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.

5.3.2. sammba.registration.anats_to_template

sammba.registration.anats_to_template(anat_filenames, head_template_filename, write_dir, brain_volume, use_rats_tool=True, registration_kind='nonlinear', brain_template_filename=None, dilated_head_mask_filename=None, convergence=0.005, maxlev=None, caching=False, verbose=1, unifize_kwargs=None, brain_masking_unifize_kwargs=None)

DEPRECATED: Function ‘anats_to_template’ has been replaced by function ‘anat_to_template’ and will be removed in future release.

Registers raw anatomical images to a given template.

Parameters

anat_filenames : list of str

Paths to the anatomical images.

head_template_filenamestr

Path to the head template.

write_dirstr

Path to an existant directory to save output files to.

brain_volumeint

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

use_rats_toolbool, optional

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

registration_kindone of {‘rigid’, ‘affine’, ‘nonlinear’}, optional

The allowed transform kind.

brain_template_filenamestr, optional

Path to a brain template. Note that this must coincide with the brain from the given head template. If None, the brain is extracted from the template with RATS.

dilated_head_mask_filenamestr, optional

Path to a dilated head mask. Note that this must be compliant with the the given head template. If None, the mask is set to the non-background voxels of the head template after one dilation.

cachingbool, optional

If True, caching is used for all the registration steps.

convergencefloat, optional

Convergence limit, passed to nipype.interfaces.afni.Allineate

maxlevint or None, optional

If not None, maximal level for the nonlinear warping. Passed to nipype.interfaces.afni.Qwarp. Lower implies faster but possibly lower precision.

verboseint, optional

Verbosity level. Note that caching implies some verbosity in any case.

unifize_kwargsdict, optional

Is passed to nipype.interfaces.afni.Unifize, to control bias correction of the template.

brain_masking_unifize_kwargsdict, optional

Is passed to nipype.interfaces.afni.Unifize, to tune the seperate bias correction step done prior to brain extraction.

Returns

data : sklearn.datasets.base.Bunch

Dictionary-like object, the interest attributes are :

• registeredlist of str.

  Paths to registered images. Note that they have undergone a bias correction step before.

• pre_transformslist of str.

  Paths to the affine transforms from the raw images to the images allineated to the template.

• transformslist of str.

  Paths to the transforms from the allineated images to the final registered images.

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