Brain region parcellation

Parcellation

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

Parcellates an input.

Input attributes:

Parameters:

• T1_inACPC_erode – Eroded AC/PC-aligned T1 input image as an existing file name
• lobar_grid – Grid file with coordinates based on the Talairach atlas as an existing file name
• lobar_tracing – Lobar tracing 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=_parcel)

Output attributes:

Parameters:

• output_image – Output image as an existing file name
• output_grid – Grid file with coordinates based on the Talairach atlas as an existing file name

Example:

>>> parcel = Parcellate()
>>> parcel.T1_inACPC_erode = '{session}_T1_inACPC_erode.nii.gz'
>>> parcel.cmdline
'lobmask {session}_T1_inACPC_erode.nii.gz {session}_T1_inACPC_erode_parcel.nii.gz 1 2'
>>> parcel.run() 

Hole-filling

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

Fill holes in a parcellation using sbl-fill_holes_in_acpc_lobmask.

Input attributes:

Parameters:

• input_parcellation – Input image 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=_filled)

Output attributes:

Parameters:output_image – Output image as an existing file name

Example:

>>> fill = FillHolesInParcellation()
>>> fill.input_parcellation = 'mni_icbm152_T1.nii.gz'
>>> fill.cmdline
'fill_holes_in_acpc_lobmask mni_icbm152_T1_seg.nii.gz mni_icbm152_T1_mask.nii.gz 5 mni_icbm152_T1_seg_filled.nii.gz'
>>> fill.run()