External Email - Use Caution
Hi,
I tried to run the recon-all command on a single participant on a high memory cluster by typing:
qlogin -q qlogin.himem.q -l h_vmem=20G,s_vmem=20G
recon-all -i 103_T1.nii.gz -s 103T -sd /data/jag/cnds/ortal/freesurftest/C103/ -all
- Most of the necessary files were created, however the aparc.a2009 files and the recon-all.done file were not.
sincerely,
Ortal Nakash
Hi Ortal
you need to send us the recon-all.log, otherwise we don't have the information we need to help you
cheers Bruce On Thu, 2 Aug 2018, Ortal Nakash wrote:
External Email - Use Caution
Hi,
I tried to run the recon-all command on a single participant on a high memory cluster by typing:
qlogin -q qlogin.himem.q -l h_vmem=20G,s_vmem=20G
recon-all -i 103_T1.nii.gz -s 103T -sd /data/jag/cnds/ortal/freesurftest/C103/ -all
- Most of the necessary files were created, however the aparc.a2009 files and the recon-all.done
file were not.
sincerely,
Ortal Nakash
External Email - Use Caution
I copied it in the attached file.
Thank you, Ortal
On Thu, Aug 2, 2018 at 12:23 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Ortal
you need to send us the recon-all.log, otherwise we don't have the information we need to help you
cheers Bruce On Thu, 2 Aug 2018, Ortal Nakash wrote:
External Email - Use CautionHi,
I tried to run the recon-all command on a single participant on a high memory cluster by typing:
qlogin -q qlogin.himem.q -l h_vmem=20G,s_vmem=20G
recon-all -i 103_T1.nii.gz -s 103T -sd /data/jag/cnds/ortal/freesurftest/C103/ -all
- Most of the necessary files were created, however the aparc.a2009 files
and the recon-all.done file were not.
sincerely,
Ortal Nakash
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
can you send it as a text file (not converted to .docx)? On Thu, 2 Aug 2018, Ortal Nakash wrote:
External Email - Use Caution
I copied it in the attached file. Thank you, Ortal
On Thu, Aug 2, 2018 at 12:23 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Ortal
you need to send us the recon-all.log, otherwise we don't have the information we need to help you cheers Bruce On Thu, 2 Aug 2018, Ortal Nakash wrote: External Email - Use Caution Hi, I tried to run the recon-all command on a single participant on a high memory cluster by typing: qlogin -q qlogin.himem.q -l h_vmem=20G,s_vmem=20G recon-all -i 103_T1.nii.gz -s 103T -sd /data/jag/cnds/ortal/freesurftest/C103/ -all - Most of the necessary files were created, however the aparc.a2009 files and the recon-all.done file were not. sincerely, Ortal Nakash
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
External Email - Use Caution
Sure, here it is.
On Thu, Aug 2, 2018 at 12:40 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
can you send it as a text file (not converted to .docx)?
On Thu, 2 Aug 2018, Ortal Nakash wrote:
External Email - Use CautionI copied it in the attached file. Thank you, Ortal
On Thu, Aug 2, 2018 at 12:23 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Ortal
you need to send us the recon-all.log, otherwise we don't have theinformation we need to help you
cheers Bruce On Thu, 2 Aug 2018, Ortal Nakash wrote: External Email - Use Caution Hi, I tried to run the recon-all command on a single participanton a high memory cluster by typing:
qlogin -q qlogin.himem.q -l h_vmem=20G,s_vmem=20G recon-all -i 103_T1.nii.gz -s 103T -sd /data/jag/cnds/ortal/freesurftest/C103/ -all - Most of the necessary files were created, however theaparc.a2009 files and the recon-all.done file were not.
sincerely, Ortal Nakash
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
hmmm, it looks like it just stopped in the middle of a process. DId it exceed some wall time limit perhaps? On Thu, 2 Aug 2018, Ortal Nakash wrote:
External Email - Use Caution
Sure, here it is.
