Re: [Freesurfer] parellizing Freesurfer
You'll find some answers here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15728.html 2011/2/26 Pablo Polosecki ppolose...@mail.rockefeller.edu Hi Pedro and everyone, Thanks so much for pointing me there. I seems like the only way to parallelize is to run several recon-all simultanously intstead of wating for one to finshe and then run the following. I wonder if you (of someone else) managed to achieve some further decrease in running times, making a single recon-all run faster or something like that. Was it any different in the Amazon EC2? It would seem that the analysis fo functional data (at least parts of it) could run in parallel, since the analysis of one voxel is independent of the rest. I would love to know if this is something people do. An ugly implementation could be to split the volumes into several small volume files and run the analysis separately and then merge back the output volumes. Has anyone done something like that or nicer? Thanks! Pablo 2011/2/26 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br Yes. Take a look at: http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.HowcanIreducethetimeofrecon-allinagroupofpatients.3F Also I have successfully executed it at Amazon EC2 instances. PPJ - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile On Sat, Feb 26, 2011 at 19:59, Pablo Polosecki ppolose...@mail.rockefeller.edu wrote: Hi all, I was wondering if someone out there has any experience trying to parallelize their analysis streams in clusters or multiprocessor machines. I was thinking also about the cloud computing services offered by Google, Amazon or other. Has anyone tried or has any plans of implementing something along those lines? Best wishes, Pablo ___ 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.
Re: [Freesurfer] parellizing Freesurfer
Thank you, Pedro. That is really useful. 2011/2/27 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br You'll find some answers here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15728.html 2011/2/26 Pablo Polosecki ppolose...@mail.rockefeller.edu Hi Pedro and everyone, Thanks so much for pointing me there. I seems like the only way to parallelize is to run several recon-all simultanously intstead of wating for one to finshe and then run the following. I wonder if you (of someone else) managed to achieve some further decrease in running times, making a single recon-all run faster or something like that. Was it any different in the Amazon EC2? It would seem that the analysis fo functional data (at least parts of it) could run in parallel, since the analysis of one voxel is independent of the rest. I would love to know if this is something people do. An ugly implementation could be to split the volumes into several small volume files and run the analysis separately and then merge back the output volumes. Has anyone done something like that or nicer? Thanks! Pablo 2011/2/26 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br Yes. Take a look at: http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.HowcanIreducethetimeofrecon-allinagroupofpatients.3F Also I have successfully executed it at Amazon EC2 instances. PPJ - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile On Sat, Feb 26, 2011 at 19:59, Pablo Polosecki ppolose...@mail.rockefeller.edu wrote: Hi all, I was wondering if someone out there has any experience trying to parallelize their analysis streams in clusters or multiprocessor machines. I was thinking also about the cloud computing services offered by Google, Amazon or other. Has anyone tried or has any plans of implementing something along those lines? Best wishes, Pablo ___ 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] parellizing Freesurfer
Hi all, I was wondering if someone out there has any experience trying to parallelize their analysis streams in clusters or multiprocessor machines. I was thinking also about the cloud computing services offered by Google, Amazon or other. Has anyone tried or has any plans of implementing something along those lines? Best wishes, Pablo ___ 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] parellizing Freesurfer
Yes. Take a look at: http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.HowcanIreducethetimeofrecon-allinagroupofpatients.3F Also I have successfully executed it at Amazon EC2 instances. PPJ - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile On Sat, Feb 26, 2011 at 19:59, Pablo Polosecki ppolose...@mail.rockefeller.edu wrote: Hi all, I was wondering if someone out there has any experience trying to parallelize their analysis streams in clusters or multiprocessor machines. I was thinking also about the cloud computing services offered by Google, Amazon or other. Has anyone tried or has any plans of implementing something along those lines? Best wishes, Pablo ___ 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.
Re: [Freesurfer] parellizing Freesurfer
Hi Pedro and everyone, Thanks so much for pointing me there. I seems like the only way to parallelize is to run several recon-all simultanously intstead of wating for one to finshe and then run the following. I wonder if you (of someone else) managed to achieve some further decrease in running times, making a single recon-all run faster or something like that. Was it any different in the Amazon EC2? It would seem that the analysis fo functional data (at least parts of it) could run in parallel, since the analysis of one voxel is independent of the rest. I would love to know if this is something people do. An ugly implementation could be to split the volumes into several small volume files and run the analysis separately and then merge back the output volumes. Has anyone done something like that or nicer? Thanks! Pablo 2011/2/26 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br Yes. Take a look at: http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.HowcanIreducethetimeofrecon-allinagroupofpatients.3F Also I have successfully executed it at Amazon EC2 instances. PPJ - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile On Sat, Feb 26, 2011 at 19:59, Pablo Polosecki ppolose...@mail.rockefeller.edu wrote: Hi all, I was wondering if someone out there has any experience trying to parallelize their analysis streams in clusters or multiprocessor machines. I was thinking also about the cloud computing services offered by Google, Amazon or other. Has anyone tried or has any plans of implementing something along those lines? Best wishes, Pablo ___ 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.
