Table 1 Neuroimaging software packages included in Lin4Neuro

3D Slicer

Tools for the segmentation, registration, and three-dimensional visualization of multi-modal image data. The package includes image analysis algorithms for diffusion tensor imaging, functional magnetic resonance imaging, and image-guided therapy.

AFNI

An environment for processing and displaying functional MRI data. It provides a complete analysis tool chain, including 3D cortical surface models and mapping of volumetric data (SUMA).

Amide

A tool for viewing and analyzing medical image data sets. It includes the simultaneous handling of multiple data sets imported from a variety of file formats, image fusion, 3D region of interest drawing and analysis, volume rendering, and rigid body alignments.

Caret

A tool which enables the user to create, view, and manipulate surface reconstructions of the cerebral and cerebellar cortex. It also displays experimental data on surfaces and volumes.

FSL

A comprehensive library of image analysis and statistical tools for fMRI, MRI, and DTI brain imaging data. Implementation of standard GLM analysis, white matter tractography, tissue segmentation, affine and non-linear co-registration, and independent component analysis.

ITK

Providing segmentation and registration algorithms in two, three, and more dimensions.

LIPSIA

A tool for data processing and evaluation of functional magnetic resonance images.

MINC-tools

Tools to manipulate MINC files.

MNI-N3

A tool for unsupervised correction of radio frequency (RF) field inhomogeneities in MR volumes.

MRIConvert

A medical image file conversion utility that converts DICOM files to NIfTI 1.1, Analyze 7.5, SPM99/Analyze, BrainVoyager, and MetaImage volume formats.

MRIcron

A GUI-based visualization and analysis tool for (functional) MRI. It can also draw anatomical regions-of-interest (ROI), or lesion mapping, as well as basic analysis of functional time series. In addition to 'mricron', the package also provides 'dcm2nii', which supports converting DICOM and PAR/REC images into the NIfTI format and 'npm' for non-parametric data analysis.

Virtual MRI

A realistic simulation of an MRI scanner. For the user it should be possible to change all the relevant settings of the virtual scanner and to adapt them to the expected pathology.

(x)Medcon

A tool to convert medical images. Supported formats are: Acr/Nema 2.0, Analyze (SPM), Concorde/μPET, DICOM 3.0, CTI ECAT 6/7, NIfTI-1, InterFile3.3, and PNG or Gif87a/89a.