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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" ahoopes@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-bounces@nmr.mgh.harvard.edu > on behalf of Ерохин Александр < erohin_a_v@mail.ru > Reply-To: Ерохин Александр < erohin_a_v@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

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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 AHOOPES@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-bounces@nmr.mgh.harvard.edu on behalf of Ерохин Александр erohin_a_v@mail.ru *Reply-To: *Ерохин Александр erohin_a_v@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)

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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" < ahoopes@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-bounces@nmr.mgh.harvard.edu on behalf of Ерохин Александр erohin_a_v@mail.ru *Reply-To: *Ерохин Александр erohin_a_v@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)

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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.

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