I've posted two scripts -- one for starting an instance and one for running freesurfer -- using Pedro's AMI. They're in Python, and require two additional Python packages which are easily installable. If people find this a good starting point, please send me suggestions or code (including suggestions to do the running Freesurfer part completely differently) but otherwise you're welcome to just copy the scripts and modify them yourselves if they're useful to you.
https://github.com/thomasballinger/remoteFreesurfer Thomas Ballinger 2011/11/11 Nick Schmansky <ni...@nmr.mgh.harvard.edu> > thanks Pedro Paulo! > > Thomas, yes that script would be useful. A handy 'use case' for a > contributor to add to that wiki page would be to show how to use your > script to process the 40 tutorial subjects we supply on our site. > > n. > > On Fri, 2011-11-11 at 09:11 -0500, Thomas Ballinger wrote: > > I had previously worked on a script which, given Amazon EC2 > > credentials, would spin up the instance, upload freesurfer data and > > run it, then send an email when done - if this would be helpful to > > anyone I'll bother to finish it, we use local compute resources so I > > never quite bothered. Now that Pedro's created the image most of the > > work is done, I had been manually configuring a clean ubuntu image > > previously. > > > > > > Thomas Ballinger > > Psychiatry Neuroimaging Lab > > Brigham and Women's Hospital > > > > 2011/11/11 Pedro Paulo de Magalhães Oliveira Junior > > <p...@netfilter.com.br> > > I've put together the basic tutorial on getting started using > > Amazon AWS system: > > > > > > It's in the same place Nick pointed > > out: https://surfer.nmr.mgh.harvard.edu/fswiki/AmazonCloud > > > > > > > > > --------------------------------------------------------------------- > > Pedro Paulo de Magalhães Oliveira Junior > > Netfilter & SpeedComm Telecom > > -- www.netfilter.com.br > > -- For > > mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 > > > > > > > > > > > > > > 2011/11/9 Nick Schmansky <ni...@nmr.mgh.harvard.edu> > > Pedro Paulo, > > > > thanks for posting the info. i've added this to the > > Download wiki page, > > and created a stub page for the Amazon Cloud: > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/AmazonCloud > > > > i've never set one up so i have no idea how to do it. > > maybe someone can > > flesh-out this page as using the ec2 seems like a > > great alternative to a > > cluster. > > > > n. > > > > > > On Wed, 2011-11-09 at 22:44 -0200, Pedro Paulo de > > Magalhães Oliveira > > Junior wrote: > > > No. This is for non GPU instances > > > > > > -- iOS 5.0 > > > > > > Em 09/11/2011, às 22:28, Satrajit Ghosh > > <sa...@mit.edu> escreveu: > > > > > > > > > > > > > hi pedro, > > > > > > > > > > > > will this work with gpu instances as well? > > > > > > > > cheers, > > > > > > > > satra > > > > > > > > 2011/11/9 Pedro Paulo de Magalhães Oliveira Junior > > > > <p...@netfilter.com.br> > > > > Some weeks ago I was asked about a public > > image (AMI) to run > > > > in the Amazon EC2 infrastructure > > > > > > > > > > > > If you want to use FreeSurfer in the EC2 > > infrastructure you > > > > can use this public AMI: > > 060244368407/FREESURFER51 > > > > > > > > > > > > Just for your information this AMI can run > > a recon-all in 23 > > > > hours in an Amazon AWS Small Instance. So > > with the current > > > > Amazon cost per Small Instance/Hour you'll > > have a recon-all > > > > for USD 2.04 > > > > > > > > > > > > Amazon request a credit card in order to > > create an account > > > > in http://aws.amazon.com > > > > > > > > > > > > Hope it helps, > > > > > > > > > > > > Pedro Paulo Jr. > > > > > > > --------------------------------------------------------------------- > > > > Pedro Paulo de Magalhães Oliveira Junior > > > > Netfilter & SpeedComm Telecom > > > > -- www.netfilter.com.br > > > > -- For > > > > mobile: > > http://itunes.apple.com/br/artist/netfilter/id365306441 > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > 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 > > > > > > > > > > > > _______________________________________________ > > 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.