On Thu, Aug 2, 2018 at 12:40 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: can you send it as a text file (not converted to .docx)? On Thu, 2 Aug 2018, Ortal Nakash wrote:
External Email - Use Caution I copied it in the attached file. Thank you, Ortal On Thu, Aug 2, 2018 at 12:23 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Ortal you need to send us the recon-all.log, otherwise we don't have the information we need to help you cheers Bruce On Thu, 2 Aug 2018, Ortal Nakash wrote: External Email - Use Caution Hi, I tried to run the recon-all command on a single participant on a high memory cluster by typing: qlogin -q qlogin.himem.q -l h_vmem=20G,s_vmem=20G recon-all -i 103_T1.nii.gz -s 103T -sd /data/jag/cnds/ortal/freesurftest/C103/ -all - Most of the necessary files were created, however the aparc.a2009 files and the recon-all.done file were not. sincerely, Ortal Nakash _______________________________________________ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
External Email - Use Caution
Do you mean that I should have used higher memory?
Is there a way to continue running it from where it stopped or should I start it all over again?
On the Freesurfer Archive there's a suggestion to use the following command: recon-all -make all -s <subjid> However, when I tried it gave an error; *ERROR: cannot find /share/apps/freesurfer/6.0.0/subjects/103T.*
On Thu, Aug 2, 2018 at 12:49 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
hmmm, it looks like it just stopped in the middle of a process. DId it exceed some wall time limit perhaps?
On Thu, 2 Aug 2018, Ortal Nakash wrote:
External Email - Use CautionSure, here it is.
On Thu, Aug 2, 2018 at 12:40 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: can you send it as a text file (not converted to .docx)? On Thu, 2 Aug 2018, Ortal Nakash wrote:
External Email - Use Caution I copied it in the attached file. Thank you, Ortal On Thu, Aug 2, 2018 at 12:23 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Ortal
you need to send us the recon-all.log, otherwise wedon't have the information we need to help you
cheers Bruce On Thu, 2 Aug 2018, Ortal Nakash wrote: External Email - Use Caution Hi, I tried to run the recon-all command on a singleparticipant on a high memory cluster by typing:
qlogin -q qlogin.himem.q -l h_vmem=20G,s_vmem=20G recon-all -i 103_T1.nii.gz -s 103T -sd /data/jag/cnds/ortal/freesurftest/C103/ -all - Most of the necessary files were created,however the aparc.a2009 files and the recon-all.done file were not.
sincerely, Ortal Nakash _______________________________________________ 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 theperson 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
External Email - Use Caution
on the log it says that cpu time is unlimited.
On Thu, Aug 2, 2018 at 12:58 PM, Ortal Nakash ortalnk1@sas.upenn.edu wrote:
Do you mean that I should have used higher memory?
Is there a way to continue running it from where it stopped or should I start it all over again?
On the Freesurfer Archive there's a suggestion to use the following command: recon-all -make all -s <subjid> However, when I tried it gave an error; *ERROR: cannot find /share/apps/freesurfer/6.0.0/subjects/103T.*
On Thu, Aug 2, 2018 at 12:49 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
hmmm, it looks like it just stopped in the middle of a process. DId it exceed some wall time limit perhaps?
On Thu, 2 Aug 2018, Ortal Nakash wrote:
External Email - Use CautionSure, here it is.
On Thu, Aug 2, 2018 at 12:40 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: can you send it as a text file (not converted to .docx)? On Thu, 2 Aug 2018, Ortal Nakash wrote:
External Email - Use Caution I copied it in the attached file. Thank you, Ortal On Thu, Aug 2, 2018 at 12:23 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Ortal
you need to send us the recon-all.log, otherwise wedon't have the information we need to help you
cheers Bruce On Thu, 2 Aug 2018, Ortal Nakash wrote: External Email - Use Caution Hi, I tried to run the recon-all command on a singleparticipant on a high memory cluster by typing:
qlogin -q qlogin.himem.q -l h_vmem=20G,s_vmem=20G recon-all -i 103_T1.nii.gz -s 103T -sd /data/jag/cnds/ortal/freesurftest/C103/ -all - Most of the necessary files were created,however the aparc.a2009 files and the recon-all.done file were not.
sincerely, Ortal Nakash _______________________________________________ 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 theperson 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
but the cluster scheduling software might have other ideas Bruce
On Thu, 2 Aug 2018, Ortal Nakash wrote:
External Email - Use Caution
on the log it says that cpu time is unlimited.
