def _get_deformable_to_raw_transformation(self, section_index):
        """
        Reads a series of transformations which take a raw image (i.e. image
        from the image stack before processing) into the deformable
        reconstruction image space.

        :param section_index: Index of the section to be extracted from the
          three-dimensional image stack and to be resliced. Note that this
          comes as section index as to be passed to the filename templates
          no the one starting from zero. The section index which starts from
          zero will be calculated automatically.
        :type section_index: int

        :return: List of itk transformations.
        :rtype: [``itk.Tranfsorm``, ...]
        """

        transforms = \
            pos_itk_transforms.itk_read_transformations_from_files(
                [self.options.section_affine_template % section_index,
                self.options.section_deformable_inv_template % section_index])
        transforms = \
            [transforms[1], transforms[0].GetInverseTransform()]

        return transforms
    def _get_atlas_to_reconstruction_coreg(self):
        """
        Reads a series of transformations which map the deformable
        reconstruction into the reference (atlas) image.

        :return: List of itk transformations.
        :rtype: [``itk.Tranfsorm``, ...]
        """

        transforms = \
            pos_itk_transforms.itk_read_transformations_from_files(
            [self.options.coregistration_affine,
             self.options.coregistration_deformable_forward])

        transforms = [transforms[0], transforms[1]]
        return transforms
    def _get_reconstruction_to_atlas_coreg(self):
        """
        Reads a series of transformations which map an 3D image from the
        reference image space (the atlas space) into the deformable
        reconstruction space.

        :return: List of itk transformations.
        :rtype: [``itk.Tranfsorm``, ...]
        """

        transforms = \
            pos_itk_transforms.itk_read_transformations_from_files(
            [self.options.coregistration_affine,
             self.options.coregistration_deformable_inverse])

        transforms = [transforms[1], transforms[0].GetInverseTransform()]
        return transforms