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-27f13...
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
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 bnniii@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-27f13...
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.
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" satra@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 bnniii@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-27f13...
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.
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 bnniii@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" satra@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 bnniii@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-27f13...
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.
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 thomasballinger@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 bnniii@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" satra@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 bnniii@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-27f13...
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
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 nicks@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 thomasballinger@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 bnniii@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" satra@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 bnniii@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-27f13...
I did not include the .license for FS as I wasn't sure about licensing issues, but I would be happy to publish an AMI with a built-in license if I get the go ahead. For now you will need to start a cluster and your license to each instance.
A few details:
Ubuntu 10.04 x86 built from StarClusters ami-8cf913e5 us-east-1 region See the StarCluster details at http://web.mit.edu/stardev/cluster/ Customizing StarCluster ( http://web.mit.edu/stardev/cluster/docs/latest/manual/create_new_ami.html ) s3fs (http://code.google.com/p/s3fs/) Freesurfer 5.1 32-bit NeuroDebian ready (so you can apt-get install mricron, fsl, nipype, etc.)
Thanks again for starting this thread, and let me know if I can help in any way. It would be great to see "cloud" resources be readily accessibly to the community with minimal effort to get a cluster with freesurfer and tools available via neurodebian up and running.
Cheers,
Nolan _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 ppj@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 nicks@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 thomasballinger@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 bnniii@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" satra@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 bnniii@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-27f13...
I did not include the .license for FS as I wasn't sure about licensing issues, but I would be happy to publish an AMI with a built-in license if I get the go ahead. For now you will need to start a cluster and your license to each instance.
A few details:
Ubuntu 10.04 x86 built from StarClusters ami-8cf913e5 us-east-1 region See the StarCluster details at http://web.mit.edu/stardev/cluster/ Customizing StarCluster ( http://web.mit.edu/stardev/cluster/docs/latest/manual/create_new_ami.html ) s3fs (http://code.google.com/p/s3fs/) Freesurfer 5.1 32-bit NeuroDebian ready (so you can apt-get install mricron, fsl, nipype, etc.)
Thanks again for starting this thread, and let me know if I can help in any way. It would be great to see "cloud" resources be readily accessibly to the community with minimal effort to get a cluster with freesurfer and tools available via neurodebian up and running.
Cheers,
Nolan _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 thomasballinger@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 ppj@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 nicks@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 thomasballinger@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 bnniii@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" satra@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 bnniii@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-27f13...
I did not include the .license for FS as I wasn't sure about licensing issues, but I would be happy to publish an AMI with a built-in license if I get the go ahead. For now you will need to start a cluster and your license to each instance.
A few details:
Ubuntu 10.04 x86 built from StarClusters ami-8cf913e5 us-east-1 region See the StarCluster details at http://web.mit.edu/stardev/cluster/ Customizing StarCluster
(http://web.mit.edu/stardev/cluster/docs/latest/manual/create_new_ami.html) s3fs (http://code.google.com/p/s3fs/) Freesurfer 5.1 32-bit NeuroDebian ready (so you can apt-get install mricron, fsl, nipype, etc.)
Thanks again for starting this thread, and let me know if I can help in any way. It would be great to see "cloud" resources be readily accessibly to the community with minimal effort to get a cluster with freesurfer and tools available via neurodebian up and running.
Cheers,
Nolan _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 bnniii@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 thomasballinger@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 <
ppj@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 <
nicks@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 thomasballinger@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 bnniii@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" satra@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 bnniii@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-27f13...
