Bet brick¶
Brain Extraction with BET (FSL)¶
By default, only the brain extraction is done, but there are severals options to generate surfaces, binary mask…
Mandatory inputs parameters:
- in_file (a string representing an existing file)
Input file to skull strip. An existing file (valid extensions: [.nii, .nii.gz]).
ex. '/home/username/data/raw_data/T1w.nii'
Optional inputs with default value parameters:
- output_type (‘NIFTI’ or ‘NIFTI_GZ’, optional, default value is NIFTI)
- Format of the output image (one of NIFTI, NIFTI_GZ).- NIFTI: *.nii- NIFTI_GZ: *.nii.gz
ex. NIFTI
- mask (a boolean, optional, default value is True)
Create binary mask image. (Maps to a command-line argument: -m.)
ex. True
- mesh (a boolean, optional, default value is False)
Generate a vtk mesh brain surface. (Maps to a command-line argument: -e.)
ex. False
- skull (a boolean, optional, default value is False)
Create skull image. (Maps to a command-line argument: -s.)
ex. False
- no_output (a boolean, optional, default value is False)
Don’t generate segmented output. (Maps to a command-line argument: -n.)
ex. False
- outline (a boolean, optional, default value is False)
Create surface outline image. (Maps to a command-line argument: -o.)
ex. False
- threshold (a boolean, optional, default value is False)
Apply thresholding to segmented brain image and mask. (Maps to a command-line argument: -t.)
ex. False
- frac (a float, optional, default value is 0.5)
Fractional intensity threshold. (Maps to a command-line argument: -f)
ex. 0.5
- vertical_gradient (a float, optional, default value is 0.0)
Vertical gradient in fractional intensity threshold (-1, 1). (Maps to a command-line argument: -g)
ex. 0.0
- functional (a boolean, optional, default value is False)
Apply to 4D fMRI data. (Maps to a command-line argument: -F.) Mutually exclusive with inputs: functional, reduce_bias, robust, padding, remove_eyes, surfaces, t2_guided.
ex. False
- padding (a boolean, optional, default value is False)
Improve BET if FOV is very small in Z (by temporarily padding end slices) (Maps to a command-line argument: -Z.) Mutually exclusive with inputs: functional, reduce_bias, robust, padding, remove_eyes, surfaces, t2_guided.
ex. False
- reduce_biais (a boolean, optional, default value is False)
Bias field and neck cleanup. (Maps to a command-line argument: -B.) Mutually exclusive with inputs: functional, reduce_bias, robust, padding, remove_eyes, surfaces, t2_guided.
ex. False
- remove_eyes (a boolean, optional, default value is False)
Eye & optic nerve cleanup (can be useful in SIENA) (Maps to a command-line argument: -S.) Mutually exclusive with inputs: functional, reduce_bias, robust, padding, remove_eyes, surfaces, t2_guided.
ex. False
- robust (a boolean, optional, default value is False)
Robust brain centre estimation (iterates BET several times). (Maps to a command-line argument: -R.) Mutually exclusive with inputs: functional, reduce_bias, robust, padding, remove_eyes, surfaces, t2_guided.
ex. False
- surfaces (a boolean, optional, default value is False)
Run bet2 and then betsurf to get additional skull and scalp surfaces (includes registrations). (Maps to a command-line argument: -A.) Mutually exclusive with inputs: functional, reduce_bias, robust, padding, remove_eyes, surfaces, t2_guided.
ex. False
Optional inputs:
- radius (a integer, optional)
Head radius in mm . (Maps to a command-line argument: -r %d.)
ex. 65
- center (a list of at most 3 items which are an integer, optional)
Center of gravity in voxels. (Maps to a command-line argument: -c %s.)
ex. [1, 1, 1]
- t2_guided (a string representing an existing file, optional)
R As with creating surfaces, when also feeding in non-brain-extracted T2 (includes registrations). (Maps to a command-line argument: -A2.) Mutually exclusive with inputs: functional, reduce_bias, robust, padding, remove_eyes, surfaces, t2_guided.
ex. '/home/username/data/raw_data/T2w.nii'
Outputs parameters:
- out_file (a pathlike object or string representing a file)
Skullstripped file (extensions: [.nii, .nii.gz])
ex. '/home/username/data/derived_data/T1w_brain.nii'
- mask_file (a pathlike object or string representing a file)
Brain mask file (extensions: [.nii, .nii.gz])
ex. '/home/username/data/derived_data/T1w_brain_mask.nii'
- mesh_vtk_file (a pathlike object or string representing a file)
Mesh file (extensions: [.vtk])
ex. '/home/username/data/derived_data/T1w_brain_mesh.vtk'
- outline_file (a pathlike object or string representing a file)
Outline file (extensions: [.nii, .nii.gz])
ex. '/home/username/data/derived_data/T1w_brain_overlay.nii'
- skull_file (a pathlike object or string representing a file)
Skull file (extensions: [.nii, .nii.gz])
ex. '/home/username/data/derived_data/T1w_brain_skull.nii'
- inskull_mask_file (a pathlike object or string representing a file)
Inskull mask (extensions: [.nii, .nii.gz])
ex. '/home/username/data/derived_data/T1w_brain_inskull_mask.nii'
- inskull_mesh_vtk_file (a pathlike object or string representing a file)
Inskull mesh (extensions [.nii, .nii.gz])
ex. '/home/username/data/derived_data/T1w_brain_inskull_mesh.nii'
- inskull_mesh_vtk_file (a pathlike object or string representing a file)
Inskull mesh (extensions [.vtk])
ex. '/home/username/data/derived_data/T1w_brain_inskull_mesh.vtk'
- outskin_mask_file (a pathlike object or string representing a file)
Outskin mask (extensions: [.nii, .nii.gz])
ex. '/home/username/data/derived_data/T1w_brain_outskin_mask.nii'
- outskin_mesh_file (a pathlike object or string representing a file)
Outskin mesh (extensions [.nii, .nii.gz])
ex. '/home/username/data/derived_data/T1w_brain_outskin_mesh.vtk'
- outskin_mesh_vtk_file (a pathlike object or string representing a file)
Outskin mesh (extensions [.vtk])
ex. '/home/username/data/derived_data/T1w_brain_outskin_mesh.vtk'
- outskull_mask_file (a pathlike object or string representing a file)
Outskull mask (extensions: [.nii, .nii.gz])
ex. '/home/username/data/derived_data/T1w_brain_outskull_mask.nii'
- outskull_mesh_vtk_file (a pathlike object or string representing a file)
Outskull mesh (extensions [.vtk])
ex. /home/username/data/derived_data/T1w_brain_outskull_mesh.vtk
- outskull_mesh_file (a pathlike object or string representing a file)
Outskull mesh (extensions [.nii, .nii.gz])
ex. /home/username/data/derived_data/T1w_brain_outskull_mesh.vtk
- skull_mask_file (a pathlike object or string representing a file)
Skull mask (extensions: [.nii, .nii.gz])
ex. '/home/username/data/derived_data/T1w_brain_skull_mask.nii'
Usefull links: