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 <[email protected]> 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 _______________________________________________ Neurodebian-users mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/neurodebian-users
