External Email - Use Caution
Greetings, esteemed Surfers! I have a .nii file that I am trying to run through recon1 and I'm not sure I have my commands correct. At first I typed this command line and received this error: recon-all -subjid 1234 -i 1234.nii -autorecon1 ERROR: You are trying to re-run an existing subject with (possibly) new input data (-i). If this is truly new input data, you should delete the subject folder and re-run, or specify a different subject name. If you are just continuing an analysis of an existing subject, then omit all -i flags.
However, if I omit the -i flag, I receive this message: recon-all -subjid 1234 -autorecon1 Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /home/scanlab1/Desktop/FSTraining_2020 Actual FREESURFER_HOME /usr/local/freesurfer Linux SCANLab-Work1 4.15.0-46-generic #49~16.04.1-Ubuntu SMP Tue Feb 12 17:45:24 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux '/usr/local/freesurfer/bin/recon-all' -> '/home/scanlab1/Desktop/FSTraining_2020/2556/scripts/recon-all.local-copy' #-------------------------------------------- #@# MotionCor Tue Nov 3 17:46:26 CST 2020 ERROR: no run data found in /home/blah/blah/blah/1234/mri. Make sure to have a volume called 001.mgz in /home/blah/blah/blah/1234/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://secure-web.cisco.com/1UQYixkLhTyJq63goY7Pg_eCT-9bgdiZTokEQSMnHq7lBQtH... Linux SCANLab-Work1 4.15.0-46-generic #49~16.04.1-Ubuntu SMP Tue Feb 12 17:45:24 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 2556 exited with ERRORS at Tue Nov 3 17:46:26 CST 2020
For more details, see the log file /home/scanlab1/Desktop/FSTraining_2020/2556/scripts/recon-all.log To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1jEiXRrElXVtXwKhwmcYmBf1ASyXbJIhbTjDDo8znrKWXGez...
It's also been approx 1 year since FS was run on our machines. Perhaps an update is needed? Thank you so much!
NOTICE: This message, including all attachments transmitted with it, is intended solely for the use of the Addressee(s) and may contain information that is PRIVILEGED, CONFIDENTIAL, and/or EXEMPT FROM DISCLOSURE under applicable law. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or use of the information contained herein is STRICTLY PROHIBITED. If you received this communication in error, please destroy all copies of the message, whether in electronic or hard copy format, as well as attachments and immediately contact the sender by replying to this email or contact the sender at the telephone numbers listed above. Thank you!
HI Kelli
It sounds like you started running at some point but didn't get very far? Try something like:
mv /home/blah/blah/blah/1234 /home/blah/blah/blah/saved.1234 recon-all -subjid 1234 -i 1234.nii -autorecon1
and see if that works (then you can probably delete the saved.1234 dir if you want) cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Kelli Ann Nini Sent: Saturday, November 7, 2020 5:28 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Recon1 command
External Email - Use Caution Greetings, esteemed Surfers! I have a .nii file that I am trying to run through recon1 and I'm not sure I have my commands correct. At first I typed this command line and received this error: recon-all -subjid 1234 -i 1234.nii -autorecon1 ERROR: You are trying to re-run an existing subject with (possibly) new input data (-i). If this is truly new input data, you should delete the subject folder and re-run, or specify a different subject name. If you are just continuing an analysis of an existing subject, then omit all -i flags.
However, if I omit the -i flag, I receive this message: recon-all -subjid 1234 -autorecon1 Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /home/scanlab1/Desktop/FSTraining_2020 Actual FREESURFER_HOME /usr/local/freesurfer Linux SCANLab-Work1 4.15.0-46-generic #49~16.04.1-Ubuntu SMP Tue Feb 12 17:45:24 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux '/usr/local/freesurfer/bin/recon-all' -> '/home/scanlab1/Desktop/FSTraining_2020/2556/scripts/recon-all.local-copy' #-------------------------------------------- #@# MotionCor Tue Nov 3 17:46:26 CST 2020 ERROR: no run data found in /home/blah/blah/blah/1234/mri. Make sure to have a volume called 001.mgz in /home/blah/blah/blah/1234/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux SCANLab-Work1 4.15.0-46-generic #49~16.04.1-Ubuntu SMP Tue Feb 12 17:45:24 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 2556 exited with ERRORS at Tue Nov 3 17:46:26 CST 2020
For more details, see the log file /home/scanlab1/Desktop/FSTraining_2020/2556/scripts/recon-all.log To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportin
It's also been approx 1 year since FS was run on our machines. Perhaps an update is needed? Thank you so much!
