Hi FS'users,
I'm trying to do the Tracula tutorial but after set the configuration file I run the command trac-all cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/Tracula_Tutorial_Public/diffusion_tutorial> trac-all -help trac-all: Command not found. I have the version: freesurfer-Linux-centos4-stable-pub-v5.0.0. How I update the to version 5.1? What I have to fix to run trac-all command?
Thanks,
Best regards
Carolina
Hi Carolina,
Tracula is a part of Stable v5.1.0 not Stable v5.0.0, so you need to update your version.
-Priti
Hi FS'users,
I'm trying to do the Tracula tutorial but after set the configuration file I run the command trac-all cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/Tracula_Tutorial_Public/diffusion_tutorial> trac-all -help trac-all: Command not found. I have the version: freesurfer-Linux-centos4-stable-pub-v5.0.0. How I update the to version 5.1? What I have to fix to run trac-all command?
Thanks,
Best regards
Carolina _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Carolina - There's info on the new release and how to install it here: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
a.y
On Tue, 16 Aug 2011, Carolina Valencia wrote:
Hi FS'users, I'm trying to do the Tracula tutorial but after set the configuration file I run the command trac-all cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/Tracula_Tutorial _Public/diffusion_tutorial> trac-all -help trac-all: Command not found. I have the version: freesurfer-Linux-centos4-stable-pub-v5.0.0. How I update the to version 5.1? What I have to fix to run trac-all command?
Thanks,
Best regards
Carolina
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. -----------------------------------------------------------------------------------
On Tue, Aug 16, 2011 at 1:42 PM, Leo Souza lsouza@nvidia.com 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
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.rge@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 lsouza@nvidia.com 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. -----------------------------------------------------------------------------------
On Wed, Aug 17, 2011 at 3:19 PM, Leo Souza lsouza@nvidia.com 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
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.rge@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 lsouza@nvidia.com 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. -----------------------------------------------------------------------------------
On Wed, Aug 17, 2011 at 5:03 PM, Leo Souza lsouza@nvidia.com wrote:
Can you provide quick instructions on how to run those tests? I am new to FreeSurfer.
I'll have to defer to others on running those two programs - it's been too long since I worked on Freesurfer. I believe the website has some general information (and should contain instructions for running 'recon-all' on ernie and bert), but only a few programs in the pipeline are accelerated. Although that could be an interesting study in itself - an Amdahl's Law analysis on the entire pipeline :-)
Richard
Hi, After update the FS version to 5.1, I follow the Tracula tutorial and run the command trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/scripts/dmrirc_single_subject It starts to run but finish with errors:
writing to /home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tutorial/Diff001/dmri/dwi_orig.nii.gz... Saving bvals and bvecs mri_probedicom --i /home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tutorial//Diff001/orig/6-1.dcm
/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tutorial/Diff001/dmri/dcminfo.dat flip4fsl /home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tutorial/Diff001/dmri/dwi_orig.nii.gz /home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tutorial/Diff001/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8 fslswapdim /home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tutorial/Diff001/dmri/dwi_orig.nii.gz x -y z /home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tutorial/Diff001/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tutorial/Diff001/dmri/dwi_orig_flip.nii.gz fslorient: error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory INFO: found /home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tutorial/Diff001/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tutorial/Diff001/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tutorial/Diff001/dmri/dwi_orig_flip.mghdti.bvecs /home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tutorial/Diff001/dmri/bvecs mv -f /home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tutorial/Diff001/dmri/dwi_orig_flip.mghdti.bvals /home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tutorial/Diff001/dmri/bvals eddy_correct /home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tutorial/Diff001/dmri/dwi_orig_flip.nii.gz /home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tutorial/Diff001/dmri/dwi.nii.gz 0 fslroi: error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory fslsplit: error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory fslmerge: error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory /bin/rm: no se puede borrar «/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tutorial/Diff001/dmri/dwi_tmp????.*»: No existe el fichero o el directorio /bin/rm: no se puede borrar «/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tutorial/Diff001/dmri/dwi_ref*»: No existe el fichero o el directorio Linux cvalencia-Precision-WorkStation-T3400 2.6.35-30-generic-pae #56-Ubuntu SMP Mon Jul 11 21:51:12 UTC 2011 i686 GNU/Linux
trac-preproc exited with ERRORS at jue ago 18 10:54:43 COT 2011
any suggestions??