On Thu, Aug 2, 2018 at 12:58 PM, Ortal Nakash ortalnk1@sas.upenn.edu wrote: Do you mean that I should have used higher memory? Is there a way to continue running it from where it stopped or should I start it all over again?
On the Freesurfer Archive there's a suggestion to use the following command: recon-all -make all -s <subjid> However, when I tried it gave an error; ERROR: cannot find /share/apps/freesurfer/6.0.0/subjects/103T.
On Thu, Aug 2, 2018 at 12:49 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: hmmm, it looks like it just stopped in the middle of a process. DId it exceed some wall time limit perhaps? On Thu, 2 Aug 2018, Ortal Nakash wrote:
External Email - Use Caution Sure, here it is. On Thu, Aug 2, 2018 at 12:40 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: can you send it as a text file (not converted to .docx)? On Thu, 2 Aug 2018, Ortal Nakash wrote: External Email - Use Caution I copied it in the attached file. Thank you, Ortal On Thu, Aug 2, 2018 at 12:23 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Ortal you need to send us the recon-all.log, otherwise we don't have the information we need to help you cheers Bruce On Thu, 2 Aug 2018, Ortal Nakash wrote: External Email - Use Caution Hi, I tried to run the recon-all command on a single participant on a high memory cluster by typing: qlogin -q qlogin.himem.q -l h_vmem=20G,s_vmem=20G recon-all -i 103_T1.nii.gz -s 103T -sd /data/jag/cnds/ortal/freesurftest/C103/ -all - Most of the necessary files were created, however the aparc.a2009 files and the recon-all.done file were not. sincerely, Ortal Nakash _______________________________________________ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
you need to specify the SUBJECTS_DIR. And yes, you might have needed more ram as the free is a lot less than the used at the start of recon-all, but some clusters also have limits on the length of time a job is allowed to run
cheers Bruce
On Thu, 2 Aug 2018, Ortal Nakash wrote:
External Email - Use Caution
Do you mean that I should have used higher memory? Is there a way to continue running it from where it stopped or should I start it all over again?
On the Freesurfer Archive there's a suggestion to use the following command: recon-all -make all -s <subjid> However, when I tried it gave an error; ERROR: cannot find /share/apps/freesurfer/6.0.0/subjects/103T.
On Thu, Aug 2, 2018 at 12:49 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: hmmm, it looks like it just stopped in the middle of a process. DId it exceed some wall time limit perhaps? On Thu, 2 Aug 2018, Ortal Nakash wrote:
External Email - Use Caution Sure, here it is. On Thu, Aug 2, 2018 at 12:40 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: can you send it as a text file (not converted to .docx)? On Thu, 2 Aug 2018, Ortal Nakash wrote: External Email - Use Caution I copied it in the attached file. Thank you, Ortal On Thu, Aug 2, 2018 at 12:23 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Ortal you need to send us the recon-all.log, otherwise we don't have the information we need to help you cheers Bruce On Thu, 2 Aug 2018, Ortal Nakash wrote: External Email - Use Caution Hi, I tried to run the recon-all command on a single participant on a high memory cluster by typing: qlogin -q qlogin.himem.q -l h_vmem=20G,s_vmem=20G recon-all -i 103_T1.nii.gz -s 103T -sd /data/jag/cnds/ortal/freesurftest/C103/ -all - Most of the necessary files were created, however the aparc.a2009 files and the recon-all.done file were not. sincerely, Ortal Nakash _______________________________________________ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Ortal Nakash