Re: [Freesurfer] Reproducible Qdec error color bar not updated when clicking reverse value.
Does anyone knows which command would exercise the GPUs using CUDA as benchmark? Thanks, Leo Souza -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, July 26, 2011 8:58 AM To: Knut J Bjuland Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] Reproducible Qdec error color bar not updated when clicking reverse value. Hi Knut, why does it need to be reversed? doug Knut J Bjuland wrote: > Hi > When I click on reverse values in Qdec the color on the hemisphere will > change, but the color bar at the bottom on the screen will stay the > same. Is there anything I can do to force Qdec to change the color bar > at the bottom of the screen? I am send along to attachment one with > reverse values and one without reversing the values. To reproduce this > error I have sent a picture of the same correlation with one exception I > have clicked on reverse value on the file named error.jpg. > > Best regards > Knut J > > > > > > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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. --- 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] How to run a benchmark on GPU with FreeSufer?
Hi Dear All, Does anyone knows how do I run a benchmark test on GPU with FreeSurfer and CUDA? Thanks, Leo Souza --- 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 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.
Re: [Freesurfer] How to run a benchmark on GPU with FreeSufer?
I want to verify what's the performance of different GPUs using FreeSurfer as Benchmark App. Thanks, Leo Souza -Original Message- From: R Edgar [mailto:freesurfer@gmail.com] Sent: Wednesday, August 17, 2011 6:20 AM To: Leo Souza; Freesurfer Mailing List Cc: Douglas N Greve Subject: Re: [Freesurfer] How to run a benchmark on GPU with FreeSufer? On Tue, Aug 16, 2011 at 1:42 PM, Leo Souza wrote: > Does anyone knows how do I run a benchmark test on GPU with FreeSurfer and > CUDA? Beyond running a comparison between [x] and [x]_cuda? If you want numbers on individual routines, then the cudatest directory holds a lot of test cases which will run one routine and compare timings (these are used by the tests under test_tm). Could you explain what information you're looking for? Richard --- 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 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.
Re: [Freesurfer] How to run a benchmark on GPU with FreeSufer?
Can you provide quick instructions on how to run those tests? I am new to FreeSurfer. Thanks, Leo Souza -Original Message- From: R Edgar [mailto:freesurfer@gmail.com] Sent: Wednesday, August 17, 2011 12:36 PM To: Leo Souza Cc: Freesurfer Mailing List; Douglas N Greve Subject: Re: [Freesurfer] How to run a benchmark on GPU with FreeSufer? On Wed, Aug 17, 2011 at 3:19 PM, Leo Souza wrote: > I want to verify what's the performance of different GPUs using FreeSurfer as > Benchmark App. In that case, the two best programs to run are mri_em_register[_cuda] for linear registration mri_ca_register[_cuda] for nonlinear registration You should know that Freesurfer quite likes the Nehalem memory hardware, whether in CPU or GPU mode. Also, mri_em_register_cuda has an additional pair of 'fast' options which cut the runtime even more (look at the top of the source file), but will sometimes give a different registration to the CPU version. Richard --- 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 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.
Re: [Freesurfer] recon-all -s exited with ERRORS
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 <mailto:rspr...@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 > > recon-all -all -i /MPRAGE.nii.gz -s 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 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.
Re: [Freesurfer] recon-all -s exited with ERRORS
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 2011/6/10mailto:rspr...@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 > > recon-all -all -i/MPRAGE.nii.gz -s 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 confident
Re: [Freesurfer] recon-all -s exited with ERRORS
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 2011/6/10mailto:rspr...@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 > > recon-all -all -i/MPRAGE.nii.gz -s 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
Re: [Freesurfer] recon-all -s exited with ERRORS
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 2011/6/10mailto:rspr...@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 > > recon-all -all -i/MPRAGE.nii.gz -s 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 cont
Re: [Freesurfer] recon-all -s exited with ERRORS
-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 2011/6/10mailto:rspr...@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 > > recon-all -all -i/MPRAGE.nii.gz -s 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
Re: [Freesurfer] recon-all -s exited with ERRORS
How long does it take to run the test? Thanks, Leo Souza From: Pedro Paulo de Magalhães Oliveira Junior [mailto:p...@netfilter.com.br] Sent: Monday, June 13, 2011 6:20 PM To: Leo Souza Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all -s exited with ERRORS recon-all -s bert -all -use-gpu -- iOS 4.3 Em 13/06/2011, às 21:30, Leo Souza mailto:lso...@nvidia.com>> escreveu: /recon-all -use-gpu --- 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 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.
