It would be great if Freesurfer maintained an official AMI. One important reason to do so is security. If the AMI is maintained by the organization, then people can feel reassured that their data is not being downloaded to a compromised instance, not that any on this board would have such malicious intent. Moreover, it could contain such scripts as makes the analysis process easier.
- Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805 2011/11/14 Pedro Paulo de Magalhães Oliveira Junior <p...@netfilter.com.br> > Ok. I'll label as private this AMI that has .license file. > > Maybe we can make a tutorial on how to create an AMI instead. > > --------------------------------------------------------------------- > Pedro Paulo de Magalhães Oliveira Junior > Netfilter & SpeedComm Telecom > -- www.netfilter.com.br > -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 > > > > > On Mon, Nov 14, 2011 at 21:07, Nick Schmansky > <ni...@nmr.mgh.harvard.edu>wrote: > >> Glad to hear it works well. To revisit the issue of the license (in the >> form of the .license file which needs to be in the $FREESURFER_HOME >> directory and the request of which is used for usage tracking), I think >> the convention to follow for any publicly available AMI freesurfer >> instances should be to not include a .license file with it, so as to >> force the download of this file (so that freesurfer usage will be >> tracked). A user need only do this once for however many times they use >> the cloud instance. >> >> N. >> >> On Mon, 2011-11-14 at 17:16 -0500, Joshua Lee wrote: >> > Thanks again Pedro. I just ran 220 brains through in day or two using >> > the cloud. Fantastic. >> > The script people have been talking about would have been useful. >> > One thing I didn't realize was that I should have moved the freesurfer >> > subject directory from /usr/local/freesurfer/subjects to the larger >> > disk that comes with the instance. I had disk-write errors because the >> > the main partition ran out of space. >> > >> > Anyway, ec2 rocks with Freesurfer. >> > - >> > >> > Joshua Lee >> > >> > Graduate Student >> > Center for Mind and Brain & >> > >> > Department of Psychology >> > >> > University of California, Davis >> > 530.747.3805 >> > >> > >> > 2011/11/12 Nolan Nichols <bnn...@uw.edu> >> > If only running a small number of instances, I think it is >> > reasonable >> > to leave the ami w/o a .license file since it is easy enough >> > to scp it >> > up to the cloud. For running a cluster it would be nice to >> > have a >> > script, perhaps using Fabric, to upload a .license file to >> > each >> > instance in a cluster. As it stands, the starcluster FS AMI >> > does not >> > have a .license file and requires one to be uploaded manually. >> > >> > Nolan >> > >> > 2011/11/12 Thomas Ballinger <thomasballin...@gmail.com>: >> > >> > > Perhaps the AMI image could be without a licence file and >> > uploading one >> > > (acquired though normal means) would be required? (I >> > suppose that's the >> > > basic solution we're looking for a clean way around) >> > > >> > > 2011/11/12 Pedro Paulo de Magalhães Oliveira Junior >> > <p...@netfilter.com.br> >> > >> >> > >> Maybe we can set up a web server in the Martinos center and >> > the AMI Image >> > >> can authenticate in it. >> > >> >> > >> --------------------------------------------------------------------- >> > >> Pedro Paulo de Magalhães Oliveira Junior >> > >> Netfilter & SpeedComm Telecom >> > >> -- www.netfilter.com.br >> > >> -- For >> > mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 >> > >> >> > >> >> > >> >> > >> >> > >> On Sat, Nov 12, 2011 at 15:28, Nick Schmansky >> > <ni...@nmr.mgh.harvard.edu> >> > >> wrote: >> > >>> >> > >>> I'm happy to see the work getting the cloud to be >> > feasible. I still need >> > >>> to catch up on this thread but one issue that I'd like to >> > sort out is >> > >>> tracking the license count. Its fine for a new user to >> > use an existing >> > >>> image, but I think there will need to be a way to remind >> > people to request >> > >>> our .license file even if they don't actually use the file >> > so that cloud >> > >>> usages get counted (license count is critical for us for >> > grant renewal >> > >>> purposes). Ideas on a clean way to do this? >> > >>> N. >> > >>> >> > >>> On Nov 12, 2011, at 11:10 AM, Thomas Ballinger >> > >>> <thomasballin...