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Volreg brick

Registers each 3D volume from the input dataset to the base volume using AFNI 3dvolreg

Mandatory inputs parameters:

• in_file (a string representing an existing file)

  Input file (valid extensions: [.nii, .nii.gz]).

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

Optional inputs with default value parameters:

• copyorigin (a boolean, optional, default value is False)

  Copy base file origin coords to output.

  ex. False
  

• interpolation (Fourier or linear or cubic or quintic or heptic, optional, default value is heptic)

  Different interpolation methods:

  • Fourier = Use a Fourier method (the default: most accurate; slowest).

  • linear = Use linear (1st order polynomial) interpolation (least accurate).

  • cubic = Use the cubic (3rd order) Lagrange polynomial interpolation.

  • quintic = Use the quintic (5th order) Lagrange polynomial interpolation.

  • heptic = Use the heptic (7th order) Lagrange polynomial interpolation.

  ex. heptic
  

• output_type (NIFTI or NIFTI_GZ, optional, default value is NIFTI)

  Format of the output image (one of NIFTI, NIFTI_GZ).

  - NIFTI: *.nii

  - NIFTI_GZ: *.nii.gz

  ex. NIFTI
  

• out_prefix (a string, optional, default value is ‘reg’)

  Prefix of the output image.

  ex. 'reg_'
  

• save_oned_matrix (a boolean, optional, default value is False)

  Save the transformation matrix oned matrix.

  ex. False
  

• save_md1d_file (a boolean, optional, default value is False)

  Save max displacement outputfile (md1d) file.

  ex. False
  

• timeshift (a boolean, optional, default value is False)

  Time shift to mean slice time offset.

  ex. False
  

• twopass (a boolean, optional, default value is False)

  Do two passes of the registration algorithm: (1) with smoothed base and data bricks, with linear interpolation, to get a crude alignment, then’ (2) with the input base and data bricks, to get a fine alignment. This method is useful when aligning high-resolution datasets that may need to be moved more than a few voxels to be aligned.

  ex. False
  

• zpad (a integer, optional, default value is 4)

  Zeropad around the edges by ‘n’ voxels during rotations.

  ex. 4
  

Optional inputs with default value parameters:

• in_weight_volume (a tuple (a string representing an existing file, Integer), optional)

  Weights for each voxel specified by a file with an optional volume number (defaults to 0). Default is Undefined (ie parameter not used).

  ex. ('/home/username/data/raw_data/mask.nii', 0)
  

Outputs parameters:

• md1d_file (a strings representing a file, optional)

  The transformation matrix (extensions: [.aff12.1D]).

  ex. '/home/username/data/derived_data/reg_func_md.1D'
  

• oned_file (a strings representing a file)

  Movement parameters file (extensions: [.txt]).

  ex. '/home/username/data/derived_data/reg_func_oned.txt'
  

• oned_matrix (a strings representing a file, optional)

  Transformation matrix (extensions: [.aff12.1D]).

  ex. '/home/username/data/derived_data/reg_func_oned_matrix.aff12.1D'
  

• out_file (a strings representing a file)

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

  ex. '/home/username/data/derived_data/reg_func.nii'
  

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Useful links:

AFNI 3dvolreg

AFNI Volreg - nipype