NOTICE: This message, including all attachments transmitted with it, is intended solely for the use of the Addressee(s) and may contain information that is PRIVILEGED, CONFIDENTIAL, and/or EXEMPT FROM DISCLOSURE under applicable law. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or use of the information contained herein is STRICTLY PROHIBITED. If you received this communication in error, please destroy all copies of the message, whether in electronic or hard copy format, as well as attachments and immediately contact the sender by replying to this email or contact the sender at the telephone numbers listed above. Thank you!
External Email - Use Caution
Dr. Fischl, Thank you so much for your reply. The brains I'm using have been processed and analyzed numerous times for a variety of projects in our department and are in several directories on the same computer. However, I copied only the .nii files over to a new directory and set the environment before attempting to run recon-1. I'm tasked with teaching FreeSurfer to our incoming lab students, so I'd like to keep the copies separate if possible. Any advice is sincerely appreciated. -Kelli
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce BFISCHL@mgh.harvard.edu Sent: Sunday, November 8, 2020 10:07 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon1 command
WARNING: This email originated outside of the University of New Orleans system. The sender of this email could not be validated and may not actually be the person in the “From” field. Do NOT click links or open attachments if the message seems suspicious in any way. Never provide your user ID or password.
HI Kelli
It sounds like you started running at some point but didn’t get very far? Try something like:
mv /home/blah/blah/blah/1234 /home/blah/blah/blah/saved.1234
recon-all -subjid 1234 -i 1234.nii -autorecon1
and see if that works (then you can probably delete the saved.1234 dir if you want)
cheers
Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Kelli Ann Nini Sent: Saturday, November 7, 2020 5:28 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Recon1 command
External Email - Use Caution
Greetings, esteemed Surfers! I have a .nii file that I am trying to run through recon1 and I'm not sure I have my commands correct. At first I typed this command line and received this error: recon-all -subjid 1234 -i 1234.nii -autorecon1
ERROR: You are trying to re-run an existing subject with (possibly)
new input data (-i). If this is truly new input data, you should delete
the subject folder and re-run, or specify a different subject name.
If you are just continuing an analysis of an existing subject, then
omit all -i flags.
However, if I omit the -i flag, I receive this message: recon-all -subjid 1234 -autorecon1
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
INFO: SUBJECTS_DIR is /home/scanlab1/Desktop/FSTraining_2020
Actual FREESURFER_HOME /usr/local/freesurfer
Linux SCANLab-Work1 4.15.0-46-generic #49~16.04.1-Ubuntu SMP Tue Feb 12 17:45:24 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
'/usr/local/freesurfer/bin/recon-all' -> '/home/scanlab1/Desktop/FSTraining_2020/2556/scripts/recon-all.local-copy'
#--------------------------------------------
#@# MotionCor Tue Nov 3 17:46:26 CST 2020
ERROR: no run data found in /home/blah/blah/blah/1234/mri. Make sure to
have a volume called 001.mgz in /home/blah/blah/blah/1234/mri/orig.
If you have a second run of data call it 002.mgz, etc.
