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Bold_mni_align pipeline

Register a mean functional image EPI in MNI space (for checking out registration)

Adapted from mriqc 22.06

Pipeline insight

Bold_mni_align combines the following pipelines and processes:
- Bias field correction (using ANTs N4BiasFieldCorrection)
(default: dimension = 3)
- Affine Initializer
- Get template from templateFlow
(default values for template : in_template = ‘MNI152NLin2009cAsym’, resolution = 2, suffix = ‘boldref’, desc =’fMRIPrep’
default values for template mask : in_template = ‘MNI152NLin2009cAsym’, resolution = 2, suffix = ‘mask’, desc =’brain’
default values for template seg : in_template = ‘MNI152NLin2009cAsym’, resolution = 1, suffix = ‘dseg’, desc =’carpet’)
- Registration
(default values:
convergence_threshold = [1e-06, 1e-06, 1e-06],
convergence_window_size = [20, 20, 10],
interpolation = ‘LanczosWindowedSinc’,
metric = [‘Mattes’, ‘Mattes’, ‘CC’],
metric_weight = [1, 1, 1],
number_of_iterations = [[10000, 1000, 100], [500, 250, 100], [100, 30, 20]],
radius_or_number_of_bins = [56, 56, 4],
sampling_percentage = [0.25, 0.25, 1.0],
sampling_strategy = [‘Regular’, ‘Regular’, ‘None’],
shrink_factors = [[4, 2, 1], [8, 4, 2], [8, 4, 2]],
smoothing_sigmas = [[4.0, 2.0, 1.0], [4.0, 2.0, 0.0], [3.0, 2.0, 1.0]],
transform_parameters = [(0.05,), (0.08,), (0.1, 3.0, 0.0)],
transforms = [‘Rigid’, ‘Affine’, ‘SyN’])
- Apply Transform
(default values: interpolation = ‘MultiLabel’)
Bold mni align pipeline

Mandatory inputs parameters

  • epi_mask (a string representing an existing file)

    Functional image brain mask (valid extensions: [.nii, .nii.gz]).

    ex. '/home/username/data/raw_data/automask_mean_reg_func_valid.nii'
  • epi_mean (a string representing an existing file)

    Mean functional image (valid extensions: [.nii, .nii.gz]).

    ex. '/home/username/data/raw_data/mean_reg_func_valid.nii'

Optional inputs parameters with a default value

  • reg_convergence_threshold (a list of items which are a float, optional)

    See Registration brick

    default value. [1e-06, 1e-06, 1e-06]
  • reg_convergence_window_size (a list of items which are an integer, optional)

    See Registration brick

    default value. [20, 20, 10]
  • reg_interpolation (Linear or NearestNeighbor or CosineWindowedSinc or WelchWindowedSinc or HammingWindowedSinc or LanczosWindowedSinc or BSpline or MultiLabel or Gaussian or GenericLabel, optional)

    See Registration brick

    default value.  'LanczosWindowedSinc'
  • reg_metric (a list of items which are CC or MeanSquares or Demon or GC or MI or mattes, optional)

    See Registration brick

    default value. ['Mattes', 'Mattes', 'CC']
  • reg_metric_weight (a list of items which are a float, optional)

    See Registration brick

    default value. [1, 1, 1]
  • reg_number_of_iteration (a list of items which are a list of item which are an integer, optional)

    See Registration brick

    default value. [[10000, 1000, 100], [500, 250, 100], [100, 30, 20]]
  • reg_radius_or_number_of_bins (a list of items which are an integer, optional)

    See Registration brick

    default value. [56, 56, 4]
  • reg_sampling_percentage (a list of items which are a float, optional)

    See Registration brick

    default value. [0.25, 0.25, 1.0]
  • reg_sampling_strategy (a list of items which are Random, Regular or None, optional)

    See Registration brick

    default value.  ['Regular', 'Regular', 'None']
  • reg_shrink_factors (a list of items which are a list of items which are an integer, optional)

    See Registration brick

    default value.  [[4, 2, 1], [8, 4, 2], [8, 4, 2]]
  • reg_smoothing_sigmas (a list of items which are a list of items which are a float, optional)

    See Registration brick

    default value. [[4.0, 2.0, 1.0], [4.0, 2.0, 0.0], [3.0, 2.0, 1.0]]
  • reg_transform_parameters (a list of items which are a tuple of the form: (a float) or a tuple of the form: (a float, a float, a float) or a tuple of the form: (a float, an integer, an integer, an integer) or a tuple of the form: (a float, an integer, a float, a float, a float, a float) or a tuple of the form: (a float, a float, a float, an integer) or a tuple of the form: (a float, an integer, an integer, an integer, an integer), optional)

    See Registration brick

    default value. [(0.05,), (0.08,), (0.1, 3.0, 0.0)]
  • reg_transforms (a list of items which are Rigid or Affine or CompositeAffine or Similarity or Translation or BSpline or GaussianDisplacementField or TimeVaryingVelocityField or TimeVaryingBSplineVelocityField or SyN or BSplineSyN or Exponential or BSplineExponential, optional)

    See Registration brick

    default value ['Rigid', 'Affine', 'SyN']
  • seg_template_res (an integer, optional)

    Seg template resolution

    default value. 1
  • template (a string, optional)

    Template name in TemplateFlow

    default value. 'MNI152NLin2009cAsym'
  • template_res (an integer, optional)

    Template resolution

    default value. 2

Outputs parameters:

  • composite_transform

    Composite transform (bold space –> MNI)

    ex. '/home/username/data/derived_data/n4c_mean_reg_func_valid_Composite.h5'
  • bias_image

    Register file (extensions: [.nii, .nii.gz]).

    ex. '/home/username/data/derived_data/n4c_mean_reg_func_valid_bias.nii'
  • epi_mni

    Bold data in template space (extensions: [.nii, .nii.gz]).

    ex. '/home/username/data/derived_data/w_n4c_mean_reg_func_valid.nii'
  • epi_parc

    Template data in bold space (extensions: [.nii, .nii.gz]).

    ex. '/home/username/data/derived_data/t_tpl-MNI152NLin2009cAsym_res-01_desc-carpet_dseg.nii'
  • inverse_composite_transform

    Inverse composite transform (MNI –> bold space)

    ex. '/home/username/data/derived_data/n4c_mean_reg_func_valid_InverseComposite.h5'

Useful links:

mriq EPI mni align pipeline