qsiprep.interfaces.anatomical module

Image tools interfaces

class qsiprep.interfaces.anatomical.DesaturateSkull(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Mandatory Inputs:

  • brain_mask_image (a pathlike object or string representing an existing file) – Binary brain mask in the same grid as skulled_t2w_image.

  • skulled_t2w_image (a pathlike object or string representing an existing file) – Skull-on T2w image.

Optional Inputs:

brain_to_skull_ratio (a float) – Ratio of signal in the brain to signal in the skull. (Nipype default value: 8.0)

Outputs:

  • desaturated_t2w (a pathlike object or string representing an existing file)

  • head_scaling_factor (a float)

class qsiprep.interfaces.anatomical.DiceOverlap(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Mandatory Inputs:

  • anatomical_mask (a pathlike object or string representing an existing file) – Mask from a T1w image.

  • dwi_mask (a pathlike object or string representing an existing file) – Mask from a DWI image.

Outputs:

dice_score (a float)

class qsiprep.interfaces.anatomical.FakeSegmentation(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Mandatory Inputs:

mask_file (a pathlike object or string representing an existing file)

Outputs:

dseg_file (a pathlike object or string representing an existing file)

class qsiprep.interfaces.anatomical.GetTemplate(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Mandatory Inputs:

template_spec (a string) – Template specification of the form <template>[+<cohort>].

Optional Inputs:

anatomical_contrast (‘T1w’ or ‘T2w’ or ‘none’)

Outputs:

  • mask_file (a pathlike object or string representing an existing file)

  • template_file (a pathlike object or string representing an existing file)

class qsiprep.interfaces.anatomical.VoxelSizeChooser(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Optional Inputs:

  • anisotropic_strategy (‘min’ or ‘max’ or ‘mean’) – (Nipype default value: min)

  • input_image (a pathlike object or string representing an existing file)

  • voxel_size (a float)

Outputs:

voxel_size (a float)

qsiprep.interfaces.anatomical.calculate_nonbrain_saturation(head_img, brain_mask_img)[source]