Arch Linux User Repository

In the current state and for the most up-to-date fresh install of Arch (well.. as far as my laptop goes..), fsl doesn' finish the build for many important functions such as melodic, fast5, extras, etc etc etc. - basically the installation is only half functional. Even slicer doesn't work.

The build.log produces many error messages, all of which is due to libgd (in extras) not compiling, an essential library the rest depends on. After some googling, I found that the culprit is in libpimg.c, which uses some global/standard library-provided constants which don't exist anymore in libvpx.

See here:
https://github.com/gagern/libgd/commit/d41eb72cd4545c394578332e5c102dee69e02ee8


Anyway... long story short, I came up with some sed lines and updated my BUILDPKG with the following lines, which fixed it all for me. Insert somewhere before:
cd "${FSLDIR}"
./build
... and just after the sed lines already in there.

### BEGIN INSERT
echo "fixing: " ${FSLDIR}/extras/src/libgd/src/webpimg.c

sed -i "s^vpx_img_wrap(\&img, IMG_FMT_I420,^vpx_img_wrap(\&img, VPX_IMG_FMT_I420,^g" "${FSLDIR}/extras/src/libgd/src/webpimg.c"

sed -i "s^img\.planes\[PLANE_Y\] = (uint8\*)(Y);^img\.planes\[VPX_PLANE_Y\] = (uint8\*)(Y);^g" "${FSLDIR}/extras/src/libgd/src/webpimg.c"
sed -i "s^img\.planes\[PLANE_U\] = (uint8\*)(U);^img\.planes\[VPX_PLANE_U\] = (uint8\*)(U);^g" "${FSLDIR}/extras/src/libgd/src/webpimg.c"
sed -i "s^img\.planes\[PLANE_V\] = (uint8\*)(V);^img\.planes\[VPX_PLANE_V\] = (uint8\*)(V);^g" "${FSLDIR}/extras/src/libgd/src/webpimg.c"
sed -i "s^img\.stride\[PLANE_Y\] = y_stride;^img\.stride\[VPX_PLANE_Y\] = y_stride;^g" "${FSLDIR}/extras/src/libgd/src/webpimg.c"
sed -i "s^img\.stride\[PLANE_U\] = uv_stride;^img\.stride\[VPX_PLANE_U\] = uv_stride;^g" "${FSLDIR}/extras/src/libgd/src/webpimg.c"
sed -i "s^img\.stride\[PLANE_V\] = uv_stride;^img\.stride\[VPX_PLANE_V\] = uv_stride;^g" "${FSLDIR}/extras/src/libgd/src/webpimg.c"
### END INSERT

Thanks for providing the PKG, hope you find this info useful.

Best wishes
Johan

Hi all,

I also managed to get fslview working with instructions at: http://neuro.debian.net/blog/2011/2011-12-12_schroot_fslview.html. Only, unlike in these instructions, squeeze no longer works for me. It's been a while, so you'd have to use jessie now. fslview is actually in the basic repositories of Debian Stable. So... replace all instances of squeeze with jessie in the following instructions at:

http://neuro.debian.net/blog/2011/2011-12-12_schroot_fslview.html

I tried to build fslview.. but.. it just takes too long at the moment. I do get this warning about QGtkStyle could not resolve GTK, but I will ignore it.

Small maintenance note, it seems that FSL source has updated to 5.0.8. I was able to install simply by changing the version number to 5.0.8 in the PKGBUILD and disabling verification checks.The current PKGBUILD file is looking for the source link given above, which no longer exists.

Thanks!

@bobschi
Thanks for continuing to look into this. If I'm understanding this correctly, they are suggesting to use a chroot of a Debian install that has all of the old libraries. Making such a pkgbuild is inconsistent with the arch way and is completely out of the question, IMO. That said, the chroot method might shine some light on how to get it to compile from source. I will take a look when I get some free time. Thanks again for following up.

@cornholio
This works for me: http://neuro.debian.net/blog/2011/2011-12-12_schroot_fslview.html

First time starting I got an error, which could be fixed by commenting out "networks": https://bbs.archlinux.org/viewtopic.php?id=100039

Maybe you can put all this information together in a PKGBUILD?

@bobschi

Yes, I consulted that page extensively when trying to get it to compile. The code is so old I had difficulty just obtaining old enough versions of some of the dependencies. Let me know if you get it working and can point me in the right direction.

@cornholio
Thank you too. Did you have a look at this?

http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/SourceCode/FslView#Preparing_a_build_environment

@bobschi
Thanks, I've updated fsl now. I have never been able to get fslview to compile. I even tried using a binary package from neurodebian but couldn't get that to work either.

New version available: 5.0.6

As I installed this version today I saw, that fslview is missing. Any ideas?

new version available: 5.0.5
To install, modify PKGBUILD to newer version:

pkgver=5.0.5
#md5sums=('b87889efb2b4a31842eca1bee97c8578') #http://fsl.fmrib.ox.ac.uk/fsl/cgi-bin/fslchecksums.pl
sha1sums=('43f831d179d7714c616fd661f18783e7be34b7d0') #self-generated