Dear all, I have created a Docker image with Freesurfer distribution (and all required dependencies).
Features:
- Only requires Docker to run (works on Linux, Mac and Windows - does not suffer from the VirtualBox bug https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42474.html ) - understands BIDS http://bids.neuroimaging.io/ formatted datasets - performs recon-all on all subjects - allows you to run each subject independently (and potentially in parallel) - automatically performs longitudinal analysis when multiple sessions are detected - creates custom group level template for your study - can be easily converted to a Singularity http://singularity.lbl.gov/ image using docker2singularity https://github.com/chrisfilo/docker2singularity tool and run on your local HPC/cluster
You can find more information here: https://github.com/BIDS-Apps/freesurfer
Please let me know what do you think!
Best, Chris
Hi Chris,
This sounds great! How does it deal with the FreeSurfer license? I know that the FreeSurfer team depends on licenses to keep track of the number of users (a key component to justifying their work when applying for grants). I'm looking forward to trying it out!
Thanks, Dan
On Tue, Aug 9, 2016 at 12:37 PM, Chris Filo Gorgolewski chris.gorgolewski@gmail.com wrote:
Dear all, I have created a Docker image with Freesurfer distribution (and all required dependencies).
Features:
Only requires Docker to run (works on Linux, Mac and Windows - does not suffer from the VirtualBox bug) understands BIDS formatted datasets performs recon-all on all subjects allows you to run each subject independently (and potentially in parallel) automatically performs longitudinal analysis when multiple sessions are detected creates custom group level template for your study can be easily converted to a Singularity image using docker2singularity tool and run on your local HPC/cluster
You can find more information here: https://github.com/BIDS-Apps/freesurfer
Please let me know what do you think!
Best, Chris
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 Dan, Users are asked to provide their license key they received from MGH after registration as a command line parameter. I also added links to the registration form.
Best, Chris
On Tue, Aug 9, 2016 at 12:24 PM, dgw dgwakeman@gmail.com wrote:
Hi Chris,
This sounds great! How does it deal with the FreeSurfer license? I know that the FreeSurfer team depends on licenses to keep track of the number of users (a key component to justifying their work when applying for grants). I'm looking forward to trying it out!
Thanks, Dan
On Tue, Aug 9, 2016 at 12:37 PM, Chris Filo Gorgolewski chris.gorgolewski@gmail.com wrote:
Dear all, I have created a Docker image with Freesurfer distribution (and all
required
dependencies).
Features:
Only requires Docker to run (works on Linux, Mac and Windows - does not suffer from the VirtualBox bug) understands BIDS formatted datasets performs recon-all on all subjects allows you to run each subject independently (and potentially in
parallel)
automatically performs longitudinal analysis when multiple sessions are detected creates custom group level template for your study can be easily converted to a Singularity image using docker2singularity
tool
and run on your local HPC/cluster
You can find more information here: https://github.com/BIDS-Apps/
freesurfer
Please let me know what do you think!
Best, Chris
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@nmr.mgh.harvard.edu
-
Chris Filo Gorgolewski -
dgw