Table 5.
A non-exhaustive list of commonly used software tools for MRI processing using atlas based methods.
| Software | Atlas building pipeline | Atlas-based processing | Type of atlas accepted in the processing |
|---|---|---|---|
| ANTs (Avants et al., 2011) – http://stnava.github.io/ANTs/ | Template Creation and Labeling pipeline | Brain extraction: ✓ | Labeled and probabilistic atlas |
| Normalization: ✓ | |||
| Brain segmentation: ✓ | |||
| NiftyReg/NiftySeg (Cardoso et al., 2013a, Ourselin et al., 2000) – http://cmictig.cs.ucl.ac.uk/wiki/index.php/Main_Page | Niftyreg Groupwise | Normalization: ✓ | Labeled, probabilistic and 4D atlas |
| Brain segmentation: ✓ | |||
| Freesurfer (Dale et al., 1999, Fischl et al., 1999) – http://freesurfer.net/ | FsAverage (only intensity average) | Cortical and subcortical segmentation: − | Labeled and probabilistic atlas |
| FSL (Jenkinson et al., 2012, Smith et al., 2004) | / | Brain extraction: – | Brain template |
| Normalization: ✓ | |||
| Brain segmentation: − | |||
| Statistical Parametric Mapping (SPM) (Ashburner and Friston, 1997) – http://www.fil.ion.ucl.ac.uk/spm/ | / | Normalization: ✓ | Labeled and probabilistic atlas |
| Brain segmentation: ✓ | Probabilistic atlas | ||
Brain atlas non-specific to the software can be integrated (✓) or not (−).