Hello Freesurfer's users,
I'm starting using FS and I have a problem running recon-all I create a folder called hptu_subj001 which contains MPRAGE.nii.gz within tutorial_subj First I convert nii.gz to mgz qith the command: recon-all -i MPRAGE.nii.gz -s hptu_subj001 and then in order to process all, I type: recon-all –i 001.mgz –subject hptu_subj001 –all
cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig> recon-all –i 001.mgz –subject hptu_subj001 –all ERROR: Flag i unrecognized. i 001.mgz subject hptu_subj001 all Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae #50-Ubuntu SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux
recon-all -s exited with ERRORS at Fri Jun 10 12:50:04 COT 2011
then I tried with:
cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj> recon-all –i MPRAGE.nii.gz –subject hptu_subj001 –all ERROR: Flag i unrecognized. i MPRAGE.nii.gz subject hptu_subj001 all Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae #50-Ubuntu SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux
recon-all -s exited with ERRORS at Fri Jun 10 12:36:24 COT 2011
How I can fix this error?
Thanks a lot,
Best regards,
Carolina
Hi Carolina,
-subject is not recognized by Freesurfer...Use -subjid or -s instead.
setenv SUBJECTS_DIR <path to tutorial data>
recon-all -all -i <path to your MPRAGE>/MPRAGE.nii.gz -s <path to freesurfer recons>/hptu_subj001
Priti
Hello Freesurfer's users,
I'm starting using FS and I have a problem running recon-all I create a folder called hptu_subj001 which contains MPRAGE.nii.gz within tutorial_subj First I convert nii.gz to mgz qith the command: recon-all -i MPRAGE.nii.gz -s hptu_subj001 and then in order to process all, I type: recon-all i 001.mgz subject hptu_subj001 all
cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig> recon-all i 001.mgz subject hptu_subj001 all ERROR: Flag i unrecognized. i 001.mgz subject hptu_subj001 all Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae #50-Ubuntu SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux
recon-all -s exited with ERRORS at Fri Jun 10 12:50:04 COT 2011
then I tried with:
cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj> recon-all i MPRAGE.nii.gz subject hptu_subj001 all ERROR: Flag i unrecognized. i MPRAGE.nii.gz subject hptu_subj001 all Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae #50-Ubuntu SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux
recon-all -s exited with ERRORS at Fri Jun 10 12:36:24 COT 2011
How I can fix this error?
Thanks a lot,
Best regards,
Carolina _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Carolina,
Sorry My bad. I was inaccurate in my previous message.
-subject should work.
Assuming that the MPRAGE of your subject is under the following directory:
/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig
set your SUBJECTS_DIR to /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig before running recon-all
setenv SUBJECTS_DIR ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig
recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject $SUBJECTS_DIR/hptu_subj001
This should create a folder where Freesurfer recons will be created:
cd ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig/hptu_subj001
Best, Priti
Hi Carolina,
-subject is not recognized by Freesurfer...Use -subjid or -s instead.
setenv SUBJECTS_DIR <path to tutorial data>
recon-all -all -i <path to your MPRAGE>/MPRAGE.nii.gz -s <path to freesurfer recons>/hptu_subj001
Priti
Hello Freesurfer's users,
I'm starting using FS and I have a problem running recon-all I create a folder called hptu_subj001 which contains MPRAGE.nii.gz within tutorial_subj First I convert nii.gz to mgz qith the command: recon-all -i MPRAGE.nii.gz -s hptu_subj001 and then in order to process all, I type: recon-all i 001.mgz subject hptu_subj001 all
cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig> recon-all i 001.mgz subject hptu_subj001 all ERROR: Flag i unrecognized. i 001.mgz subject hptu_subj001 all Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae #50-Ubuntu SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux
recon-all -s exited with ERRORS at Fri Jun 10 12:50:04 COT 2011
then I tried with:
cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj> recon-all i MPRAGE.nii.gz subject hptu_subj001 all ERROR: Flag i unrecognized. i MPRAGE.nii.gz subject hptu_subj001 all Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae #50-Ubuntu SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux
recon-all -s exited with ERRORS at Fri Jun 10 12:36:24 COT 2011
How I can fix this error?
