[Neurodebian-users] ND menus

Wed Mar 2 00:04:01 UTC 2016

Yaroslav,

I think maybe I screwed something up with the recent updating of the
FSL 5.1 menu item for the neurodebian-desktop.

It seemed to install but not launch FSL.  In trying to figure out what
might be up, I looked at the nd-autoinstall and it looks like the
correct command to run is, from a command line,

$ sudo nd-autoinstall -e /usr/share/fsl/5.0/etc/fslconf/fsl.sh -p
fsl-5.0-core fsl

However, when I put that in the desktop file, it installs
fsl-5.0-core, but it doesn't seem to run fsl.

Not sure how to proceed.  Am I missing something obvious again?

-- 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