Author: Andreas Hadjiprocpis (andreashad2@gmail.com)
My work at the Institute of Neurology (UCL, Queen Square, London).
It is a toolkit of reading and analysing brain MRI scans.
The analysis consists of segmenting multiple sclerosis lesions and brain gray and white matter and CSF (the fluid in the brain).
There are also a lot of auxiliary utilities (e.g. clustering) all written in C for efficiency.
All files in this repo are for browsing only. If you want to install then you need to download only the tarball:
https://raw.githubusercontent.com/hadjiprocopis/medical-image-analysis/master/iontoolkit-2.0.0.tar.gz
Extract the files from the tar file using
tar xvzf iontoolkit-2.0.0.tar.gz
change dir to application:
cd iontoolkit-2.0.0
configure (note that below we configure for the install dir to be at
$HOME/usr, which means a folder in you home dir so that we avoid
requesting root privileges for installing files. This is the best
option in my opinion. Then all binaries will be placed in $HOME/usr/bin
and include files and libraries in $HOME/usr/include and $HOME/usr/lib
respectively. Alternatively, if you do have root privileges do not
specify --prefix in the command below. And all files will be installed
in system default locations. The other two options are required and please
do not forget them. Later GNU compiler versions are so pedantic they will
fail on very stupid warnings.):
./configure --prefix=$HOME/usr --disable-werror --disable-debug
compile:
make clean; make all
install in specified installation dir:
make install
In order to execute a command:
$HOME/usr/bin/UNCtest -o output.unc
This will produce a test UNC file as specified.
If you have $HOME/usr/bin in your path
(e.g. EXPORT PATH="$PATH:$HOME/usr/bin")
then you do not need to prefix each command with the
path.
This suite of programs and libraries has an important dependency : FFTW3. This is a Fast Fourier Transform library by the good people Matteo Frigo and Steven G. Johnson, see "The Design and Implementation of FFTW3," Proceedings of the IEEE 93 (2), 216–231 (2005). Invited paper, Special Issue on Program Generation, Optimization, and Platform Adaptation. (see http://www.fftw.org/ for downloading). Thanks to them!