Thanks a lot,
Best regards,
Carolina _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks a lot, it works. just waiting 24 hours.
Best regards,
Carolina
2011/6/10 rspriti@nmr.mgh.harvard.edu
Hi Carolina,
Sorry My bad. I was inaccurate in my previous message.
-subject should work.
Assuming that the MPRAGE of your subject is under the following directory:
/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig
set your SUBJECTS_DIR to /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig before running recon-all
setenv SUBJECTS_DIR ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig
recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject $SUBJECTS_DIR/hptu_subj001
This should create a folder where Freesurfer recons will be created:
cd
~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig/hptu_subj001
Best, Priti
Hi Carolina,
-subject is not recognized by Freesurfer...Use -subjid or -s instead.
setenv SUBJECTS_DIR <path to tutorial data>
recon-all -all -i <path to your MPRAGE>/MPRAGE.nii.gz -s <path to freesurfer recons>/hptu_subj001
Priti
Hello Freesurfer's users,
I'm starting using FS and I have a problem running recon-all I create a folder called hptu_subj001 which contains MPRAGE.nii.gz within tutorial_subj First I convert nii.gz to mgz qith the command: recon-all -i MPRAGE.nii.gz -s hptu_subj001 and then in order to process all, I type: recon-all –i 001.mgz –subject hptu_subj001 –all
cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig>
recon-all –i 001.mgz –subject hptu_subj001 –all ERROR: Flag i unrecognized. i 001.mgz subject hptu_subj001 all Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae #50-Ubuntu SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux
recon-all -s exited with ERRORS at Fri Jun 10 12:50:04 COT 2011
then I tried with:
cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj>
recon-all –i MPRAGE.nii.gz –subject hptu_subj001 –all ERROR: Flag i unrecognized. i MPRAGE.nii.gz subject hptu_subj001 all Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae #50-Ubuntu SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux
recon-all -s exited with ERRORS at Fri Jun 10 12:36:24 COT 2011
How I can fix this error?
Thanks a lot,
Best regards,
Carolina _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
--
Hi Carolina,
Do you know how can I run Freesurfer just to get some Benchmark Numbers and to Check GPU Performance using Cuda?
Thanks, *Leo Souza*
On 06/13/2011 07:04 AM, Carolina Valencia wrote:
Thanks a lot, it works. just waiting 24 hours.
Best regards,
Carolina
2011/6/10 <rspriti@nmr.mgh.harvard.edu mailto:rspriti@nmr.mgh.harvard.edu>
Hi Carolina, Sorry My bad. I was inaccurate in my previous message. -subject should work. Assuming that the MPRAGE of your subject is under the following directory: /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig set your SUBJECTS_DIR to /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig before running recon-all setenv SUBJECTS_DIR ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject $SUBJECTS_DIR/hptu_subj001 This should create a folder where Freesurfer recons will be created: cd ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig/hptu_subj001 Best, Priti > Hi Carolina, > > -subject is not recognized by Freesurfer...Use -subjid or -s instead. > > setenv SUBJECTS_DIR <path to tutorial data> > > recon-all -all -i <path to your MPRAGE>/MPRAGE.nii.gz -s <path to > freesurfer recons>/hptu_subj001 > > Priti > >> Hello Freesurfer's users, >> >> I'm starting using FS and I have a problem running recon-all >> I create a folder called hptu_subj001 which contains MPRAGE.nii.gz >> within >> tutorial_subj >> First I convert nii.gz to mgz qith the command: >> recon-all -i MPRAGE.nii.gz -s hptu_subj001 >> and then in order to process all, I type: >> recon-all –i 001.mgz –subject hptu_subj001 –all >> >> cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig> >> recon-all –i 001.mgz –subject hptu_subj001 –all >> ERROR: Flag i unrecognized. >> i 001.mgz subject hptu_subj001 all >> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae >> #50-Ubuntu >> SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux >> >> recon-all -s exited with ERRORS at Fri Jun 10 12:50:04 COT 2011 >> >> then I tried with: >> >> cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj> >> recon-all –i MPRAGE.nii.gz –subject hptu_subj001 –all >> ERROR: Flag i unrecognized. >> i MPRAGE.nii.gz subject hptu_subj001 all >> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae >> #50-Ubuntu >> SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux >> >> recon-all -s exited with ERRORS at Fri Jun 10 12:36:24 COT 2011 >> >> How I can fix this error? >> >> Thanks a lot, >> >> Best regards, >> >> Carolina >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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.--
----------------------------------------------------------------------------------- This email message is for the sole use of the intended recipient(s) and may contain confidential information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. -----------------------------------------------------------------------------------
When you run recon-all, it will create a recon-all-status file in the scripts directory. This has the start times of all the processes, so you can work out how long each took. This will be wall clock time, so take that into account.
