hi jens, if you search the archives, there is a post that lists the minimal set of files needed for running recon-all.
i used a tool called cde to create it: http://www.pgbovine.net/cde.html this reduces the archive down to about 650MB comprising binaries and atlases. this wouldn't be for general purpose freesurfer processing, just for running recon-all. cheers, satra On Wed, Nov 19, 2014 at 8:40 AM, Jens Offenbach <wolle5...@gmx.de> wrote: > I have corresponding setup modules for auto-deployment and configuration > in the cloud, but it still takes some time (even in the local cloud > network) to transfer the archive from the fileserver to the virtual machine > and especially to untar that archive. A manual untar took nearly 20 > minutes, that's too slow for on-demand provisioning. I think the "subjects" > folder can be removed. It seems to contain only example mri data, but I > want to make sure not to remove anything that is actually required for > analysis purposes. I need a minimum archive file which is able to perform > the pipeline execution. > > Yes, we have a cloud portal, where different consumers can request the > freesurfer service after uploading their mri raw files. The virtual > machines are created and configured on the fly starting from a raw OS > image. When the freesurfer run terminates the virtual machines are > destroyed and the whole procedures starts again if someone requests a new > freesurfer service (Create and start a virtual machine, transfer freesurfer > archive, untar that archive, set environmement variables ...). We only want > to parallelize different freesurfer jobs and not the freesurfer pipeline > itself. We do not have a medical background. > > Regards, > Jens > > Gesendet: Mittwoch, 19. November 2014 um 13:14 Uhr > Von: "Krieger, Donald N." <krieg...@upmc.edu> > An: "'Freesurfer support list'" <freesurfer@nmr.mgh.harvard.edu> > Betreff: Re: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and > 5.3.0-patch > Dear Jens, > > I can offer just a bit of information and I also have a question. > We are using Fedora 11.0 on an x86_64 box and both the Centos 4 and Centos > 6 compiles work. > The package appears to be self-contained as I have seen no faults on > failures to find shared libraries. > We simply untar freesurfer to a convenient location and set the PATH and > FREESURFERHOME environment variables accordingly. > I see no reason why that shouldn't work in a cloud solution except that I > do not know what you have in mind as a use for your solution. > Will there be a group of users who are provided access so that they can > run freesurfer on an image data set through a portal to your cloud? > Are you using the cloud to distribute the calculation to many machines? > If so, what is the "granularity" of this, e.g. does one freesurfer run get > one machine? > > Regards, > > Don > > > Don Krieger, Ph.D. > Department of Neurological Surgery > University of Pittsburgh > (412)648-9654 Office > (412)521-4431 Cell/Text > > > > -----Original Message----- > > From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- > > boun...@nmr.mgh.harvard.edu] On Behalf Of Jens Offenbach > > Sent: Wednesday, November 19, 2014 5:47 AM > > To: freesurfer@nmr.mgh.harvard.edu > > Subject: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and > 5.3.0- > > patch > > > > 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[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[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 >
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