> > I did not include the .license for FS as I wasn't sure about
licensing
> issues, but I would be happy to publish an AMI with a built-in
license
> if I get the go ahead. For now you will need to start a cluster and > your license to each instance. > > A few details: > > Ubuntu 10.04 x86 > built from StarClusters ami-8cf913e5 > us-east-1 region > See the StarCluster details at http://web.mit.edu/stardev/cluster/ > Customizing StarCluster > > (
http://web.mit.edu/stardev/cluster/docs/latest/manual/create_new_ami.html)
> s3fs (http://code.google.com/p/s3fs/) > Freesurfer 5.1 32-bit > NeuroDebian ready (so you can apt-get install mricron, fsl, nipype, > etc.) > > Thanks again for starting this thread, and let me know if I can help > in any way. It would be great to see "cloud" resources be readily > accessibly to the community with minimal effort to get a cluster
with
> freesurfer and tools available via neurodebian up and running. > > Cheers, > > Nolan > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to
whom
> it is > addressed. If you believe this e-mail was sent to you in error and
the
> e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to
you
> in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to
you
in error but does not contain patient information, please contact the sender
and
properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom
it
is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to
you in
error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 bnniii@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 <thomasballinger@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 <ppj@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 <nicks@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 >>> <thomasballinger@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 <bnniii@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" <satra@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 <bnniii@uw.edu> wrote: >>>>>> >>>>>> Thanks, Pedro! >>>>>> >>>>>> I am glad to see that you posted a public AMI for freesurfer. And >>>>>> thanks to Thomas for producin documentation on how to use it. >>>>>> >>>>>> This thread inspired me share a StarCluster AMI (ami-27f1384e in the >>>>>> us-east-1 region) that I built for batch FS jobs, which includes the >>>>>> initial setup for installing tools from the NeuroDebian repository. >>>>>> I've also been playing around with using s3fs, which allows Amazon's >>>>>> S3 to be mounted as a drive and accessed directly as the >>>>>> "subjects_dir". >>>>>> >>>>>> The AMI can be launched here: >>>>>> >>>>>> https://console.aws.amazon.com/ec2/home?region=us-east-1#launchAmi=ami-27f1384e >>>>>> >>>>>> I did not include the .license for FS as I wasn't sure about licensing >>>>>> issues, but I would be happy to publish an AMI with a built-in license >>>>>> if I get the go ahead. For now you will need to start a cluster and >>>>>> your license to each instance. >>>>>> >>>>>> A few details: >>>>>> >>>>>> Ubuntu 10.04 x86 >>>>>> built from StarClusters ami-8cf913e5 >>>>>> us-east-1 region >>>>>> See the StarCluster details at http://web.mit.edu/stardev/cluster/ >>>>>> Customizing StarCluster >>>>>> >>>>>> (http://web.mit.edu/stardev/cluster/docs/latest/manual/create_new_ami.html) >>>>>> s3fs (http://code.google.com/p/s3fs/) >>>>>> Freesurfer 5.1 32-bit >>>>>> NeuroDebian ready (so you can apt-get install mricron, fsl, nipype, >>>>>> etc.) >>>>>> >>>>>> Thanks again for starting this thread, and let me know if I can help >>>>>> in any way. It would be great to see "cloud" resources be readily >>>>>> accessibly to the community with minimal effort to get a cluster with >>>>>> freesurfer and tools available via neurodebian up and running. >>>>>> >>>>>> Cheers, >>>>>> >>>>>> Nolan >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> The information in this e-mail is intended only for the person to whom >>>>>> it is >>>>>> addressed. If you believe this e-mail was sent to you in error and the >>>>>> e-mail >>>>>> contains patient information, please contact the Partners Compliance >>>>>> HelpLine at >>>>>> http://www.partners.org/complianceline . If the e-mail was sent to you >>>>>> in error >>>>>> but does not contain patient information, please contact the sender >>>>>> and properly >>>>>> dispose of the e-mail. >>>>>> >>>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> The information in this e-mail is intended only for the person to whom >>>> it is >>>> addressed. If you believe this e-mail was sent to you in error and the >>>> e-mail >>>> contains patient information, please contact the Partners Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was sent to you >>>> in error >>>> but does not contain patient information, please contact the sender and >>>> properly >>>> dispose of the e-mail. >>>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to whom it >>> is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >> > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 nicks@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 bnniii@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 <thomasballinger@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 <ppj@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 <nicks@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 >>> <thomasballinger@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 <bnniii@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" <satra@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 <bnniii@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-27f13...