Thanks,
Carolina
2011/8/16 Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu
Hi Carolina - There's info on the new release and how to install it here: https://surfer.nmr.mgh.**harvard.edu/fswiki/**ReleaseNoteshttps://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
a.y
On Tue, 16 Aug 2011, Carolina Valencia wrote:
Hi FS'users,
I'm trying to do the Tracula tutorial but after set the configuration file I run the command trac-all cvalencia-Precision-**WorkStation-T3400:~/**freesurfer/subjects/Tracula_* *Tutorial _Public/diffusion_tutorial> trac-all -help trac-all: Command not found. I have the version: freesurfer-Linux-centos4-**stable-pub-v5.0.0. How I update the to version 5.1? What I have to fix to run trac-all command?
Thanks,
Best regards
Carolina
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/**compliancelinehttp://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.
Hm, it seems like all FSL commands give you a shared library error. Were you able to run FSL commands properly before updating freesusrfer?
On Thu, 18 Aug 2011, Carolina Valencia wrote:
Hi,After update the FS version to 5.1, I follow the Tracula tutorial and run the command trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/scripts/dmrirc_single_subject It starts to run but finish with errors: writing to/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto rial/Diff001/dmri/dwi_orig.nii.gz... Saving bvals and bvecs mri_probedicom --i/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto rial//Diff001/orig/6-1.dcm >/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto rial/Diff001/dmri/dcminfo.dat flip4fsl/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto rial/Diff001/dmri/dwi_orig.nii.gz/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto rial/Diff001/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8 fslswapdim/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto rial/Diff001/dmri/dwi_orig.nii.gz x -y z/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto rial/Diff001/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto rial/Diff001/dmri/dwi_orig_flip.nii.gz fslorient: error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory INFO: found/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto rial/Diff001/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto rial/Diff001/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto rial/Diff001/dmri/dwi_orig_flip.mghdti.bvecs/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto rial/Diff001/dmri/bvecs mv -f/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto rial/Diff001/dmri/dwi_orig_flip.mghdti.bvals/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto rial/Diff001/dmri/bvals eddy_correct/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto rial/Diff001/dmri/dwi_orig_flip.nii.gz/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tuto rial/Diff001/dmri/dwi.nii.gz 0 fslroi: error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory fslsplit: error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory fslmerge: error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory /bin/rm: no se puede borrar«/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tut orial/Diff001/dmri/dwi_tmp????.*»: No existe el fichero o el directorio /bin/rm: no se puede borrar«/home/cvalencia/freesurfer/subjects/Tracula_Tutorial_Public//diffusion_tut orial/Diff001/dmri/dwi_ref*»: No existe el fichero o el directorio Linux cvalencia-Precision-WorkStation-T3400 2.6.35-30-generic-pae #56-Ubuntu SMP Mon Jul 11 21:51:12 UTC 2011 i686 GNU/Linux
trac-preproc exited with ERRORS at jue ago 18 10:54:43 COT 2011
any suggestions??
Thanks,
Carolina
2011/8/16 Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu
Hi Carolina - There's info on the new release and how to install it here: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes a.yOn Tue, 16 Aug 2011, Carolina Valencia wrote:
Hi FS'users, I'm trying to do the Tracula tutorial but after set the configuration file I run the command trac-allcvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/Tracula_Tutoria l _Public/diffusion_tutorial> trac-all -help trac-all: Command not found. I have the version: freesurfer-Linux-centos4-stable-pub-v5.0.0. How I update the to version 5.1? What I have to fix to run trac-all command?
Thanks, Best regards CarolinaThe 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.
Yes, I was able to run FSL commands, but normally I usually use the FSL GUI, but now you're pointing this out, I try to run the commands that did not run with tracula and shows me the same error about loading shared libraries. How I can fix this?
Carolina
2011/8/18 Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu
Hm, it seems like all FSL commands give you a shared library error. Were you able to run FSL commands properly before updating freesusrfer?
