External Email - Use Caution Hi Aleksandr,
You could try making a minimal container with reprozip https://www.reprozip.org/ Only recon-all should be less than a Gb. -Paul On Wed, Apr 22, 2020 at 5:31 PM Hoopes, Andrew <ahoo...@mgh.harvard.edu> wrote: > I don’t have an exact number, but I believe the minimal compiled > distribution is less than 2GB. > > Andrew > > > > *From: *<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Ерохин > Александр <erohin_...@mail.ru> > *Reply-To: *Ерохин Александр <erohin_...@mail.ru>, FS Help < > freesurfer@nmr.mgh.harvard.edu> > *Date: *Wednesday, April 22, 2020 at 12:35 PM > *To: *FS Help <freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] (no subject) > > > > * External Email - Use Caution * > > Hi Andrew, > > > > Alright, many thanks for the hint! I started experimenting myself with > file exclusion, but is seems I've excluded too much and recon-all is not > able to complete successfully anymore. > > > > Regarding this MINIMAL flag option — could you please tell an approximate > distribution size with it is specified? > > Does it worth the trouble? > > > > Regards, > > Aleksandr. > > > > > > Понедельник, 20 апреля 2020, 19:36 +03:00 от "Hoopes, Andrew" < > ahoo...@mgh.harvard.edu>: > > > Hi Aleksandr, > > > > Yes, this is an unfortunate limitation, but we are working towards making > freesurfer more modular in the future. There’s no single straightforward > solution to cutting down the distribution, but you do have a couple of > options. > > > > The BIDS group has created a minimal FS6 docker container that removes a > lot of unnecessary subject data for recon-all. Their dockerfile is > available at > https://github.com/BIDS-Apps/freesurfer/blob/master/Dockerfile and you > can mimic that second wget command to download a filtered version of FS. > > > > Also, if you’re familiar with the development process, you can build your > own freesurfer distribution following the instructions at > https://surfer.nmr.mgh.harvard.edu/fswiki/BuildGuide. There is a cmake > flag `MINIMAL` that will only build core recon-all components if it is set > to ON. This is a more complete option than the first, but also much more > time consuming… > > > > Hope that helps, > > Andrew Hoopes > > > > *From: *<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Ерохин > Александр <erohin_...@mail.ru> > *Reply-To: *Ерохин Александр <erohin_...@mail.ru>, FS Help < > freesurfer@nmr.mgh.harvard.edu> > *Date: *Sunday, April 19, 2020 at 1:49 PM > *To: *FS Help <freesurfer@nmr.mgh.harvard.edu> > *Subject: *[Freesurfer] (no subject) > > > > * External Email - Use Caution * > > Hello together, > > > > The FreeSurfer distribution takes * 10G* of the disk space in my local > installation. It has numerous tools, but it’s not modular, or at lest it’s > very hard to tell boundaries between modules. > > > > E.g. /bin folder contains around 860 executables all in one place. > > > > Is it possible to trim down the distribution provided to minimize the size > but keep it functional in terms of computation for *recon-all* steps? > > For example trim away all GUI executables and support libraries. > > > > As far as I can see, the directories taking most of the space are: > > > > 2.2G *./subjects* > 3.1G *./average* > 2.5G *./bin* > 1.3G *./lib* > > > > But I am not sure what could be removed and what not in order to keep all > recon-all steps functional. > > > > Many thanks, > > Aleksandr. > > > > > > _______________________________________________ > 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