doug
Leo Souza wrote:
Hi Carolina,
Do you know how can I run Freesurfer just to get some Benchmark Numbers and to Check GPU Performance using Cuda?
Thanks, *Leo Souza*
On 06/13/2011 07:04 AM, Carolina Valencia wrote:
Thanks a lot, it works. just waiting 24 hours.
Best regards,
Carolina
2011/6/10 <rspriti@nmr.mgh.harvard.edu mailto:rspriti@nmr.mgh.harvard.edu>
Hi Carolina, Sorry My bad. I was inaccurate in my previous message. -subject should work. Assuming that the MPRAGE of your subject is under the following directory: /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig set your SUBJECTS_DIR to /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig before running recon-all setenv SUBJECTS_DIR ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject $SUBJECTS_DIR/hptu_subj001 This should create a folder where Freesurfer recons will be created: cd ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig/hptu_subj001 Best, Priti > Hi Carolina, > > -subject is not recognized by Freesurfer...Use -subjid or -s instead. > > setenv SUBJECTS_DIR <path to tutorial data> > > recon-all -all -i <path to your MPRAGE>/MPRAGE.nii.gz -s <path to > freesurfer recons>/hptu_subj001 > > Priti > >> Hello Freesurfer's users, >> >> I'm starting using FS and I have a problem running recon-all >> I create a folder called hptu_subj001 which contains MPRAGE.nii.gz >> within >> tutorial_subj >> First I convert nii.gz to mgz qith the command: >> recon-all -i MPRAGE.nii.gz -s hptu_subj001 >> and then in order to process all, I type: >> recon-all –i 001.mgz –subject hptu_subj001 –all >> >> cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig> >> recon-all –i 001.mgz –subject hptu_subj001 –all >> ERROR: Flag i unrecognized. >> i 001.mgz subject hptu_subj001 all >> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae >> #50-Ubuntu >> SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux >> >> recon-all -s exited with ERRORS at Fri Jun 10 12:50:04 COT 2011 >> >> then I tried with: >> >> cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj> >> recon-all –i MPRAGE.nii.gz –subject hptu_subj001 –all >> ERROR: Flag i unrecognized. >> i MPRAGE.nii.gz subject hptu_subj001 all >> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae >> #50-Ubuntu >> SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux >> >> recon-all -s exited with ERRORS at Fri Jun 10 12:36:24 COT 2011 >> >> How I can fix this error? >> >> Thanks a lot, >> >> Best regards, >> >> Carolina >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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.--
This email message is for the sole use of the intended recipient(s) and may contain confidential information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Yes, I did that, but it doesn't actually uses the GPU to do that, only CPU.
GPU percentage is 0%. (you can check it by do running: "nvidia-smi -q -d UTILIZATION -l 3" if your'e using any recent drivers.
Thanks, *Leo Souza*
On 06/13/2011 02:44 PM, Douglas N Greve wrote:
When you run recon-all, it will create a recon-all-status file in the scripts directory. This has the start times of all the processes, so you can work out how long each took. This will be wall clock time, so take that into account.
doug
Leo Souza wrote:
Hi Carolina,
Do you know how can I run Freesurfer just to get some Benchmark Numbers and to Check GPU Performance using Cuda?
