General

class sbl.sabre.interfaces.MakeIsotropic(command=None, **inputs)

Creates an image with isotropic voxel dimensions using the command sb-make_isotropic.

Input attributes:

Parameters:

• input_image – Input image as an existing file name
• output_image – Output image as a file name (optional, if output_image_suffix is not provided)
• output_image_suffix – Output image suffix as a string (optional, if output_image is not provided, default=_iso086)

Output attributes:

Parameters:output_image – Output image as an existing file name

Example:

>>> iso = MakeIsotropic()
>>> iso.input_image = '{session}_T1.nii.gz'
>>> iso.cmdline
'make_isotropic {session}_T1.nii.gz {session}_T1_iso086.nii.gz'
>>> iso.run() 

class sbl.sabre.interfaces.Erode(command=None, **inputs)

Erode an image using sb-erode.

Input attributes:

Parameters:

• input_image – Input image as an existing file name
• input_segmentation – Input segmentation as an existing file name
• output_image – Output image as a file name (optional, if output_suffix is not provided)
• output_suffix – Output suffix as a string (optional, if output_image is not provided, default=_eroded)

Output attributes:

Parameters:output_image – Output image as an existing file name

Example:

>>> erode = Erode()
>>> erode.input_segmentation = 'mni_icbm152_T1.nii.gz'
>>> erode.cmdline
'erode {session}_T1.nii.gz {session}_T1_seg.nii.gz {session}_T1_erode.nii.gz'
>>> erode.run()