Table 2.
A non-exhaustive list of automated software used to process structural MRI and DTI data.
| Software | Description | Methods Papers | Measurements | Notes | Base | Website |
|---|---|---|---|---|---|---|
| 3D Slicer | Software package for visualization and image analysis. | Fedorov et al. (2012) | Cortical volume, Subcortical volume, DTI | Freely available; Open Source; Ongoing updates | Surgical Planning Lab, Boston, USA | www.slicer.org/ |
| AFNI | Software package for mapping human brain activity, with add-on programs and toolboxes that allow for cortical surface-based analysis (SUMA), and DTI tractography analysis (FATCAT). | Cox (1996), Cox and Hyde (1997) and Taylor and Saad (2013) | Cortical volume, Subcortical volume, DTI | Freely available; Open Source; Ongoing updates; Interacts with FreeSurfer and FSL | National Institute of Mental Health, Bethesda, USA | www.afni.nimh.nih.gov/ |
| Caret | Surface and volume-based software package for structural and functional analyses of the cerebral and cerebellar cortex. | Van Essen and Dierker (2007) and Van Essen (2012) | Surface measures, Myelin mapping, Cortical depth | Freely available; Open Source; Ongoing updates; Interacts with FreeSurfer | Van Essen Lab, St. Louis, USA | www.brainvis.wustl.edu/wiki/index.php |
| CIVET | Surface-based human brain image-processing pipeline for corticometric, morphometric and volumetric analyses. | Zijdenbos et al. (2002) | Cortical thickness, Surfrace area, Mean curvature, Gyrification index | Freely available; Ongoing updates | McConnell Brain Imaging Center, Montreal, Canada | www.bic.mni.mcgill.ca/ServicesSoftware/CIVET/ |
| ExploreDTI | Toolbox for exploratory diffusion tensor MRI and fiber tractography | Leemans et al. (2009) | DTI | Freely available; Ongoing updates | Image Sciences Institute, University Medical Center Utrecht, Netherlands | www.exploredti.com/ |
| FreeSurfer | Surface- and volume-based software suite for processing and analyzing brain MR images. FreeSurfer reconstructs the cortical surface, segments subcortical structures, and provides a number of labeling and statistical analysis options. | Dale et al. (1999), Fischl et al. (1999) and Reuter et al. (2012) | Cortical volume, Subcortical volume, Cortical thickness, DTI, Surfrace area, Mean curvature, Gyrification index | Freely available; Open Source; Ongoing updates; Interacts with Caret and FSL; Calculates DTI metrics via TRACULA; Has longitudinal pipeline | Laboratory for Computational Neuroimaging, Boston, USA | www.surfer.nmr.mgh.harvard.edu/ |
| FSL | Comprehensive library of analysis tools for fMRI, MRI and DTI brain imaging data. | Jenkinson et al. (2012) and Smith et al. (2004) | Gray matter concentration, volumetry, DTI, fMRI | Freely available; Ongoing updates; Interacts with FreeSurfer | Analysis Group, FMRIB, Oxford, UK | www.fsl.fmrib.ox.ac.uk/fsl/fslwiki/ |
| LL method | The Longitudinal registration and Longitudinal classification (LL) method measures structural volume changes in longitudinal MRI scans in which participant-specific information is used for both registration and segmentation. | Aubert-Broche et al. (2013) | Cortical volume, Subcortical volume | Not available for public use; Specific to longitudinal designs | McConnell Brain Imaging Center, Montreal, Canada | N/A |
| QUARC | Quantitative anatomical regional change (QUARC) is a nonlinear registration method that measures longitudinal change on a voxel-wise basis. | Holland and Dale (2011) | Cortical volume, Subcortical volume | Not available for public use; Specific to longitudinal designs; Interacts with FreeSurfer | Multimodal Imaging Laboratory, San Diego, USA | N/A |
| VBM | Voxel-based morphometry (VBM) is a technique that measures the concentration of gray matter within each voxel of the brain, and provides voxel-wise comparisons of local tissue volumes within a group or across groups. | Ashburner and Friston (2000) | Gray matter concentration or signal intensity | Freely available; Ongoing updates; Has longitudinal pipeline; Interacts with SPM | Functional Imaging Laboratory, London, UK | www.fil.ion.ucl.ac.uk/spm/dbm.neuro.uni-jena.de/vbm/ |