Thanks, *Leo Souza*
On 06/13/2011 07:04 AM, Carolina Valencia wrote:
Thanks a lot, it works. just waiting 24 hours.
Best regards,
Carolina
2011/6/10<rspriti@nmr.mgh.harvard.edu mailto:rspriti@nmr.mgh.harvard.edu>
Hi Carolina, Sorry My bad. I was inaccurate in my previous message. -subject should work. Assuming that the MPRAGE of your subject is under the following directory: /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig set your SUBJECTS_DIR to /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig before running recon-all setenv SUBJECTS_DIR ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject $SUBJECTS_DIR/hptu_subj001 This should create a folder where Freesurfer recons will be created: cd ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig/hptu_subj001 Best, Priti > Hi Carolina, > > -subject is not recognized by Freesurfer...Use -subjid or -s instead. > > setenv SUBJECTS_DIR<path to tutorial data> > > recon-all -all -i<path to your MPRAGE>/MPRAGE.nii.gz -s<path to > freesurfer recons>/hptu_subj001 > > Priti > >> Hello Freesurfer's users, >> >> I'm starting using FS and I have a problem running recon-all >> I create a folder called hptu_subj001 which contains MPRAGE.nii.gz >> within >> tutorial_subj >> First I convert nii.gz to mgz qith the command: >> recon-all -i MPRAGE.nii.gz -s hptu_subj001 >> and then in order to process all, I type: >> recon-all –i 001.mgz –subject hptu_subj001 –all >> >> cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig> >> recon-all –i 001.mgz –subject hptu_subj001 –all >> ERROR: Flag i unrecognized. >> i 001.mgz subject hptu_subj001 all >> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae >> #50-Ubuntu >> SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux >> >> recon-all -s exited with ERRORS at Fri Jun 10 12:50:04 COT 2011 >> >> then I tried with: >> >> cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj> >> recon-all –i MPRAGE.nii.gz –subject hptu_subj001 –all >> ERROR: Flag i unrecognized. >> i MPRAGE.nii.gz subject hptu_subj001 all >> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae >> #50-Ubuntu >> SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux >> >> recon-all -s exited with ERRORS at Fri Jun 10 12:36:24 COT 2011 >> >> How I can fix this error? >> >> Thanks a lot, >> >> Best regards, >> >> Carolina >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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.--
This email message is for the sole use of the intended recipient(s) and may contain confidential information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sorry my typos, got a weird keyboard here.
Thanks, *Leo Souza*
On 06/13/2011 03:27 PM, Leo Souza wrote:
Yes, I did that, but it doesn't actually uses the GPU to do that, only CPU.
GPU percentage is 0%. (you can check it by do running: "nvidia-smi -q -d UTILIZATION -l 3" if youŕe using any recent drivers.
Thanks, *Leo Souza*
On 06/13/2011 02:44 PM, Douglas N Greve wrote:
When you run recon-all, it will create a recon-all-status file in the scripts directory. This has the start times of all the processes, so you can work out how long each took. This will be wall clock time, so take that into account.
doug
Leo Souza wrote:
Hi Carolina,
Do you know how can I run Freesurfer just to get some Benchmark Numbers and to Check GPU Performance using Cuda?
Thanks, *Leo Souza*
On 06/13/2011 07:04 AM, Carolina Valencia wrote:
Thanks a lot, it works. just waiting 24 hours.
