Fluid attenuated inversion recovery

This module performs normalization of the T2/FLAIR images based on the gray and white matter modes. The image is then registered to nativepro, then mapped to fsnative, fsLR-5k, fsLR-32k, and fsaverage5 surfaces.



Prerequisites 🖐🏼

You need to run -proc_structural, -proc_surf and -post_structural before this stage

  • GM and WM segmentation of flair

  • Bias field correction weighted by white matter

  • Get the mode for each tissue: GM and WM

  • Normalize intensities by peak of WM (mode). This normalization will center the peak of the WM mode intensity at ZERO.

  • Brains mask of the normalized flair

  • Registration of flair to nativepro

  • Map flair midthickness to fsLR-32k, fsLR-5k and fsaverage5