPK or epk) For several subjects with failed recon-all commands, I re-ran the command individually: recon-all -s subjectname -qcashe (output from the terminal window) It could also be that recon-all was running at one point but died in an unexpected way. If it is th
Re: [Freesurfer] Freesurfer recon-all qcache partial failure
The command should look like this 'recon-all -s subjid -qcache -all -i input-file' From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Asuka Toyofuku Sent: Monday, January 15, 2024 9:45 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer recon-all qcache partial failure External Email - Use Caution Dear Yujing, Thank you very much for your kind help. So, you're saying I need more directive other than -qcashe? My command was; for d in Te* te* EPK* epk* do recon-all -s $d -qcache done Do you think I should add another directive, such as -all or -autorecon-all? So, the command line looks like this? recon-all -s -subjid -qcashe - autorecon-all I ran recon-all -qcashe not on the fsaverage folder, but in the SUBJECT_DIR. In the previous post, I attached the wrong recon-all log (which was from fsaverage>scripts folder), but now I'm attaching the recon-all log file from a random subject folder. Could you please look and check this recon-all as well? Many thanks! Best, Asuka From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Huang, Yujing mailto:yhuan...@mgh.harvard.edu>> Sent: 12 January 2024 14:24 To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Freesurfer recon-all qcache partial failure Your recon-all command doesn't have the directive to tell it what to run. You also need to specify input files for your initial run. See this wiki page for detail MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all<https://secure-web.cisco.com/11Bilsco5cPfi23kohUaJckmoejScJgxCVT9TueKMZWvsx7dAntYubRwWYXHtGKljKeBLeTqzQQ5UePuZUZnRFzxae5FFSuLRLH4HzelINkwLs96J8N2iaElEUM_9YKPg9etzBOD8OEAuG2UfdHxpyONcBHtLAn_f6EkrCSoSjzjNvXi_oX7KVCXXUF3o5g3Bjyz-ezPwcZ5YFtvqdbIYv52nG9qbUuOOaolTNutoq-ibvyTwQgNV48YK3yt4Hsi_B54h6NAIo1rBwTyHrWCfvL9-lF9ZVJPN9vRL5Pst33y1_GcnaQjVirIdC2QsnN3-/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all> The recon-all.log attached contains runs between 2009 and 2010 on subject 'fsaverage'. 'fsaverage' is an average subject comes with Freesurfer distribution in $FREESURFER_HOME/subjects/. fsaverage is a template brain based on a combination of 40 MRI scans of real brains. It can be used as a common space for group comparison. You don't want to run recon-all on it. Your SUBJECTS_DIR should not set to your Freesurfer download/install directory. Set it to some other directory where you have the write permission. You should see 'fsaverage' as a symbolic link in your SUBJECTS_DIR. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Asuka Toyofuku Sent: Friday, January 12, 2024 4:31 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Freesurfer recon-all qcache partial failure External Email - Use Caution Dear Freesurfer researchers, I have an issue with recon-all-qcashe results. (please find the recon-all.log attached.) The command created fsaverage mgh files (e.g., lh.thickness.fsaverage.mgh), but it did not create fsaverage files with different smoothing levels (e.g., lh.thickness.fwhm10.fsaverage.mgh, lh.thickness.fwhm15.fsaverage.mgh, lh.thickness.fwhm20.fsaverage.mgh...etc) in the individual subject "surf" folder. I used the command below: for d in Te* te* EPK* epk* do recon-all -s $d -qcache done (Subjects names start from either Te, te, EPK or epk) For several subjects with failed recon-all commands, I re-ran the command individually: recon-all -s subjectname -qcashe (output from the terminal window) It could also be that recon-all was running at one point but died in an unexpected way. If it is the case that there is a process running, you can kill it and start over or just let it run. If the process has died, you should type: rm /media/m-proc/Vol03/FREESURFER7_SUBJECTS/teen_subject_name/scripts/IsRunning.lh+rh **Try to copy the line and then rerun again with the quche code. I'm currently using freesurfer-x86_64-redhat-linux-gnu-dev4-20090216. Do you have any ideas why the command did not produce different fwhm files? I'm thinking about re-running the recon-all again, so I would appreciate it if you could help me modify the commands. Thank you very much in advance. Best regards, Asuka ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Please note that this e-mail is not secure (encrypted). If you do not wish to continue communica
