Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
As requested I removed the AMI image because that image contains a .license file. I can republish the image when we find a solution for the licensing issue. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 2011/11/15 Joshua Lee jki...@ucdavis.edu 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.eduwrote: 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. ___ 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] Amazon EC2 Version of FreeSurfer 5.1 Available
Hi PPJ, I would rather people use FS without licenses than find themselves unable to use it, so why not leave it for now. Can you put a request that they first download a license or register on your website? Alternatively, can you just remove the .license file from the AMI forcing the users to get one? thanks for making this available Bruce On Fri, 18 Nov 2011, Pedro Paulo de Magalhães Oliveira Junior wrote: As requested I removed the AMI image because that image contains a .license file. I can republish the image when we find a solution for the licensing issue. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom-- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 2011/11/15 Joshua Lee jki...@ucdavis.edu 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. ___ 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] Amazon EC2 Version of FreeSurfer 5.1 Available
I have restored the image: 060244368407/FREESURFER51 I'll create a web service that can log the number of instances spawned. Is that ok with you? - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 2011/11/18 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi PPJ, I would rather people use FS without licenses than find themselves unable to use it, so why not leave it for now. Can you put a request that they first download a license or register on your website? Alternatively, can you just remove the .license file from the AMI forcing the users to get one? thanks for making this available Bruce On Fri, 18 Nov 2011, Pedro Paulo de Magalhães Oliveira Junior wrote: As requested I removed the AMI image because that image contains a .license file. I can republish the image when we find a solution for the licensing issue. --**--**- Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom-- www.netfilter.com.br -- For mobile: http://itunes.apple.**com/br/artist/netfilter/** id365306441 http://itunes.apple.com/br/artist/netfilter/id365306441 2011/11/15 Joshua Lee jki...@ucdavis.edu 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 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. 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. ___ 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] Amazon EC2 Version of FreeSurfer 5.1 Available
When I used the AMI, (maybe not Pedro's), so I sftp'd a license file to each instance prior to running an analysis. Not a big deal. I didn't get a new license for each instance, but copied the same one to multiple instances. Joshua 2011/11/18 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br I have restored the image: 060244368407/FREESURFER51 I'll create a web service that can log the number of instances spawned. Is that ok with you? - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 2011/11/18 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi PPJ, I would rather people use FS without licenses than find themselves unable to use it, so why not leave it for now. Can you put a request that they first download a license or register on your website? Alternatively, can you just remove the .license file from the AMI forcing the users to get one? thanks for making this available Bruce On Fri, 18 Nov 2011, Pedro Paulo de Magalhães Oliveira Junior wrote: As requested I removed the AMI image because that image contains a .license file. I can republish the image when we find a solution for the licensing issue. --**--** - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom-- www.netfilter.com.br -- For mobile: http://itunes.apple.**com/br/artist/netfilter/** id365306441 http://itunes.apple.com/br/artist/netfilter/id365306441 2011/11/15 Joshua Lee jki...@ucdavis.edu 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 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. 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. ___ 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
Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
Long term, after we put together an 'official' instance of the AMI with scripts (which might well be an instance that Pedro Paulo created) I think sftp'ing the .license file to each instance is the way to go. The .license file need only apply to the user (not each instance or run). N. On Fri, 2011-11-18 at 08:00 -0800, Joshua Lee wrote: When I used the AMI, (maybe not Pedro's), so I sftp'd a license file to each instance prior to running an analysis. Not a big deal. I didn't get a new license for each instance, but copied the same one to multiple instances. Joshua 2011/11/18 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br I have restored the image: 060244368407/FREESURFER51 I'll create a web service that can log the number of instances spawned. Is that ok with you? - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 2011/11/18 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi PPJ, I would rather people use FS without licenses than find themselves unable to use it, so why not leave it for now. Can you put a request that they first download a license or register on your website? Alternatively, can you just remove the .license file from the AMI forcing the users to get one? thanks for making this available Bruce On Fri, 18 Nov 2011, Pedro Paulo de Magalhães Oliveira Junior wrote: As requested I removed the AMI image because that image contains a .license file. I can republish the image when we find a solution for the licensing issue. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom-- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 2011/11/15 Joshua Lee jki...@ucdavis.edu 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:
Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