Best regards,
Carolina
2011/6/10<rspriti@nmr.mgh.harvard.edu mailto:rspriti@nmr.mgh.harvard.edu>
Hi Carolina, Sorry My bad. I was inaccurate in my previous message. -subject should work. Assuming that the MPRAGE of your subject is under the following directory: /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig set your SUBJECTS_DIR to /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig before running recon-all setenv SUBJECTS_DIR ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject $SUBJECTS_DIR/hptu_subj001 This should create a folder where Freesurfer recons will be created: cd ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig/hptu_subj001 Best, Priti > Hi Carolina, > > -subject is not recognized by Freesurfer...Use -subjid or -s instead. > > setenv SUBJECTS_DIR<path to tutorial data> > > recon-all -all -i<path to your MPRAGE>/MPRAGE.nii.gz -s<path to > freesurfer recons>/hptu_subj001 > > Priti > >> Hello Freesurfer's users, >> >> I'm starting using FS and I have a problem running recon-all >> I create a folder called hptu_subj001 which contains MPRAGE.nii.gz >> within >> tutorial_subj >> First I convert nii.gz to mgz qith the command: >> recon-all -i MPRAGE.nii.gz -s hptu_subj001 >> and then in order to process all, I type: >> recon-all –i 001.mgz –subject hptu_subj001 –all >> >> cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig> >> recon-all –i 001.mgz –subject hptu_subj001 –all >> ERROR: Flag i unrecognized. >> i 001.mgz subject hptu_subj001 all >> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae >> #50-Ubuntu >> SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux >> >> recon-all -s exited with ERRORS at Fri Jun 10 12:50:04 COT 2011 >> >> then I tried with: >> >> cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj> >> recon-all –i MPRAGE.nii.gz –subject hptu_subj001 –all >> ERROR: Flag i unrecognized. >> i MPRAGE.nii.gz subject hptu_subj001 all >> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae >> #50-Ubuntu >> SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux >> >> recon-all -s exited with ERRORS at Fri Jun 10 12:36:24 COT 2011 >> >> How I can fix this error? >> >> Thanks a lot, >> >> Best regards, >> >> Carolina >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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.--
This email message is for the sole use of the intended recipient(s) and may contain confidential information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Try adding -use-cuda to recon-all
Leo Souza wrote:
Yes, I did that, but it doesn't actually uses the GPU to do that, only CPU.
GPU percentage is 0%. (you can check it by do running: "nvidia-smi -q -d UTILIZATION -l 3" if your'e using any recent drivers.
Thanks, *Leo Souza*
On 06/13/2011 02:44 PM, Douglas N Greve wrote:
When you run recon-all, it will create a recon-all-status file in the scripts directory. This has the start times of all the processes, so you can work out how long each took. This will be wall clock time, so take that into account.
doug
Leo Souza wrote:
Hi Carolina,
Do you know how can I run Freesurfer just to get some Benchmark Numbers and to Check GPU Performance using Cuda?
Thanks, *Leo Souza*
On 06/13/2011 07:04 AM, Carolina Valencia wrote:
Thanks a lot, it works. just waiting 24 hours.
Best regards,
Carolina
2011/6/10 <rspriti@nmr.mgh.harvard.edu mailto:rspriti@nmr.mgh.harvard.edu>
Hi Carolina, Sorry My bad. I was inaccurate in my previous message. -subject should work. Assuming that the MPRAGE of your subject is under the following directory: /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig set your SUBJECTS_DIR to /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig before running recon-all setenv SUBJECTS_DIR ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject $SUBJECTS_DIR/hptu_subj001 This should create a folder where Freesurfer recons will be created: cd ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig/hptu_subj001 Best, Priti > Hi Carolina, > > -subject is not recognized by Freesurfer...Use -subjid or -s instead. > > setenv SUBJECTS_DIR <path to tutorial data> > > recon-all -all -i <path to your MPRAGE>/MPRAGE.nii.gz -s <path to > freesurfer recons>/hptu_subj001 > > Priti > >> Hello Freesurfer's users, >> >> I'm starting using FS and I have a problem running recon-all >> I create a folder called hptu_subj001 which contains MPRAGE.nii.gz >> within >> tutorial_subj >> First I convert nii.gz to mgz qith the command: >> recon-all -i MPRAGE.nii.gz -s hptu_subj001 >> and then in order to process all, I type: >> recon-all –i 001.mgz –subject hptu_subj001 –all >> >> cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig> >> recon-all –i 001.mgz –subject hptu_subj001 –all >> ERROR: Flag i unrecognized. >> i 001.mgz subject hptu_subj001 all >> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae >> #50-Ubuntu >> SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux >> >> recon-all -s exited with ERRORS at Fri Jun 10 12:50:04 COT 2011 >> >> then I tried with: >> >> cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj> >> recon-all –i MPRAGE.nii.gz –subject hptu_subj001 –all >> ERROR: Flag i unrecognized. >> i MPRAGE.nii.gz subject hptu_subj001 all >> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae >> #50-Ubuntu >> SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux >> >> recon-all -s exited with ERRORS at Fri Jun 10 12:36:24 COT 2011 >> >> How I can fix this error? >> >> Thanks a lot, >> >> Best regards, >> >> Carolina >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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.--
This email message is for the sole use of the intended recipient(s) and may contain confidential information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Okay,
Let me see what's gonna happen.