Re: [Freesurfer] Freesurfer recon-all qcache partial failure
Your recon-all command doesn't have the directive to tell it what to run. You also need to specify input files for your initial run. See this wiki page for detail https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all The recon-all.log attached contains runs between 2009 and 2010 on subject 'fsaverage'. 'fsaverage' is an average subject comes with Freesurfer distribution in $FREESURFER_HOME/subjects/. fsaverage is a template brain based on a combination of 40 MRI scans of real brains. It can be used as a common space for group comparison. You don't want to run recon-all on it. Your SUBJECTS_DIR should not set to your Freesurfer download/install directory. Set it to some other directory where you have the write permission. You should see 'fsaverage' as a symbolic link in your SUBJECTS_DIR. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Asuka Toyofuku Sent: Friday, January 12, 2024 4:31 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer recon-all qcache partial failure External Email - Use Caution Dear Freesurfer researchers, I have an issue with recon-all-qcashe results. (please find the recon-all.log attached.) The command created fsaverage mgh files (e.g., lh.thickness.fsaverage.mgh), but it did not create fsaverage files with different smoothing levels (e.g., lh.thickness.fwhm10.fsaverage.mgh, lh.thickness.fwhm15.fsaverage.mgh, lh.thickness.fwhm20.fsaverage.mgh...etc) in the individual subject "surf" folder. I used the command below: for d in Te* te* EPK* epk* do recon-all -s $d -qcache done (Subjects names start from either Te, te, EPK or epk) For several subjects with failed recon-all commands, I re-ran the command individually: recon-all -s subjectname -qcashe (output from the terminal window) It could also be that recon-all was running at one point but died in an unexpected way. If it is the case that there is a process running, you can kill it and start over or just let it run. If the process has died, you should type: rm /media/m-proc/Vol03/FREESURFER7_SUBJECTS/teen_subject_name/scripts/IsRunning.lh+rh **Try to copy the line and then rerun again with the quche code. I'm currently using freesurfer-x86_64-redhat-linux-gnu-dev4-20090216. Do you have any ideas why the command did not produce different fwhm files? I'm thinking about re-running the recon-all again, so I would appreciate it if you could help me modify the commands. Thank you very much in advance. Best regards, Asuka ___ 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.
[Freesurfer] Freesurfer recon-all qcache partial failure
External Email - Use Caution Dear Freesurfer researchers, I have an issue with recon-all-qcashe results. (please find the recon-all.log attached.) The command created fsaverage mgh files (e.g., lh.thickness.fsaverage.mgh), but it did not create fsaverage files with different smoothing levels (e.g., lh.thickness.fwhm10.fsaverage.mgh, lh.thickness.fwhm15.fsaverage.mgh, lh.thickness.fwhm20.fsaverage.mgh...etc) in the individual subject "surf" folder. I used the command below: for d in Te* te* EPK* epk* do recon-all -s $d -qcache done (Subjects names start from either Te, te, EPK or epk) For several subjects with failed recon-all commands, I re-ran the command individually: recon-all -s subjectname -qcashe (output from the terminal window) It could also be that recon-all was running at one point but died in an unexpected way. If it is the case that there is a process running, you can kill it and start over or just let it run. If the process has died, you should type: rm /media/m-proc/Vol03/FREESURFER7_SUBJECTS/teen_subject_name/scripts/IsRunning.lh+rh **Try to copy the line and then rerun again with the quche code. I'm currently using freesurfer-x86_64-redhat-linux-gnu-dev4-20090216. Do you have any ideas why the command did not produce different fwhm files? I'm thinking about re-running the recon-all again, so I would appreciate it if you could help me modify the commands. Thank you very much in advance. Best regards, Asuka recon-all.log Description: recon-all.log ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
