.TH NIPY_4D_REALIGN "1" "February 2023" "" "User Commands"
.SH NAME
.B nipy_4d_realign
\(en Command-line wrapper for \fBSpaceTimeRealign
.SH SYNOPSIS
.B nipy_4d_realign
.RB [ \-h ]
.RB [ \-\-slice_order\ \fIString ]
.RB [ \-\-slice_dim\ \fIInt ]
.RB [ \-\-slice_dir\ \fIInt ]
.RB [ \-\-make_figure\ \fIBool ]
.RB [ \-\-save_path\ \fIString ]
.RB [ \-\-save_params\ \fIBool ]
.I Float
.I File
.SH OPTIONS
.SS "POSITIONAL ARGUMENTS"
.TP
.I Float
The TR of the measurement
.TP
.I File
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
.BR np.sort(list_of_files) .
The outputs will be
.RB \(oq *_mc.par \(cq
(containing 3 translation and three rotation parameters)
and
.RB \(oq *_mc.nii.gz \(cq
containing the motion corrected data
(unless
.RB \(oq apply \(cq
is set to
.BR False )
.SS "OPTIONAL ARGUMENTS"
.TP
.BR \-h ,\  \-\-help
Show a help message and exit
.TP
.B \-\-slice_order\ \fIString
The order of slice aquisition
.RB {\(oq ascending \(cq,
.RB \(oq descending \(cq
.RI ( default ),
or the name of a function from
.BR nipy.algorithms.slicetiming.timefuncs }
.TP
.B \-\-slice_dim\ \fIInt
Integer denoting the axis in
.I images
that is the slice axis.
In a 4D image, this will often be
.RB axis\ =\  2
.RI ( default ).
.TP
.B \-\-slice_dir\ \fIInt
.B 1
if the slices were acquired slice 0 first
.RI ( default ),
slice \-1 last,
or
.B \-1
if acquire slice \-1 first,
slice 0 last.
.TP
.B \-\-make_figure\ \fIBool
Whether to generate a
.RB \(oq .png \(cq
figure with the motion parameters across runs.
.RB { True ,
.BR False }.
.IR Default :
.B False
.TP
.B \-\-save_path\ \fIString
Full path to a file-system location for the output files.
Defaults to the same location as the input files.
.TP
.B \-\-save_params\ \fIBool
Whether to save the motion corrections parameters
(3 rotations, 3 translations).
.RB { True ,
.RB False }.
.IR Default :
.BR False .
.IR NOTE :
The rotations are not Euler angles, but a rotation vector.
Use
.B nipy.algorithms.registration.to_matrix44
to convert to a 4-by-4 affine matrix.
.SH "SEE ALSO"
.BR nipy_3dto4d (1),
.BR nipy_4dto3d (1),
.BR nipy_diagnose (1),
.BR nipy_tsdiffana (1)