[Neurodebian-users] ND menus

Fri Feb 5 00:33:44 UTC 2016

Yaroslav,

Thanks for the helpful information.  I'll go see if I can read source.

In the meantime, you said:

    Although the question would be more of "what
    should a user get when he wants to run FSL"

I am greedy also, but I try to be circumspect.  I think there are many
people who will want the full suite of programs, help files, and etc.,
but not necessarily want the sample data, the atlas, etc.  None of the
labs for which I've installed FSL has ever asked for the data included
in the bare 'fsl' package.

There isn't right now a menu option to install the FSL data
separately.  I'm not sure what that would 'do' once the data was
installed, but I think something that captures that spirit is what is
wanted here.

Thoughts on that?  In the meantime, I will look at source and make the
more minimal changes and try to get some sort of pull request
submitted.

Thanks,  -- bennet

On Thu, Feb 4, 2016 at 4:51 PM, Yaroslav Halchenko
<debian at onerussian.com> wrote:
>
> On Thu, 04 Feb 2016, Bennet Fauber wrote:
>
>> I would like to update the neurodebian-desktop menu items for FSL and
>> FSLView, but it seems to be a bit more involved than simply changing
>> version numbers.
>
>> The layout for the fsl program seems to have changed since FSL 4.1.
>> As near as I can tell from looking at the current menu item for FSL
>> 4.1, it will request the autoinstaller install the fsl-4.1 and
>> fsl4.1-fsl .deb packages.
>
>> When I manually installed 'fsl', which is labeled as a 'dummy
>> package', it seems to have installed many FSL packages, some of which
>> are clearly data, so I am confident that is the wrong thing to include
>> there.
>
> fsl-core probably would be the right target if you wanted a skinnier
> installation.  It is also a 'dummy' one which depends on correctly
> versioned fsl*-core.  Although the question would be more of "what
> should a user get when he wants to run FSL" -- should it be just a core
> or full deployment?    greedy me would prefer "full" one ;)
>
>> Am I interpreting things correctly that the FSL 4.1 entry should
>> changed so that it is labeled FSL 5.0 (without the minor version,
>> which seems to be 5.0.9) and that it should install fsl-core, which is
>> labeled 'metapackage for the latest version' and appears to be for
>> 5.0.9-2, and that will install the binaries without the data?
>
> yeap
>
>> I ask because if that includes FSLView, which has its own menu item
>> with a discrete autoinstall option, then the FSL 5 menu item should
>> not install FSLView.
>
> nah -- let it install fslview as well ;)  but for fslview leave its own
> fslview package
>
>> I am not finding a good way to list what packages a metapackage will
>> actually install.  I tried
>
>> $ apt-cache showpkg fsl-core
>
>> but the output is a bit baffling for this neophyte, e.g.,
>> 5.0.9-2~nd15.04+1 - fsl-5.0-core (0 (null)) -- which seems fine -- but
>> that is followed by fsl (3 5.0.3) fsl:i386 (3 5.0.3) etc.  That seems
>> to imply dependencies on older versions.  I am further confused by the
>> Provides: section, which says it provides 5.0.9-2~nd15.04+1 -
>> 5.0.7-4-.  Does it provide both versions 5.0.9-2 and 5.0.7-4?
>
> I guess you see that indeed two versions are provided -- one comes from
> stock ubuntu may be and  another one from neurodebian.  run
>
> apt-cache policy fsl-core
>
> to see detail.  But for the sake of adjusting .desktop files shouldn't
> matter
>
>> If that is not enough bafflement for you, I am further confused
>> because the FSL web site seems to be distributing FSLView 3.1
>
>> http://fsl.fmrib.ox.ac.uk/fsl/fslview/
>
> well -- web  is the 'web of many lies' ;)
>
> ;)  that is the point of 'modularization'.  fslview is like an
> independent project within fsl, which hasn't changed for a while!  So
> its package wasn't updated.  When fslview sources do get updated then
> we update fslview package as well.  So it is indeed of 4.0.1 version
>
>> but the FSL web site seems to be in transition, as the link to Build
>> from sources on that page leads to a page that does not yet exist.
>> When I installed the fsl binary distribution for CentOS6-64, it seems
>> to have come with an FSLView 3.1 binary.  The FSLView, program that
>> comes with ND lists itself as 4.0.1.  (Is the source code newer and
>> the FSL binary distribution out of date?)
>
> more like their fslview  page is out of date. I believe recent fsl still
> comes with that fslview 4.0.1
>
>> If there is some obvious documentation that I should know about for
>> how the Debian FSL packages are made that I should go read, please let
>> me know.
>
> sources sources!
>
> http://git.debian.org/?p=pkg-exppsy/fsl.git
> debian/ directory has all the sources and there is README.Debian-source
> which explains some gory details.
>
>> Sorry, Yaroslav.  I did warn you.
>
> ;)  just don't dig too deep.  adjust the way you see the best fit, send
> PR and if I see that something needs tuning I will comment on.
>
> --
> Yaroslav O. Halchenko
> Center for Open Neuroscience     http://centerforopenneuroscience.org
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
> WWW:   http://www.linkedin.com/in/yarik