Thanks, *Leo Souza*
On 06/13/2011 04:10 PM, Douglas N Greve wrote:
Try adding -use-cuda to recon-all
Leo Souza wrote:
Yes, I did that, but it doesn't actually uses the GPU to do that, only CPU.
GPU percentage is 0%. (you can check it by do running: "nvidia-smi -q -d UTILIZATION -l 3" if your'e using any recent drivers.
Thanks, *Leo Souza*
On 06/13/2011 02:44 PM, Douglas N Greve wrote:
When you run recon-all, it will create a recon-all-status file in the scripts directory. This has the start times of all the processes, so you can work out how long each took. This will be wall clock time, so take that into account.
doug
Leo Souza wrote:
Hi Carolina,
Do you know how can I run Freesurfer just to get some Benchmark Numbers and to Check GPU Performance using Cuda?
Thanks, *Leo Souza*
On 06/13/2011 07:04 AM, Carolina Valencia wrote:
Thanks a lot, it works. just waiting 24 hours.
Best regards,
Carolina
2011/6/10<rspriti@nmr.mgh.harvard.edu mailto:rspriti@nmr.mgh.harvard.edu>
Hi Carolina, Sorry My bad. I was inaccurate in my previous message. -subject should work. Assuming that the MPRAGE of your subject is under the following directory: /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig set your SUBJECTS_DIR to /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig before running recon-all setenv SUBJECTS_DIR ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject $SUBJECTS_DIR/hptu_subj001 This should create a folder where Freesurfer recons will be created: cd ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig/hptu_subj001 Best, Priti > Hi Carolina, > > -subject is not recognized by Freesurfer...Use -subjid or -s instead. > > setenv SUBJECTS_DIR<path to tutorial data> > > recon-all -all -i<path to your MPRAGE>/MPRAGE.nii.gz -s<path to > freesurfer recons>/hptu_subj001 > > Priti > >> Hello Freesurfer's users, >> >> I'm starting using FS and I have a problem running recon-all >> I create a folder called hptu_subj001 which contains MPRAGE.nii.gz >> within >> tutorial_subj >> First I convert nii.gz to mgz qith the command: >> recon-all -i MPRAGE.nii.gz -s hptu_subj001 >> and then in order to process all, I type: >> recon-all –i 001.mgz –subject hptu_subj001 –all >> >> cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig> >> recon-all –i 001.mgz –subject hptu_subj001 –all >> ERROR: Flag i unrecognized. >> i 001.mgz subject hptu_subj001 all >> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae >> #50-Ubuntu >> SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux >> >> recon-all -s exited with ERRORS at Fri Jun 10 12:50:04 COT 2011 >> >> then I tried with: >> >> cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj> >> recon-all –i MPRAGE.nii.gz –subject hptu_subj001 –all >> ERROR: Flag i unrecognized. >> i MPRAGE.nii.gz subject hptu_subj001 all >> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae >> #50-Ubuntu >> SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux >> >> recon-all -s exited with ERRORS at Fri Jun 10 12:36:24 COT 2011 >> >> How I can fix this error? >> >> Thanks a lot, >> >> Best regards, >> >> Carolina >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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.--
This email message is for the sole use of the intended recipient(s) and may contain confidential information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-use-cuda is invalid I think, but I did -use-gpu and see what I get:
[root@cuda-final2 bin]# ./recon-all -use-gpu Testing for CUDA device: nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2010 NVIDIA Corporation Built on Thu_Nov__4_12:44:17_PDT_2010 Cuda compilation tools, release 3.2, V0.2.1221
Driver : 4.0 Runtime : 3.20
Acquiring CUDA device Using default device CUDA device: Tesla C2050 stable5
NVIDIA driver version info: NVRM version: NVIDIA UNIX x86_64 Kernel Module 270.41.23 Sun Jun 5 22:11:38 PDT 2011
ERROR: must specify a subject id [root@cuda-final2 bin]#
Thanks, *Leo Souza*
On 06/13/2011 04:10 PM, Douglas N Greve wrote:
Try adding -use-cuda to recon-all
Leo Souza wrote:
Yes, I did that, but it doesn't actually uses the GPU to do that, only CPU.
