Building Fabber¶

In most cases you don’t need to build Fabber - executables covering a variety of models are available in FSL (v6.0.1 or later recommended). You might need to use the following instructions, however if you:

• Need to install updated code which has not yet been released in FSL
• Want to write your own model or otherwise modify the code

Building Fabber using an installed FSL distribution¶

You will need FSL to build Fabber - it requires a number of libraries distributed as part of FSL. In addition the Fabber Makefile is based around the FSL build system.

Note

An additional cmake based build system also exists for use particularly on Windows. We will not describe this here.

Setting up an FSL development environment¶

First you need to have your system set up to compile FSL code. If you’re already building other FSL tools from source you’ve probably already done this, and can skip this section. Otherwise, run the following commands:

source $FSLDIR/etc/fslconf/fsl-devel.sh export FSLDEVDIR=<prefix to install into> export PATH=$FSLDEVDIR/bin:$PATH  Note you may want to put this in your .profile or .bash_profile script if you are going to be doing a lot of recompiling FSLDEVDIR is an alternate prefix to FSLDIR which is used to store updated code separately from the official FSL release. You might want to set it to something in your home directory, e.g. $HOME/fsldev. Most FSL-based scripts should use code installed in FSLDEVDIR in preference to the main FSL release code.

Note

This is not always necessary - it depends on the system you’re building on. So try skipping to the ‘Building…’ sections below and come back if you get compiler/linker errors.

Firstly, if you’re getting errors trying to build you need to do make clean and (to be safe!) rm depend.mk before building again with new settings. Also note that the FSL build system changed in v6.0.3 - here we provide only information for the new build system.

The relevant settings are in \$FSLDIR/config/buildSettings.mk. In particular you may need to modify ARCHFLAGS for your system - be careful as there are separate definitions for Linux and Mac (‘Darwin’) systems, so make sure you change the right one!

For recent versions of Ubuntu, you need to turn off use of the C++11 ABI as FSL libraries are not compiled using this. To do this add the following to ARCHFLAGS:

-D_GLIBCXX_USE_CXX11_ABI=0 -no-pie


If you are having difficulty with other systems, please raise an issue and we will investigate.

Building fabber_core¶

You can probably skip this if you are just building an updated model library. If you need to recompile the core, however, it should be a case of:

cd fabber_core
make install


This approach uses the same build tools as the rest of FSL which is important on some platforms, notably OSX. It will install the updated code into whatever prefix you selected as FSLDEVDIR.

Building new or updated model libraries¶

Model libraries are distributed separately from the Fabber core. If you need an updated version of a model library, for example the ASL model library, you first need to get the source code for the models library. A number of model libraries are available in our Github repositories all named fabber_models_<name>.

Then to build and install the updated model libraries you would then run, for example:

cd fabber_models_asl
make install


If you want to create your own model to use with the Fabber core model fitting engine, see Building a new model library. Once you’ve designed and coded your model there are two ways to incorporate it into the Fabber system:

Adding models directly to the core¶

If you wish, you can add your own models directly into the Fabber source tree and build the executable as above. This is not generally recommended because your model will be built into the core executable, however it can be the quickest way to get an existing model built in. You will need to follow these steps:

fabber_core/fwdmodel_mine.cc

1. Edit Makefile to add your model to the list of core objects, e.g.
COREOBJS =  fwdmodel_mine.o noisemodel.o fwdmodel.o inference.o fwdmodel_linear.o fwdmodel_poly.o convergence.o motioncorr.o priors.o transforms.o

1. Run make install again to build and install a new executable
This is the preferred approach if you want to distribute your new models. A template for a new model library including a simple sine-function implementation is included with the Fabber source code in fabber_core/examples. See Building a new model library for a full tutorial on this example which includes how to set up the build scripts.