######################################################################### This repository contains code fixes in order to run on the cluster. Follow the directions below as well as copying the following directories which are available from the downloadable package on the FSL website (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX): compiled/ mask_files/ training_files/ ######################################################################### ------------------------------------------------------- FIX - FMRIB's ICA-based Xnoiseifier Gholamreza Salimi-Khorshidi and Stephen Smith, FMRIB Analysis Group MATLAB compilation/wrapper Duncan Mortimer Copyright (C) 2012-2013 University of Oxford ------------------------------------------------------- ========= SETUP ========= Requires: R (and maybe R-devel), with the following commands run (ideally as root) to install packages: install.packages("kernlab") install.packages("ROCR") install.packages("class") install.packages("party") install.packages("e1071") install.packages("randomForest") Requires: FSL Requires: MATLAB Runtime Component: If there is a folder 'compiled' in the FIX folder then the MATLAB portions have been compiled for running without MATLAB. The required MATLAB runtime is included in 'compiled/`OS`/`arch`'. To install this follow these instructions (starting from this folder) Linux: cd compiled/Linux/x86_64 (...or compiled/Linux/i386 if you have a 32 bit OS and FIX has been compiled for this platform) cp MCRInstaller.zip /tmp ( cd /tmp; unzip MCRInstaller.zip && ./install ) Follow the instructions from this point - note where you have installed this as you will need to change the FSL_FIX_MCRROOT variable in 'settings.sh' to refer to this location. OS X: cd compiled/Darwin/x86_64 (...or compiled/Darwin/i386 on OS X 10.6) cp MCRInstaller.zip /tmp ( cd /tmp; unzip MCRInstaller.zip && ./install ) NB Mathworks only supports installation of one copy of the MATLAB Compiler Runtime at a time on OS X - if you have already installed a different version and rely on it for other software you should not use the compiled version. or: MATLAB, with the following toolboxes: signal or: Octave (>=3.4), with the following toolboxes: io (miscellaneous 1.0.11 for 3.4) statistics (1.1.3 for 3.4) specfun general control (2.2.5 for 3.4) (struct for 3.4) (optim for 3.4) signal nan To install these toolboxes, use the script setup_octave.sh - this will ask for a 'sudo' password if required (use -g option to install globally rather than for just this user account). Octave 3.4 ========== EPEL on Centos/RedHat/Scientific Linux provides Octave 3.4 which cannot install several packages from Octave forge, so download the following from http://sourceforge.net/projects/octave/files/Octave%20Forge%20Packages/Individual%20Package%20Releases/ miscellaneous-1.0.11.tar.gz statistics-1.1.3.tar.gz control-2.2.5.tar.gz signal-1.1.2.tar.gz Change to the folder where these have been downloaded to and install with: octave --eval 'pkg install -auto -forge io; pkg install -auto miscellaneous-1.0.11.tar.gz; \ pkg install -auto statistics-1.1.3.tar.gz; pkg install -auto -forge specfun; pkg install -auto -forge general; \ pkg install -auto control-2.2.5.tar.gz; pkg install -auto -forge struct; pkg instal -auto -forge optim; \ pkg install -auto signal-1.1.2.tar.gz;' To install system-wide run Octave as an admin user and add the option '-global' to each 'pkg install' command. Octave 3.6 ========== Install the required packages using: octave --eval 'pkg install -auto -forge io; pkg install -auto -forge statistics; \ pkg install -auto -forge specfun; pkg install -auto -forge general; \ pkg install -auto -forge control; pkg install -auto -forge signal;' To install system-wide run Octave as an admin user and add the option '-global' to each 'pkg install' command. ============= Configuration ============= Setup: edit the "settings.sh" script to reflect your system setup - descriptions of the options are given in this file. If using the compiled MATLAB version, make sure that FSL_FIX_MCRROOT is set to the location of the MATLAB Compiler Runtime you installed as per the instructions above. Setup for using inside HCP pipelines (only needed for HCP): Ensure the FSL_FIX_CIFTIRW and FSL_FIX_WBC variables in settings.sh are pointed at your HCP Workbench MATLAB CIFTIRW and Workbench folders respectively. ================== MATLAB Compilation ================== The MATLAB .m files can be compiled to allow fix to run without requiring MATLAB licenses (especially useful where it will be run on a cluster). To compile, ensure you have the MATLAB compiler toolbox installed and GNU make (Centos/RedHat/Scientific Linux: sudo yum -y install make Ubuntu/Debian: sudo apt-get install make OS X: Install XCode and the command line tools (XCode Preferences > Downloads) ) then issue the following command from within the fix folder: ./build_MATLAB This will install the binaries into 'compiled/`OS`/`arch`' (eg compiled/Darwin/x86_64 or compiled/Linux/x86_64) and create a file 'MCR.version' containing the version number of the MATLAB Compiler Runtime necessary to run this programs. Install this into a suitable location following these instructions ------------------------------------------------------- ============= USAGE ============= See usage instructions at the FSL Wiki: http://www.fmrib.ox.ac.uk/fsl/FIX -------------------------------------------------------