Table 3.
Standard software tools for MRI processing and their application for pediatric data.
| Software tool | MRI processing | Application in studies on young children |
|---|---|---|
| Autoseg (Wang et al., 2014) – https://www.nitrc.org/projects/autoseg/ | N4 bias field correction, noise reduction, rigid registration, skull-stripping, intensity rescaling, multi-atlas segmentation | Group comparisons based on brain volumes (Hazlett et al., 2017, Hazlett et al., 2012) |
| BrainVISA/Anatomist (Rivière et al., 2003) – http://brainvisa.info | Data visualization, manual tissue labeling | Segmentation of planum temporale (Vanderauwera et al., 2016) |
| Freesurfer (Dale et al., 1999, Fischl et al., 1999) – http://freesurfer.net/ | Motion correction, brain extraction, volumetric segmentation, surface extraction, cortical parcellation and reconstruction longitudinal processing and analysis | Morphometric analysis (Brown et al., 2012) Graph theory analysis based on structural correlation network (Hosseini et al., 2013, Im et al., 2016) |
| Correlation between structural measures and risk factors (Black et al., 2012) | ||
| Group comparisons based on cortical thickness (Clark et al., 2014, Yang et al., 2015) | ||
| Hippocampus segmentation (Krogsrud et al., 2014) | ||
| Longitudinal volumetric analysis (Lebel and Beaulieu, 2011) | ||
| FSL (Jenkinson et al., 2012, Smith et al., 2004) https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/ | ||
| - BET (Smith, 2002) | Brain extraction | Brain masking (Brain Development Cooperative Group, 2012b, Nordahl et al., 2011, Shaw et al., 2009, Shen et al., 2013) |
| - FAST (Zhang et al., 2001) | Brain segmentation | Structural correlation network based on cortical thickness (Nie et al., 2013) |
| - SIENA (Smith et al., 2002) | Cross-sectional and longitudinal analysis of brain changes | Morphometric analysis (Clark et al., 2014) |
| ITK-SNAP (Yushkevich et al., 2006) – http://www.itksnap.org/pmwiki/pmwiki.php | Manual and semi-automated brain segmentation | Segmentation of lateral ventricles and caudate (Hazlett et al., 2012, Knickmeyer et al., 2008) |
| The McConnell Brain Imaging Centre software toolboxhttp://www.bic.mni.mcgill.ca/software/ | ||
| - ANIMAL (Collins et al., 1995, Collins et al., 1994) | Anatomical labeling | Morphometric analysis (Brain Development Cooperative Group, 2012a, Castellanos et al., 2002, Hazlett et al., 2017) |
| - CIVET | Analysis of cortical surfaces | Group comparison based on cortical thickness (Shaw et al., 2009, Shaw et al., 2007) |
| - INSECT (Collins et al., 1999) | Multi-modal tissue classification | |
| - mni_autoreg (Collins et al., 1994) | MRI linear registration | |
| Statistical Parametric Mapping (SPM) (Ashburner and Friston, 1997) – http://www.fil.ion.ucl.ac.uk/spm/ | Brain segmentation, bias correction, spatial normalization | Voxel-based morphometry (Black et al., 2012, Raschle et al., 2011) |