@gmail.com> wrote: >> > >>> >> > >>> Satra, the ipython example looks great. The scripts I >> > posted also use >> > >>> fabric for running Freesurfer, but don't download >> > Freesurfer due to it >> > >>> already being installed on Pedro's image. I agree with >> > Satra that >> > >>> individually administered instances might work better for >> > those wishing to >> > >>> run a few cases with Freesurfer, particularly due to the >> > predictable long >> > >>> running time (lessening the benefits of job distribution) >> > and ability of a >> > >>> recon-all job to efficiently use all of a ec2 small >> > instance's cpu. I think >> > >>> starcluster is pretty awesome, and I would love to push >> > people in that >> > >>> direction, but it won't be quite as push-button, and the >> > benefits may be >> > >>> minimal for small use cases. That's not to say there >> > aren't plenty of folks >> > >>> who would rather use Nolan's solution (me for one :)) >> > >>> Tom >> > >>> >> > >>> >> > >>> On Sat, Nov 12, 2011 at 9:14 AM, Nolan Nichols >> > <bnn...@uw.edu> wrote: >> > >>>> >> > >>>> Hi Satra, >> > >>>> >> > >>>> Fabric does look nice, thanks for pointing it out and for >> > a link to the >> > >>>> ipython_in_a_box example. >> > >>>> >> > >>>> That framework might work for what I had in mind for >> > freesurfer and >> > >>>> starcluster, which uses the same idea to keep the initial >> > AMI footprint >> > >>>> smaller/flexible. >> > >>>> >> > >>>> Cheers, >> > >>>> >> > >>>> Nolan >> > >>>> >> > >>>> On Nov 12, 2011 7:32 AM, "Satrajit Ghosh" <sa...@mit.edu> >> > wrote: >> > >>>>> >> > >>>>> hi nolan, >> > >>>>> i think starcluster is a great way to create a cluster >> > on aws. but for >> > >>>>> those wanting to create a single instance and install >> > things on an ami >> > >>>>> without actually having a large ami, fabric might be a >> > good option. >> > >>>>> fabric: >> > >>>>> http://docs.fabfile.org/en/1.3.2/index.html >> > >>>>> example: (another neurodebian ami) >> > >>>>> >> > >> https://github.com/wholeslide/ipython_in_a_box/blob/master/fabfile.py >> > >>>>> cheers, >> > >>>>> >> > >>>>> satra >> > >>>>> >> > >>>>> On Sat, Nov 12, 2011 at 6:11 AM, Nolan Nichols >> > <bnn...@uw.edu> wrote: >> > >>>>>> >> > >>>>>> Thanks, Pedro! >> > >>>>>> >> > >>>>>> I am glad to see that you posted a public AMI for >> > freesurfer. And >> > >>>>>> thanks to Thomas for producin documentation on how to >> > use it. >> > >>>>>> >> > >>>>>> This thread inspired me share a StarCluster AMI >> > (ami-27f1384e in the >> > >>>>>> us-east-1 region) that I built for batch FS jobs, which >> > includes the >> > >>>>>> initial setup for installing tools from the NeuroDebian >> > repository. >> > >>>>>> I've also been playing around with using s3fs, which >> > allows Amazon's >> > >>>>>> S3 to be mounted as a drive and accessed directly as >> > the >> > >>>>>> "subjects_dir". >> > >>>>>> >> > >>>>>> The AMI can be launched here: >> > >>>>>> >> > >>>>>> >> > >> https://console.aws.amazon.com/ec2/home?region=us-east-1#launchAmi=ami-27f1384e >> > >>>>>> >> > >>>>>> I did not include the .license for FS as I wasn't sure >> > about licensing >> > >>>>>> issues, but I would be happy to publish an AMI with a >> > built-in license >> > >>>>>> if I get the go ahead. For now you will need to start a >> > cluster and >> > >>>>>> your license to each instance. >> > >>>>>> >> > >>>>>> A few details: >> > >>>>>> >> > >>>>>> Ubuntu 10.04 x86 >> > >>>>>> built from StarClusters ami-8cf913e5 >> > >>>>>> us-east-1 region >> > >>>>>> See the StarCluster details at >> > http://web.mit.edu/stardev/cluster/ >> > >>>>>> Customizing StarCluster >> > >>>>>> >> > >>>>>> >> > ( >> http://web.mit.edu/stardev/cluster/docs/latest/manual/create_new_ami.html >> ) >> > >>>>>> s3fs (http://code.google.com/p/s3fs/) >> > >>>>>> Freesurfer 5.1 32-bit >> > >>>>>> NeuroDebian ready (so you can apt-get install mricron, >> > fsl, nipype, >> > >>>>>> etc.) >> > >>>>>> >> > >>>>>> Thanks again for starting this thread, and let me know >> > if I can help >> > >>>>>> in any way. It would be great to see "cloud" resources >> > be readily >> > >>>>>> accessibly to the community with minimal effort to get >> > a cluster with >> > >>>>>> freesurfer and tools available via neurodebian up and >> > running. >> > >>>>>> >> > >>>>>> Cheers, >> > >>>>>> >> > >>>>>> Nolan >> > >>>>>> _______________________________________________ >> > >>>>>> 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 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 >> > >> > >> >> >
_______________________________________________ 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.
