Series Type: Structural

The structural pipeline simulates the acquisition of a single volume using gradient echo, spin echo, or inversion recoverycontrast, motion optionally applied and an image acquired at the specified acquisition resolution. Typically this is used togenerate the structural images such as T1w or FLAIR that ASL images are registered to.

All parameters have defaults if omitted; the default parameters result in spin echo contrast with TE=5ms and TR=300m and an acquisition voxel size of 1x1x1mm.

All strings are case-insensitive, for example “ge”, “GE” and “Ge” are all valid.

Images generated by the structural pipeline will be stored in a subdirectory names “anat”.

Single value parameters

The following parameters are applied to every volume that is generated by the DRO.

acq_matrix

(array of integers, optional) A 3-entry array defining the acquisition matrix size [Ni, Nj, Nk]. Defaults to [197, 233, 189].

acq_contrast

(string, optional) Defines the MRI signal model to use. “ge” for Gradient Echo, “se” for Spin Echo. See MriSignalFilter for implementation details. Defaults to "se".

desired_snr

(float, optional) The signal-to-noise ratio. If this has value of 0, then no noise will be added. See AddComplexNoiseFilter for implementation details. Defaults to 50.0.

random_seed

(int, optional) Seed to control the determinism of any pseudo-random behaviour in the pipeline, for example the noise added to images. Defaults to 0.

echo_time

(float, optional) The time in seconds after the excitation pulse that the MRI signal is acquired. This parameter generally affects the T2 or T2* contrast. Defaults to 0.005.

repetition_time

(float, optional) The time in seconds between successive excitation pulses. This parameter affects the T1 contrast. Defaults to 0.3.

rot_z

(float, optional) Rotation of the ground truth model in world space about the z-axis in degrees. See TransformResampleImageFilter for implementation details. Defaults to 0.0.

rot_y

(float, optional) Rotation of the ground truth model in world space about the y-axis in degrees. Defaults to 0.0.

rot_x

(float, optional) Rotation of the ground truth model in world space about the x-axis in degrees. Defaults to 0.0.

transl_x

(float, optional) Translation of the ground truth model in world space along the x-axis in mm. Defaults to``0.0``.

transl_y

(float, optional) Translation of the ground truth model in world space along the y-axis in mm. Defaults to 0.0.

transl_z

(float, optional) Translation of the ground truth model in world space along the z-axis in mm. Defaults to 0.0.

output_image_type

(string, optional) Specifies the image type of the output image: “magnitude”, “phase”, “real”, “imaginary”, “complex”. Defaults to "magnitude".

modality

(string, optional) Describes the intent of the generated image, for example “T1w”, “T2w”, “FLAIR”, “anat”. The actual image contrast may or may not actually be representative of this as it is dependent on other parameters. Output BIDS files are names according to this field. Defaults to "anat".