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
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
Terminal:
$ micapipe -bids <BIDS-directory> -sub <subject_id> -out <outputDirectory> -proc_flair <options>
Optional arguments:
-proc_flair has one optional argument;
Optional argument |
Description |
|---|---|
|
String to manually identify the T2/FLAIR scan for processing (eg. anat/sub-001_<flairScanStr>.nii[.gz]) Default=’FLAIR’ |
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