nipy_4d_realign - Man Page

nipy_4d_realign – Command-line wrapper for SpaceTimeRealign


nipy_4d_realign [-h] [--slice_order String] [--slice_dim Int] [--slice_dir Int] [--make_figure Bool] [--save_path String] [--save_params Bool] Float File


Positional Arguments


The TR of the measurement


Path to a nifti file, or to a folder containing nifti files. If a path to a folder is provided, the order of motion correction will be np.sort(list_of_files). The outputs will be ‘*_mc.par’ (containing 3 translation and three rotation parameters) and ‘*_mc.nii.gz’ containing the motion corrected data (unless ‘apply’ is set to False)

Optional Arguments


Show a help message and exit

--slice_order String

The order of slice aquisition {‘ascending’, ‘descending’ (default), or the name of a function from nipy.algorithms.slicetiming.timefuncs}

--slice_dim Int

Integer denoting the axis in images that is the slice axis. In a 4D image, this will often be axis = 2 (default).

--slice_dir Int

1 if the slices were acquired slice 0 first (default), slice -1 last, or -1 if acquire slice -1 first, slice 0 last.

--make_figure Bool

Whether to generate a ‘.png’ figure with the motion parameters across runs. {True, False}. Default: False

--save_path String

Full path to a file-system location for the output files. Defaults to the same location as the input files.

--save_params Bool

Whether to save the motion corrections parameters (3 rotations, 3 translations). {True, False}. Default: False. NOTE: The rotations are not Euler angles, but a rotation vector. Use nipy.algorithms.registration.to_matrix44 to convert to a 4-by-4 affine matrix.

See Also

nipy_3dto4d(1), nipy_4dto3d(1), nipy_diagnose(1), nipy_tsdiffana(1)

Referenced By

nipy_3dto4d(1), nipy_4dto3d(1), nipy_diagnose(1), nipy_tsdiffana(1).

February 2023