We are currently working on a solution that brings FreeSurfer in the cloud. Unfortunately, we are facing a lot of problems. Hopefully, someone can help me:
I want to run FreeSurfer on Ubuntu 14.04 or 14.10. What package is required to download (CentOS 4 x86_64 (64b))? Does it work anyway on the Ubuntu family? On the FTP server I have found a patch for 5.3.0, but I am not sure how to apply it or if I must apply it? The Readme says to replace “mri_segstats”. What about the other files “recon-all, fsfast, tksurferfv, …”? I want to reduce the archive to its bare minimum, otherwise the automated deployment process takes too long. It should contain only those files which are necessary to execute the pipeline without any viewer or examples. Which files and folders can be deleted safely? The most important issue is to monitor the FreeSurfer pipeline execution. I know that the scripts folder contains some status files which offer important data helping me to monitor the pipeline execution progress of “recon-all”. Unfortunately, that is not enough… If one step takes e.g. approximately 20 hours, I have to say something about the progress within this current step. Is there any possibility to monitor the progress of a single step. We need something that allows us to say e.g. that Step “CA Reg” has 34 % of its work done so far which means that the overall pipeline progress is e.g. 63 %. Is it possible to say that a specific step takes a specific portion of the overall pipeline execution time. What influences this portion (format or quality of input, platform, …)? Thank you very much for your help! Regards Jens _______________________________________________ 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.