>>>>>> >>>>>> I did not include the .license for FS as I wasn't sure about licensing >>>>>> issues, but I would be happy to publish an AMI with a built-in license >>>>>> if I get the go ahead. For now you will need to start a cluster and >>>>>> your license to each instance. >>>>>> >>>>>> A few details: >>>>>> >>>>>> Ubuntu 10.04 x86 >>>>>> built from StarClusters ami-8cf913e5 >>>>>> us-east-1 region >>>>>> See the StarCluster details at http://web.mit.edu/stardev/cluster/ >>>>>> Customizing StarCluster >>>>>> >>>>>> (http://web.mit.edu/stardev/cluster/docs/latest/manual/create_new_ami.html)
>>>>>> s3fs (http://code.google.com/p/s3fs/) >>>>>> Freesurfer 5.1 32-bit >>>>>> NeuroDebian ready (so you can apt-get install mricron, fsl, nipype, >>>>>> etc.) >>>>>> >>>>>> Thanks again for starting this thread, and let me know if I can help >>>>>> in any way. It would be great to see "cloud" resources be readily >>>>>> accessibly to the community with minimal effort to get a cluster with >>>>>> freesurfer and tools available via neurodebian up and running. >>>>>> >>>>>> Cheers, >>>>>> >>>>>> Nolan >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> The information in this e-mail is intended only for the person to whom >>>>>> it is >>>>>> addressed. If you believe this e-mail was sent to you in error and the >>>>>> e-mail >>>>>> contains patient information, please contact the Partners Compliance >>>>>> HelpLine at >>>>>> http://www.partners.org/complianceline . If the e-mail was sent to you >>>>>> in error >>>>>> but does not contain patient information, please contact the sender >>>>>> and properly >>>>>> dispose of the e-mail. >>>>>> >>>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> The information in this e-mail is intended only for the person to whom >>>> it is >>>> addressed. If you believe this e-mail was sent to you in error and the >>>> e-mail >>>> contains patient information, please contact the Partners Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was sent to you >>>> in error >>>> but does not contain patient information, please contact the sender and >>>> properly >>>> dispose of the e-mail. >>>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to whom it >>> is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >> > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 ppj@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 nicks@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 bnniii@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 <thomasballinger@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 <ppj@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 <nicks@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 >>> <thomasballinger@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 <bnniii@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" <satra@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 <bnniii@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-27f13...
>>>>>> >>>>>> I did not include the .license for FS as I wasn't sure about licensing >>>>>> issues, but I would be happy to publish an AMI with a built-in license >>>>>> if I get the go ahead. For now you will need to start a cluster and >>>>>> your license to each instance. >>>>>> >>>>>> A few details: >>>>>> >>>>>> Ubuntu 10.04 x86 >>>>>> built from StarClusters ami-8cf913e5 >>>>>> us-east-1 region >>>>>> See the StarCluster details at http://web.mit.edu/stardev/cluster/ >>>>>> Customizing StarCluster >>>>>> >>>>>> (http://web.mit.edu/stardev/cluster/docs/latest/manual/create_new_ami.html )
>>>>>> s3fs (http://code.google.com/p/s3fs/) >>>>>> Freesurfer 5.1 32-bit >>>>>> NeuroDebian ready (so you can apt-get install mricron, fsl, nipype, >>>>>> etc.) >>>>>> >>>>>> Thanks again for starting this thread, and let me know if I can help >>>>>> in any way. It would be great to see "cloud" resources be readily >>>>>> accessibly to the community with minimal effort to get a cluster with >>>>>> freesurfer and tools available via neurodebian up and running. >>>>>> >>>>>> Cheers, >>>>>> >>>>>> Nolan >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> The information in this e-mail is intended only for the person to whom >>>>>> it is >>>>>> addressed. If you believe this e-mail was sent to you in error and the >>>>>> e-mail >>>>>> contains patient information, please contact the Partners Compliance >>>>>> HelpLine at >>>>>> http://www.partners.org/complianceline . If the e-mail was sent to you >>>>>> in error >>>>>> but does not contain patient information, please contact the sender >>>>>> and properly >>>>>> dispose of the e-mail. >>>>>> >>>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> The information in this e-mail is intended only for the person to whom >>>> it is >>>> addressed. If you believe this e-mail was sent to you in error and the >>>> e-mail >>>> contains patient information, please contact the Partners Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was sent to you >>>> in error >>>> but does not contain patient information, please contact the sender and >>>> properly >>>> dispose of the e-mail. >>>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to whom it >>> is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >> > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 jkilee@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 ppj@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 nicks@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.
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 jkilee@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 ppj@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 nicks@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.
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 fischl@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 jkilee@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 <ppj@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 nicks@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.
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 ppj@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 fischl@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 jkilee@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 < ppj@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 nicks@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.
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 ppj@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 <fischl@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 <jkilee@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 <ppj@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 <nicks@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/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.
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 nicks@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 ppj@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 <fischl@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 <jkilee@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 <ppj@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 <nicks@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/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
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 nicks@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 > <ppj@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 <fischl@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 <jkilee@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 <ppj@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 > <nicks@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/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
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Bruce Fischl -
Joshua Lee -
Nick Schmansky -
Nolan Nichols -
Pedro Paulo de Magalhães Oliveira Junior -
Satrajit Ghosh -
Thomas Ballinger