1NIPY_4D_REALIGN(1)               User Commands              NIPY_4D_REALIGN(1)
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NAME

6       nipy_4d_realign – Command-line wrapper for SpaceTimeRealign
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SYNOPSIS

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

14   POSITIONAL ARGUMENTS
15       Float  The TR of the measurement
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17       File   Path to a nifti file, or to a folder containing nifti files.  If
18              a path to a folder is provided, the order of  motion  correction
19              will  be np.sort(list_of_files).  The outputs will be ‘*_mc.par’
20              (containing 3 translation and  three  rotation  parameters)  and
21              ‘*_mc.nii.gz’  containing the motion corrected data (unless ‘ap‐
22              ply’ is set to False)
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24   OPTIONAL ARGUMENTS
25       -h, --help
26              Show a help message and exit
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28       --slice_order String
29              The order of slice aquisition  {‘ascending’,  ‘descending’  (de‐
30              fault), or the name of a function from nipy.algorithms.slicetim‐
31              ing.timefuncs}
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33       --slice_dim Int
34              Integer denoting the axis in images that is the slice axis.   In
35              a 4D image, this will often be axis = 2 (default).
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37       --slice_dir Int
38              1  if the slices were acquired slice 0 first (default), slice -1
39              last, or -1 if acquire slice -1 first, slice 0 last.
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41       --make_figure Bool
42              Whether to generate a ‘.png’ figure with the  motion  parameters
43              across runs.  {True, False}.  Default: False
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45       --save_path String
46              Full  path  to a file-system location for the output files.  De‐
47              faults to the same location as the input files.
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49       --save_params Bool
50              Whether to save the motion corrections parameters (3  rotations,
51              3 translations).  {True, False}.  Default: False.  NOTE: The ro‐
52              tations are not  Euler  angles,  but  a  rotation  vector.   Use
53              nipy.algorithms.registration.to_matrix44  to convert to a 4-by-4
54              affine matrix.
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SEE ALSO

57       nipy_3dto4d(1), nipy_4dto3d(1), nipy_diagnose(1), nipy_tsdiffana(1)
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61                                 February 2023              NIPY_4D_REALIGN(1)
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