qsirecon.interfaces.anatomical module

Image tools interfaces

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

Bases: SimpleInterface

Mandatory Inputs:

sh_nifti (a string or os.PathLike object referring to an existing file)

Optional Inputs:

order (2 or 4 or 6 or 8) – (Nipype default value: 2)

Outputs:

  • q2_file (a string or os.PathLike object)

  • q4_file (a string or os.PathLike object)

  • q6_file (a string or os.PathLike object)

  • q8_file (a string or os.PathLike object)

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

Bases: SimpleInterface

Mandatory Inputs:

template_name (a string)

Outputs:

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

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

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

Bases: SimpleInterface

Get only the useful files from a QSIPrep anatomical output.

Many of the preprocessed outputs aren’t useful for reconstruction (mainly anything that has been mapped forward into template space).

Mandatory Inputs:

  • infant_mode (a boolean)

  • recon_input_dir (a string or os.PathLike object referring to an existing directory)

Optional Inputs:

  • subject_id (a string)

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

Outputs:

  • acpc_aparc (a pathlike object or string representing a file)

  • acpc_aseg (a pathlike object or string representing a file)

  • acpc_brain_mask (a pathlike object or string representing a file)

  • acpc_csf_probseg (a pathlike object or string representing a file)

  • acpc_gm_probseg (a pathlike object or string representing a file)

  • acpc_preproc (a pathlike object or string representing a file)

  • acpc_seg (a pathlike object or string representing a file)

  • acpc_to_template_xfm (a pathlike object or string representing a file)

  • acpc_wm_probseg (a pathlike object or string representing a file)

  • orig_to_acpc_xfm (a pathlike object or string representing a file)

  • template_to_acpc_xfm (a pathlike object or string representing a file)

class qsirecon.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)

qsirecon.interfaces.anatomical.calculate_steinhardt(sh_l, sh_m, data, q_num)[source]
qsirecon.interfaces.anatomical.get_l_m(lmax)[source]