hi nick, i really like pedro's idea of tracking through instance tracking as opposed to licenses. on a separate project we are setting up the ability to pull up as many instances as necessary and install whatever software environment that's needed to run your analysis. we'll try to ensure that each person has a license file in their folder that we can pull. however given the current licensing of freesurfer, one can easily remove the license components. that's why i feel the instance tracking is painless and provides you with a better estimate of the number of times freesurfer is run. as an example, at mit we have a single license which everybody uses and that's not a great way for you to track the number of projects or subjects run through freesurfer. cheers, satra 2011/11/18 Nick Schmansky ni...@nmr.mgh.harvard.edu Long term, after we put together an 'official' instance of the AMI with scripts (which might well be an instance that Pedro Paulo created) I think sftp'ing the .license file to each instance is the way to go. The .license file need only apply to the user (not each instance or run). N. On Fri, 2011-11-18 at 08:00 -0800, Joshua Lee wrote: When I used the AMI, (maybe not Pedro's), so I sftp'd a license file to each instance prior to running an analysis. Not a big deal. I didn't get a new license for each instance, but copied the same one to multiple instances. Joshua 2011/11/18 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br I have restored the image: 060244368407/FREESURFER51 I'll create a web service that can log the number of instances spawned. Is that ok with you? - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 2011/11/18 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi PPJ, I would rather people use FS without licenses than find themselves unable to use it, so why not leave it for now. Can you put a request that they first download a license or register on your website? Alternatively, can you just remove the .license file from the AMI forcing the users to get one? thanks for making this available Bruce On Fri, 18 Nov 2011, Pedro Paulo de Magalhães Oliveira Junior wrote: As requested I removed the AMI image because that image contains a .license file. I can republish the image when we find a solution for the licensing issue. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom-- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 2011/11/15 Joshua Lee jki...@ucdavis.edu 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
Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
Hi Satra we did originally consider tracking usage in that way, but it seemed invasive and a bit creepy to have FreeSurfer keeping track of what you were up to and reporting back to us, so ultimately we decided not to Bruce On Fri, 18 Nov 2011, Satrajit Ghosh wrote: hi nick, i really like pedro's idea of tracking through instance tracking as opposed to licenses. on a separate project we are setting up the ability to pull up as many instances as necessary and install whatever software environment that's needed to run your analysis. we'll try to ensure that each person has a license file in their folder that we can pull. however given the current licensing of freesurfer, one can easily remove the license components. that's why i feel the instance tracking is painless and provides you with a better estimate of the number of times freesurfer is run. as an example, at mit we have a single license which everybody uses and that's not a great way for you to track the number of projects or subjects run through freesurfer. cheers, satra 2011/11/18 Nick Schmansky ni...@nmr.mgh.harvard.edu Long term, after we put together an 'official' instance of the AMI with scripts (which might well be an instance that Pedro Paulo created) I think sftp'ing the .license file to each instance is the way to go. The .license file need only apply to the user (not each instance or run). N. On Fri, 2011-11-18 at 08:00 -0800, Joshua Lee wrote: When I used the AMI, (maybe not Pedro's), so I sftp'd a license file to each instance prior to running an analysis. Not a big deal. I didn't get a new license for each instance, but copied the same one to multiple instances. Joshua 2011/11/18 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br I have restored the image: 060244368407/FREESURFER51 I'll create a web service that can log the number of instances spawned. Is that ok with you? - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 2011/11/18 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi PPJ, I would rather people use FS without licenses than find themselves unable to use it, so why not leave it for now. Can you put a request that they first download a license or register on your website? Alternatively, can you just remove the .license file from the AMI forcing the users to get one? thanks for making this available Bruce On Fri, 18 Nov 2011, Pedro Paulo de Magalhães Oliveira Junior wrote: As requested I removed the AMI image because that image contains a .license file. I can republish the image when we find a solution for the licensing issue. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom-- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 2011/11/15 Joshua Lee jki...@ucdavis.edu 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. -
Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
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
Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
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.
Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
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.eduwrote: 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 :))
Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
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.
Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
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.
Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
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 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
Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
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
Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
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.eduwrote: 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
Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
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.eduwrote: 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
Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
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
Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
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.
Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
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.
Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
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
Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
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
Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
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] Amazon EC2 Version of FreeSurfer 5.1 Available
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.
Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
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 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] Amazon EC2 Version of FreeSurfer 5.1 Available
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 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] Amazon EC2 Version of FreeSurfer 5.1 Available
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
Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
Tomorrow I'll post a tutorial. It's quite simple - 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.
