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FLAIR

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.

-proc_flair

Prerequisites 🖐🏼

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

Processing steps

  • 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

Usage

Terminal:

$ micapipe -bids <BIDS-directory> -sub <subject_id> -out <outputDirectory> -proc_flair <options>

Optional arguments: -proc_flair has one optional argument;

Optional argument Description
-flairScanStr <path> String to manually identify the T2/FLAIR scan for processing (eg. anat/sub-001<flairScanStr>.nii[.gz]) Default='FLAIR'

Outputs

Directories created or populated by -proc_flair:

  • <outputDirectory>/micapipe/<sub>/maps
  • <outputDirectory>/micapipe/<sub>/xfm

Files generated by -proc_flair:

  • Registration ouputs stored in <outputDirectory>/micapipe/<sub>/maps:

    • <sub>_<hemi>_surf-fsaverage5_label-midthickness_flair.func.gii
    • <sub>_<hemi>_surf-fsaverage5_label-white_flair.func.gii
    • <sub>_<hemi>_surf-fsLR-32k_label-midthickness_flair.func.gii
    • <sub>_<hemi>_surf-fsLR-32k_label-white_flair.func.gii
    • <sub>_<hemi>_surf-fsLR-5k_label-midthickness_flair.func.gii
    • <sub>_<hemi>_surf-fsLR-5k_label-white_flair.func.gii
    • <sub>_<hemi>_surf-fsnative_label-midthickness_flair.func.gii
    • <sub>_<hemi>_surf-fsnative_label-white_flair.func.gii
    • <sub>_space-nativepro_map-flair.json
    • <sub>_space-nativepro_map-flair.nii.gz

  • Output stored in <outputDirectory>/micapipe/<sub>/xfm

    • <sub>_from-flair_to-nativepro_mode-image_desc-affine_0GenericAffine.mat