GPU percentage is 0%. (you can check it by do running: "nvidia-smi -q -d UTILIZATION -l 3" if your'e using any recent drivers.
Thanks, *Leo Souza*
On 06/13/2011 02:44 PM, Douglas N Greve wrote:
When you run recon-all, it will create a recon-all-status file in the scripts directory. This has the start times of all the processes, so you can work out how long each took. This will be wall clock time, so take that into account.
doug
Leo Souza wrote:
Hi Carolina,
Do you know how can I run Freesurfer just to get some Benchmark Numbers and to Check GPU Performance using Cuda?
Thanks, *Leo Souza*
On 06/13/2011 07:04 AM, Carolina Valencia wrote:
Thanks a lot, it works. just waiting 24 hours.
Best regards,
Carolina
2011/6/10<rspriti@nmr.mgh.harvard.edu mailto:rspriti@nmr.mgh.harvard.edu>
Hi Carolina, Sorry My bad. I was inaccurate in my previous message. -subject should work. Assuming that the MPRAGE of your subject is under the following directory: /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig set your SUBJECTS_DIR to /freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig before running recon-all setenv SUBJECTS_DIR ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject $SUBJECTS_DIR/hptu_subj001 This should create a folder where Freesurfer recons will be created: cd ~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig/hptu_subj001 Best, Priti > Hi Carolina, > > -subject is not recognized by Freesurfer...Use -subjid or -s instead. > > setenv SUBJECTS_DIR<path to tutorial data> > > recon-all -all -i<path to your MPRAGE>/MPRAGE.nii.gz -s<path to > freesurfer recons>/hptu_subj001 > > Priti > >> Hello Freesurfer's users, >> >> I'm starting using FS and I have a problem running recon-all >> I create a folder called hptu_subj001 which contains MPRAGE.nii.gz >> within >> tutorial_subj >> First I convert nii.gz to mgz qith the command: >> recon-all -i MPRAGE.nii.gz -s hptu_subj001 >> and then in order to process all, I type: >> recon-all –i 001.mgz –subject hptu_subj001 –all >> >> cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig> >> recon-all –i 001.mgz –subject hptu_subj001 –all >> ERROR: Flag i unrecognized. >> i 001.mgz subject hptu_subj001 all >> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae >> #50-Ubuntu >> SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux >> >> recon-all -s exited with ERRORS at Fri Jun 10 12:50:04 COT 2011 >> >> then I tried with: >> >> cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj> >> recon-all –i MPRAGE.nii.gz –subject hptu_subj001 –all >> ERROR: Flag i unrecognized. >> i MPRAGE.nii.gz subject hptu_subj001 all >> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae >> #50-Ubuntu >> SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux >> >> recon-all -s exited with ERRORS at Fri Jun 10 12:36:24 COT 2011 >> >> How I can fix this error? >> >> Thanks a lot, >> >> Best regards, >> >> Carolina >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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.--
This email message is for the sole use of the intended recipient(s) and may contain confidential information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Carolina Valencia -
Douglas N Greve -
Leo Souza -
rspriti＠nmr.mgh.harvard.edu