On Thu, 18 Aug 2011, Carolina Valencia wrote:
Hi,After update the FS version to 5.1, I follow the Tracula tutorial and
run
the command trac-all -prep -c $TUTORIAL_DATA/diffusion_**tutorial/scripts/dmrirc_**single_subject It starts to run but finish with errors: writing to/home/cvalencia/freesurfer/**subjects/Tracula_Tutorial_** Public//diffusion_tuto rial/Diff001/dmri/dwi_orig.**nii.gz... Saving bvals and bvecs mri_probedicom --i/home/cvalencia/freesurfer/**subjects/Tracula_Tutorial_ **Public//diffusion_tuto rial//Diff001/orig/6-1.dcm >/home/cvalencia/freesurfer/** subjects/Tracula_Tutorial_**Public//diffusion_tuto rial/Diff001/dmri/dcminfo.dat flip4fsl/home/cvalencia/**freesurfer/subjects/Tracula_** Tutorial_Public//diffusion_**tuto rial/Diff001/dmri/dwi_orig.**nii.gz/home/cvalencia/** freesurfer/subjects/Tracula_**Tutorial_Public//diffusion_**tuto rial/Diff001/dmri/dwi_orig_**flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8 fslswapdim/home/cvalencia/**freesurfer/subjects/Tracula_** Tutorial_Public//diffusion_**tuto rial/Diff001/dmri/dwi_orig.**nii.gz x -y z/home/cvalencia/freesurfer/** subjects/Tracula_Tutorial_**Public//diffusion_tuto rial/Diff001/dmri/dwi_orig_**flip.nii.gz fslorient -forceradiological/home/**cvalencia/freesurfer/subjects/** Tracula_Tutorial_Public//**diffusion_tuto rial/Diff001/dmri/dwi_orig_**flip.nii.gz fslorient: error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory INFO: found/home/cvalencia/**freesurfer/subjects/Tracula_** Tutorial_Public//diffusion_**tuto rial/Diff001/dmri/dwi_orig.**mghdti.bvals, converting to FSL format INFO: found/home/cvalencia/**freesurfer/subjects/Tracula_** Tutorial_Public//diffusion_**tuto rial/Diff001/dmri/dwi_orig.**mghdti.bvecs, converting to FSL format mv -f/home/cvalencia/freesurfer/**subjects/Tracula_Tutorial_** Public//diffusion_tuto rial/Diff001/dmri/dwi_orig_**flip.mghdti.bvecs/home/** cvalencia/freesurfer/subjects/**Tracula_Tutorial_Public//**diffusion_tuto rial/Diff001/dmri/bvecs mv -f/home/cvalencia/freesurfer/**subjects/Tracula_Tutorial_** Public//diffusion_tuto rial/Diff001/dmri/dwi_orig_**flip.mghdti.bvals/home/** cvalencia/freesurfer/subjects/**Tracula_Tutorial_Public//**diffusion_tuto rial/Diff001/dmri/bvals eddy_correct/home/cvalencia/**freesurfer/subjects/Tracula_** Tutorial_Public//diffusion_**tuto rial/Diff001/dmri/dwi_orig_**flip.nii.gz/home/cvalencia/** freesurfer/subjects/Tracula_**Tutorial_Public//diffusion_**tuto rial/Diff001/dmri/dwi.nii.gz 0 fslroi: error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory fslsplit: error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory fslmerge: error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory /bin/rm: no se puede borrar«/home/cvalencia/** freesurfer/subjects/Tracula_**Tutorial_Public//diffusion_tut orial/Diff001/dmri/dwi_tmp????**.*»: No existe el fichero o el directorio /bin/rm: no se puede borrar«/home/cvalencia/** freesurfer/subjects/Tracula_**Tutorial_Public//diffusion_tut orial/Diff001/dmri/dwi_ref*»: No existe el fichero o el directorio Linux cvalencia-Precision-**WorkStation-T3400 2.6.35-30-generic-pae #56-Ubuntu SMP Mon Jul 11 21:51:12 UTC 2011 i686 GNU/Linux
trac-preproc exited with ERRORS at jue ago 18 10:54:43 COT 2011
any suggestions??
Thanks,
Carolina
2011/8/16 Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu
Hi Carolina - There's info on the new release and how to install it here: https://surfer.nmr.mgh.**harvard.edu/fswiki/**ReleaseNotes<https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes> a.yOn Tue, 16 Aug 2011, Carolina Valencia wrote:
Hi FS'users, I'm trying to do the Tracula tutorial but after set the configuration file I run the command trac-allcvalencia-Precision-**WorkStation-T3400:~/**freesurfer/subjects/Tracula_* *Tutoria l _Public/diffusion_tutorial> trac-all -help trac-all: Command not found. I have the version: freesurfer-Linux-centos4-**stable-pub-v5.0.0. How I update the to version 5.1? What I have to fix to run trac-all command?
Thanks, Best regards CarolinaThe 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/**compliancelinehttp://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
-
Anastasia Yendiki -
Carolina Valencia -
Leo Souza -
Priti Srinivasan -
R Edgar