MRI-Preprocessing

MR Images Preprocessing Pipeline

• Inhomogeneity Correction
• Brain Extraction (Skull Stripping)
• Co-registration
• Tissue class segmentation
• Intensity Normalization

MR Image Data Preprocessing Tools

Inhomogeneity Correction

• N3
• N4 newer and presumably better, but in some cases N3 seems to work better. I think both tools are implemented as part of the ANTs suite of tools

Intensity Normalization

• ITK NormalizeImageFilter

Skull Stripping

• BET this is part of the FSL suite that is quite straightforward to install in ubuntu. However, there are a lot parameters to tune and sometimes it just fails for some reasons
• Robex
• FreeSurfer
• Multi-atlas skull stripping (MASS)
• AFNI

Affine Registration

• ANTS
• Fsl FLIRT
• FreeSurfer

Image Viewers

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• Slicer comes with a lot of useful packages to process images, including most of those mentioned above.
• ImageJ
• FslView