Note

This page is a reference documentation. It only explains the function signature, and not how to use it. Please refer to the user guide for the big picture.

5.3.4. sammba.registration.coregister_fmri_session

sammba.registration.coregister_fmri_session(session_data, t_r, write_dir, brain_volume, use_rats_tool=True, slice_timing=True, prior_rigid_body_registration=False, caching=False, voxel_size_x=0.1, voxel_size_y=0.1, verbose=True, **environ_kwargs)

DEPRECATED: Function ‘coregister_fmri_session’ is deprecated and will be removed in future release. Use class ‘Coregistrator’ instead.

Coregistration of the subject’s functional and anatomical images. The functional volume is aligned to the anatomical, first with a rigid body registration and then on a per-slice basis (only a fine correction, this is mostly for correction of EPI distortion).

Parameters

session_data : sammba.registration.SessionData

Single animal data, giving paths to its functional and anatomical image, as well as it identifier.

t_r : float

Repetition time for the EPI, in seconds.

write_dir : str

Directory to save the output and temporary images.

brain_volume : int

Volume of the brain in mm3 used for brain extraction. Typically 400 for mouse and 1800 for rat.

use_rats_tool : bool, optional

If True, brain mask is computed using RATS Mathematical Morphology. Otherwise, a histogram-based brain segmentation is used.

prior_rigid_body_registration : bool, optional

If True, a rigid-body registration of the anat to the func is performed prior to the warp. Useful if the images headers have missing/wrong information.

voxel_size_x : float, optional

Resampling resolution for the x-axis, in mm.

voxel_size_y : float, optional

Resampling resolution for the y-axis, in mm.

caching : bool, optional

Wether or not to use caching.

verbose : bool, optional

If True, all steps are verbose. Note that caching implies some verbosity in any case.

environ_kwargs : extra arguments keywords

Extra arguments keywords, passed to interfaces environ variable.

Returns

the same sequence with each animal_data updated: the following attributes

are added

  • output_dir_str

    Path to the output directory.

  • coreg_func_str

    Path to paths to the coregistered functional image.

  • coreg_anat_str

    Path to paths to the coregistered functional image.

  • coreg_transform_str

    Path to the transform from anat to func.

Notes

If use_rats_tool is turned on, RATS tool is used for brain extraction and has to be cited. For more information, see RATS