Automask brick¶

Create a brain-only mask of the image using AFNI 3dAutomask¶

AFNI 3dClipLevel algorithm is used to find clipping level and after an erosion/dilation step, only the largest connected component of the supra-threshold voxels are kept.

Be careful this program by itself does NOT do ‘skull-stripping’.

Mandatory inputs parameters:

in_file (a string representing an existing file)
Input image (valid extensions: [.nii, .nii.gz]). Input dataset can be 4DEPI or a skull-stripped anatomical.
ex. '/home/username/data/raw_data/func.nii'

Optional inputs with default value parameters:

clfrac (a float, optional, default value is 0.5)
Sets the clip level fraction (must be 0.1-0.9). A small value will tend to make the mask larger.
ex. 0.5
out_brain_suffix (a string, optional, default value is ‘_masked’)
Suffix of the brain masked image.
ex. '_masked'
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
out_prefix (a string, optional, default value is ‘automask’)
Prefix of the output image.
ex. 'automask_'

Optional inputs parameters:

dilate (an integer, optional)
Dilate the mask outwards. Default is Undefined (ie parameter not used).
ex. 1
erode (an integer, optional)
Erode the mask inwards. Default is Undefined (ie parameter not used).
ex. 1

Outputs parameters:

out_brain (a strings representing a file)
Masked image (extensions: [.nii, .nii.gz]).
ex. '/home/username/data/derived_data/func_masked.nii'
out_file (a strings representing a file)
Brain mask image (extensions: [.nii, .nii.gz]).
ex. '/home/username/data/derived_data/automask_func.nii'

Useful links:

AFNI 3dAutomask

AFNI 3dAutomask - nipype