See also: http://secure-web.cisco.com/1K1UWo6yjlzKPnx8ZzHCZXX0yjG2qBUWcvpBNuB8ejSW-zXL...https://secure-web.cisco.com/1XmF2hq0ynrYUSHhpakdzBns7IF7IAQizGno9mghzMczNeIIHshC_H2E9ghuwePacEyXUPjSIDCqJeKI5h7dTblTen4_6tORF8-xEm7nyRkrXvnCILp2-rPmJ-H4i25tbK55V9c-e6k-VC3pnDKEUbzofOBKXCjoIyfIgBPuTnNi86i5ZJKsf6EkadfMhsiSHOvVEVyjHIcNJI3C8tc6kgwKPz_jqGomQDlgoSerE9Vuaqr5qCgDmkyGoIfL9Gwq3-wkq1PoKlbvcLc1mo93kHQ/https%3A%2F%2Fnam12.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fsurfer.nmr.mgh.harvard.edu%252Ffswiki%252FFsTutorial%252FConversion%26data%3D04%257C01%257Cknallen1%2540my.uno.edu%257Cd1166d295e5a4f9129fd08d884007305%257C31d4dbf540044469bfeedf294a9de150%257C0%257C0%257C637404484769176619%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3D%252FSDW2NLc8qibs29r7v8cZFJg8Bdb0TLWKJGuyQMqTeU%253D%26reserved%3D0
Linux SCANLab-Work1 4.15.0-46-generic #49~16.04.1-Ubuntu SMP Tue Feb 12 17:45:24 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 2556 exited with ERRORS at Tue Nov 3 17:46:26 CST 2020
For more details, see the log file /home/scanlab1/Desktop/FSTraining_2020/2556/scripts/recon-all.log
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1ZgnAnzWo2pnr4gPeAlszFG07dIRTwhbNlnEs1dT87pP1oP1...https://secure-web.cisco.com/1ebwEFFSRf2fkEyuaf2K-ZGR7Xq7HS0ujZadhGo9BnVcvk-a5XAkM2za5S5fxd5BnmyREotljsiPlqez672NxGMazjjddTQiP4fYptIlZ1mjU-rfWuZhONWopAzWAfkZxG_pkX9-5BoLMuWOMbemqyAnmyovC_D20xl2EEFAGBX31WWQdv5UcLoC9bU83Dmvh_5fSDiCxfaB_U7oZjXa4ugvVkdexRpKVM_k8kFgQxuSe8y1Igvd2KjAvEzY0rQChdCzvUd1R-BhLUaJ4EahZJQ/https%3A%2F%2Fnam12.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fsurfer.nmr.mgh.harvard.edu%252Ffswiki%252FBugReportin%26data%3D04%257C01%257Cknallen1%2540my.uno.edu%257Cd1166d295e5a4f9129fd08d884007305%257C31d4dbf540044469bfeedf294a9de150%257C0%257C0%257C637404484769176619%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DOeRGPqn1Kub%252BM4S6RyUcBXgku0dQDBHs206eg%252FnWhT4%253D%26reserved%3D0
It's also been approx 1 year since FS was run on our machines. Perhaps an update is needed? Thank you so much!
NOTICE: This message, including all attachments transmitted with it, is intended solely for the use of the Addressee(s) and may contain information that is PRIVILEGED, CONFIDENTIAL, and/or EXEMPT FROM DISCLOSURE under applicable law. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or use of the information contained herein is STRICTLY PROHIBITED. If you received this communication in error, please destroy all copies of the message, whether in electronic or hard copy format, as well as attachments and immediately contact the sender by replying to this email or contact the sender at the telephone numbers listed above. Thank you!
I think you can still do what Bruce suggested and keep things separate. What's the problem?
On 11/10/2020 1:11 PM, Kelli Ann Nini wrote:
External Email - Use Caution
Dr. Fischl, Thank you so much for your reply. The brains I'm using have been processed and analyzed numerous times for a variety of projects in our department and are in several directories on the same computer. However, I copied only the .nii files over to a new directory and set the environment before attempting to run recon-1. I'm tasked with teaching FreeSurfer to our incoming lab students, so I'd like to keep the copies separate if possible. Any advice is sincerely appreciated. -Kelli
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce BFISCHL@mgh.harvard.edu *Sent:* Sunday, November 8, 2020 10:07 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Recon1 command
*WARNING: This email originated outside of the University of New Orleans system. The sender of this email could not be validated and may not actually be the person in the “From” field. Do NOT click links or open attachments if the message seems suspicious in any way. Never provide your user ID or password.*
HI Kelli
It sounds like you started running at some point but didn’t get very far? Try something like:
mv /home/blah/blah/blah/1234 /home/blah/blah/blah/saved.1234
recon-all -subjid 1234 -i 1234.nii -autorecon1
and see if that works (then you can probably delete the saved.1234 dir if you want)
cheers
Bruce
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Kelli Ann Nini *Sent:* Saturday, November 7, 2020 5:28 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Recon1 command
* External Email - Use Caution *
Greetings, esteemed Surfers! I have a .nii file that I am trying to run through recon1 and I'm not sure I have my commands correct. At first I typed this command line and received this error: recon-all -subjid 1234 -i 1234.nii -autorecon1
ERROR: You are trying to re-run an existing subject with (possibly)
new input data (-i). If this is truly new input data, you should delete
the subject folder and re-run, or specify a different subject name.
If you are just continuing an analysis of an existing subject, then
omit all -i flags.
However, if I omit the -i flag, I receive this message: recon-all -subjid 1234 -autorecon1
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
INFO: SUBJECTS_DIR is /home/scanlab1/Desktop/FSTraining_2020
Actual FREESURFER_HOME /usr/local/freesurfer
Linux SCANLab-Work1 4.15.0-46-generic #49~16.04.1-Ubuntu SMP Tue Feb 12 17:45:24 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
'/usr/local/freesurfer/bin/recon-all' -> '/home/scanlab1/Desktop/FSTraining_2020/2556/scripts/recon-all.local-copy'
#--------------------------------------------
#@# MotionCor Tue Nov 3 17:46:26 CST 2020
ERROR: no run data found in /home/blah/blah/blah/1234/mri. Make sure to
have a volume called 001.mgz in /home/blah/blah/blah/1234/mri/orig.
If you have a second run of data call it 002.mgz, etc.
See also: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion https://secure-web.cisco.com/1XmF2hq0ynrYUSHhpakdzBns7IF7IAQizGno9mghzMczNeIIHshC_H2E9ghuwePacEyXUPjSIDCqJeKI5h7dTblTen4_6tORF8-xEm7nyRkrXvnCILp2-rPmJ-H4i25tbK55V9c-e6k-VC3pnDKEUbzofOBKXCjoIyfIgBPuTnNi86i5ZJKsf6EkadfMhsiSHOvVEVyjHIcNJI3C8tc6kgwKPz_jqGomQDlgoSerE9Vuaqr5qCgDmkyGoIfL9Gwq3-wkq1PoKlbvcLc1mo93kHQ/https%3A%2F%2Fnam12.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fsurfer.nmr.mgh.harvard.edu%252Ffswiki%252FFsTutorial%252FConversion%26data%3D04%257C01%257Cknallen1%2540my.uno.edu%257Cd1166d295e5a4f9129fd08d884007305%257C31d4dbf540044469bfeedf294a9de150%257C0%257C0%257C637404484769176619%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3D%252FSDW2NLc8qibs29r7v8cZFJg8Bdb0TLWKJGuyQMqTeU%253D%26reserved%3D0
Linux SCANLab-Work1 4.15.0-46-generic #49~16.04.1-Ubuntu SMP Tue Feb 12 17:45:24 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 2556 exited with ERRORS at Tue Nov 3 17:46:26 CST 2020
For more details, see the log file /home/scanlab1/Desktop/FSTraining_2020/2556/scripts/recon-all.log
To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportin https://secure-web.cisco.com/1ebwEFFSRf2fkEyuaf2K-ZGR7Xq7HS0ujZadhGo9BnVcvk-a5XAkM2za5S5fxd5BnmyREotljsiPlqez672NxGMazjjddTQiP4fYptIlZ1mjU-rfWuZhONWopAzWAfkZxG_pkX9-5BoLMuWOMbemqyAnmyovC_D20xl2EEFAGBX31WWQdv5UcLoC9bU83Dmvh_5fSDiCxfaB_U7oZjXa4ugvVkdexRpKVM_k8kFgQxuSe8y1Igvd2KjAvEzY0rQChdCzvUd1R-BhLUaJ4EahZJQ/https%3A%2F%2Fnam12.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fsurfer.nmr.mgh.harvard.edu%252Ffswiki%252FBugReportin%26data%3D04%257C01%257Cknallen1%2540my.uno.edu%257Cd1166d295e5a4f9129fd08d884007305%257C31d4dbf540044469bfeedf294a9de150%257C0%257C0%257C637404484769176619%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DOeRGPqn1Kub%252BM4S6RyUcBXgku0dQDBHs206eg%252FnWhT4%253D%26reserved%3D0
It's also been approx 1 year since FS was run on our machines. Perhaps an update is needed? Thank you so much!
NOTICE: This message, including all attachments transmitted with it, is intended solely for the use of the Addressee(s) and may contain information that is PRIVILEGED, CONFIDENTIAL, and/or EXEMPT FROM DISCLOSURE under applicable law. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or use of the information contained herein is STRICTLY PROHIBITED. If you received this communication in error, please destroy all copies of the message, whether in electronic or hard copy format, as well as attachments and immediately contact the sender by replying to this email or contact the sender at the telephone numbers listed above. Thank you!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Fischl, Bruce -
Kelli Ann Nini