Perelman School of Medicine at the University of Pennsylvania

Section for Biomedical Image Analysis (SBIA)

participating with CBICA

Required Packages and Optional Packages - GONDOLA


Required Packages

The following software has to be installed in order to build and run GONDOLA.

Package

Version

Description

BASIS

2.0

A meta-project developed at SBIA to standardize and simplify the software development.

CMake

2.8.4

The build of the software packages developed at SBIA is based on CMake, a cross-platform, open-source build tool. This tool can be used to configure the build system for various build tools which perform the actual build.

ITK

3.18

The ITK has to be build with the same compiler as the one used to build the MEX-files and MATLAB executable. Moreover, CMAKE_CXX_FLAGS and CMAKE_C_FLAGS has to include the -fPIC option for GCC. Although there have been major changes in ITK 4.0, this software should also work well with this version of the ITK as only the image IO classes are being used.

Jython

2.2

Jython is a Java implementation of the Python language interpreter. It enables the use of Java classes in scripts using the Python language and is in particular required by the command-line tools which determine the best parameters for each classifier and train them as these make use of the Weka Java API.

LIBLINEAR

1.8

LIBLINEAR is a fast linear SVM solver used in the GONDOLA optimization procedure. Make sure that you compile both LIBLINEAR and its MEX-files.

MATLAB

R2009b

An important part of this software has been written in MATLAB. Note that the Image Processing Toolbox is in particular required.

Python

2.6

The scripts for the cross-validation experiments are implemented in Python.

SBIAUtilities

1.0

The sbiautilities.pyxel Python module is used to read and write spreadsheets with the results of the cross-validation experiments in the CSV format.

Weka

3.7.3

Weka is a collection of machine learning algorithms for data mining tasks. It is used for the classification task.