Hello,

I successfully - assuming so - installed FSL 5.0 from the Debian repository. In the ./profile I set the path as explained on the Neurodebian webpage:

# set PATH for FSL 5.0
FSLDIR=/usr/share/fsl/5.0
. ${FSLDIR}/etc/fslconf/fsl.sh
PATH=${FSLDIR}/bin:${PATH}
export FSLDIR PATH

As a next step I wanted to install FRIEND for FSL, however, apparently the "buildAllLinux.sh" file which should compile the binaries into the application folder looks for the following paths:

$FSLDIR/extras/src/...
$FSLDIR/src/...

which are not present in my fsl directory. Present are the following folders:bin, data, doc, etc and tcl

I know that this is a rather specific question but I wanted to give it a try here as I don't know where to search for an answer anymore. I appreciate any tips and help.

Best,
Marcel

>>
>> Did you download the source code?
>
> http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Fs...
>
>
>

Hi Vanessa

I appreciate your fast answer.
I contacted Neurodebian on how to get the source code for Ubuntu 14.04, however till now I did not receive an answr. Your link describes it for Centos and I haven't found a tar-file for Ubuntu 14.04 yet.

Any idea?

Best,
Marcel

Hi Marcel,

You want to download "uncompiled sources" (see attached image).  That should have the complete data and extras folder, if I remember correctly.  Let me know if you run into trouble and I can poke around a bit!

Best,

Vanessa

Hi Vanessa

Thank you. I successfully downloaded the source files, however, I got stuck at the following stage "./build". It gives me the following error message:
"

Building projects - see build.log file for progress...
Finished build : end of log file shows ...

!!ERROR in BUILD!!
Could not make the following projects successfully:
extras utils znzlib niftiio fslio giftiio miscmaths newimage libvis first_lib meshclass fslvtkio basisfield warpfns bint shapeModel MVdisc fslsurface libmeshutils avwutils bet2 cluster fast4 feat5 film filmbabe flirt fabber mcflirt melodic misc_c miscvis mm gps randomise siena slicetimer susan tbss fnirt fugue asl_mfree fdt first possum flameo oxford_asl qboot topup ptx2 lesions eddy
!!ERROR in INSTALL!!
Could not fully install the following projects successfully:
misc_tcl

"

Thank you so much for the support. I attached you the build.log file as well.

Best,
Marcel

I've successfully used the neurodebian on many Ubuntu machines including 14.04. The instructions are fairly direct.

http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Fs...

Hi Marcel,

Did you install all the prerequisite packages? The Instructions show using the package manager "Yum" however on ubuntu you would need to use apt-get. Most of the time when a build fails it is because you don't have the necessary prerequisites, and if you scroll up when you see it trying to build there are probably error messages about libraries not being found.

So try installing all the required packages and then build again ;)

Best,

Vanessa

Hi Benett.

The installation is not the problem. FSL was successfully installed with the link you provided. However, this installation lacks the source and extra folders which I need for FRIEND.

Thank you,
Marcel

Hi Vanessa

To be honest I tried without that as apt-get didn't find these.

E: Unable to locate package expat-devel
E: Unable to locate package libX11-devel
E: Unable to locate package mesa-libGL-devel
E: Unable to locate package zlib-devel

But apparently, I need to find those somehow.

Best,
Marcel

Hi Marcel,

Give me a few minutes - I'll see if I can find those packages.

Best,

Vanessa

Expat:
sudo apt-get install libexpat1-dev

If you need to install from source:
http://glacier.lbl.gov/build_versions.ht...

LibX11:
sudo apt-get install libx11-dev

Mesa Graphics Library
http://www.mesa3d.org/vmware-guest.html

ZLib
sudo apt-get install zlib1g-dev libncurses5-dev

or source:
http://www.zlib.net/

Hi Vanessa

Are there some more packages one needs? Apparently, it was able to build "extras", however I get still a similar error:

!!ERROR in BUILD!!
Could not make the following projects successfully:
utils niftiio fslio giftiio miscmaths newimage libvis first_lib meshclass fslvtkio basisfield warpfns bint shapeModel MVdisc fslsurface libmeshutils avwutils bet2 cluster fast4 feat5 film filmbabe flirt fabber mcflirt melodic misc_c miscvis mm gps randomise siena slicetimer susan tbss fnirt fugue asl_mfree fdt first possum flameo oxford_asl qboot topup ptx2 lesions eddy

!!ERROR in INSTALL!!
Could not fully install the following projects successfully:
misc_tcl

Thank you for your big support and help. I am sorry that takes so long:-/

Best,
Marcel

Hi Marcel,

Wasn't your goal to just compile the extras? All of those packages in that error message are available with the compiled version for Ubuntu (that you already installed, correct?), so why are you aiming to recompile from source?  

Best,

Vanessa

My goal is actually to create the extra and src folders in my /usr/share/fsl/5.0 folder. However, I am not sure how to do that exactly. I assume you cannot just copy them over or can I?

I had the same error to build source code of FSL 5 on Ubuntu 14.04 at the first time.
I solved this problem by changing the default gcc setting that FSL used.

In $FSLDIR/config
1. delete the gnu_64-gcc4.8 folder
2. duplicate the gnu_64-gcc4.4 folder and rename it to gnu_64-gcc4.8

That works for me.
I think the setting files in gnu_64-gcc4.8 doesn't work well with ubuntu.
But the old version is fine

Hope it helps

Yuankai

Ubuntu is good.