Package Details: fsl 5.0.10-2

Git Clone URL: https://aur.archlinux.org/fsl.git (read-only)
Package Base: fsl
Description: A comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data
Upstream URL: http://www.fmrib.ox.ac.uk/fsl/
Licenses: custom
Submitter: fishburn
Maintainer: fishburn
Last Packager: fishburn
Votes: 8
Popularity: 0.011692
First Submitted: 2012-07-02 23:36
Last Updated: 2017-11-26 05:53

Latest Comments

dvogel commented on 2018-01-11 12:51

Hey Fishburn, thanks for the package. I had issues building the package, however found fixes: - rebuilt newmat with -fPIC in CCFLAGS (solves linking issues, suggested in build.log) - changed include directories in externallibs.mk to vtk8 since vtk headers were not found with vtk6 (even though the latter is installed).

For now I only tested bet with this build.

fishburn commented on 2017-11-26 05:46

I updated the checksums, bumped the pkgver (since I don't know what changed since the checksums changed), and got it building again.

@rafaqzsu
@AKSoo
@jnvandermeer
Would appreciate if you could verify its working on your end.

rafaqzsu commented on 2017-11-24 05:12

Still broken

==> Validating source files with sha1sums...
fsl-5.0.10-sources.tar.gz ... FAILED
fsl-5.0.10-feeds.tar.gz ... FAILED
systemvars.mk ... Passed
externallibs.mk ... Passed
fsl_exec.patch ... Passed
==> ERROR: One or more files did not pass the validity check!

AKSoo commented on 2017-07-21 04:39

The tar.gz's from FMRIB fail the sha1sum validation.

The build fails as well. I believe 'fftw' and 'boost' (for the headers) should be included as dependencies.

Some entries in 'externallibs.mk' has header and library directories swapped.

fishburn commented on 2017-06-13 17:15

Updated to 5.0.10 and passes all FEEDS build tests

jnvandermeer commented on 2017-03-16 07:28

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



jnvandermeer commented on 2017-03-13 07:11

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.

reecestevens commented on 2015-02-03 23:11

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!

fishburn commented on 2014-06-12 01:21

@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.

bobschi commented on 2014-06-11 13:17

@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?

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