hi jens, here is the post - the links were all broken, but i've updated them below. note that this run was from nov 2013. i would recommend doing a run with all the current patches installed.
---- an update on the files needed for a vanilla recon-all run (evaluation done using cde:http://www.pgbovine.net/cde.html): freesurfer files: https://www.dropbox.com/s/ei3m9dcvq8zemps/fslist.txt?dl=0 all files (fs + system+ output): https://www.dropbox.com/s/1rjk7s0qyzn2hm5/allfiles.txt?dl=0 size of fs components (641M): https://www.dropbox.com/s/mmcadnp63ao4dv8/size.txt?dl=0 one thing that surprised me a bit was that no component of fsaverage appeared to be used (other than the directory being touched). this could be something the program missed, or is actually true. ---- cheers, satra On Wed, Nov 19, 2014 at 5:03 PM, Jens Offenbach <wolle5...@gmx.de> wrote: > Hi satra, > I have tried to find some posts about the minimum files required to run > recon-all, but I cannot find anything. Could you please try to find the > post in the archives and provide me the link? > > Thank you very much! > > > > Gesendet: Mittwoch, 19. November 2014 um 15:23 Uhr > Von: "Satrajit Ghosh" <sa...@mit.edu> > An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > Betreff: Re: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and > 5.3.0-patch > > 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[ > 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[krieg...@upmc.edu]> > An: "'Freesurfer support list'" <freesurfer@nmr.mgh.harvard.edu[ > 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[ > freesurfer-boun...@nmr.mgh.harvard.edu] [mailto:freesurfer-[freesurfer-] > > boun...@nmr.mgh.harvard.edu[boun...@nmr.mgh.harvard.edu]] On Behalf Of > Jens Offenbach > > Sent: Wednesday, November 19, 2014 5:47 AM > > To: freesurfer@nmr.mgh.harvard.edu[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[Freesurfer@nmr.mgh.harvard.edu] > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer[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][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[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[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[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 >
_______________________________________________ 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.
