Generate5ttfsl brick¶

Generate a five-tissues-type (5TT) segmented tissue image with FSL¶

The generated 5TT image is suitable for use in Anatomically-Constrained Tractography (ACT).

(mrtrix 5ttgen fsl command)

Mandatory inputs parameters:

in_file (a string representing an existing file)
Input T1w image (valid extensions: [.mif, .nii, .nii.gz]).
ex. '/home/username/data/raw_data/T1w.mif'

Optional inputs with default value parameters:

no_crop (a boolean, default value is False, optional)
Do NOT crop the resulting 5TT image to reduce its size (keep the same dimensions as the input image)
ex. False
sgm_amyg_hipp (a boolean, default value is False, optional)
Represent the amygdalae and hippocampi as sub-cortical grey matter in the 5TT image
ex. False
premasked (a boolean, default value is False, optional)
Indicate that brain masking has already been applied to the input image
ex. False

Optional inputs parameters:

in_mask (a string representing an existing file, optional)
Manually provide a brain mask, rather than deriving one in the script (valid extensions: [.mif, .nii, .nii.gz]).
ex. '/home/username/data/derived_data/brainmask.mif'
t2_image (a string representing an existing file, optional)
Provide a T2-weighted image in addition to the default T1-weighted image; this will be used as a second input to FSL FAST(valid extensions: [.mif, .nii, .nii.gz]).
ex. '/home/username/data/derived_data/T2.nii'

Outputs parameters:

out_file (a pathlike object or string representing a file)
The output 5TT image.
ex. '/home/username/data/derived_data/T1w_5tt.mif'

Useful links: