.TH NIPY_DIAGNOSE "1" "February 2023" "" "User Commands"
.SH NAME
.B nipy_diagnose
\(en Calculate and write results for diagnostic screen
.SH SYNOPSIS
.B nipy_diagnose
.RB [ \-h ]
.RB [ \-\-out\-path\ \fIOUT_PATH ]
.RB [ \-\-out\-fname\-label\ \fIOUT_FNAME_LABEL ]
.RB [ \-\-ncomponents\ \fINCOMPONENTS ]
.RB [ \-\-time\-axis\ \fITIME_AXIS ]
.RB [ \-\-slice\-axis\ \fISLICE_AXIS ]
.I filename
.SH DESCRIPTION
.BR nipy_diagnose (1)
will generate a series of diagnostic images
for a 4D fMRI image volume.
The following images will be generated.
.RI < ext >
is the input filename extension (e.g.\ \(oq\fB.nii\fR\(cq):
.RS +7n
.IP \(bu 2
.B components_\fR<\fIlabel\fR>\fB.png\fR\ :
plots of PCA basis vectors
.IP \(bu 2
.B max_\fR<\fIlabel\fR><\fIext\fR>\ :
max image
.IP \(bu 2
.B mean_\fR<\fIlabel\fR><\fIext\fR>\ :
mean image
.IP \(bu 2
.B min_\fR<\fIlabel\fR><\fIext\fR>\ :
min image
.IP \(bu 2
.B pca_\fR<\fIlabel\fR><\fIext\fR>\ :
4D image of PCA component images
.IP \(bu 2
.B pcnt_var_\fR<\fIlabel\fR>\fB.png\fR\ :
percent variance scree plot for PCA components
.IP \(bu 2
.B std_\fR<\fIlabel\fR><\fIext\fR>\ :
standard deviation image
.IP \(bu 2
.B tsdiff_\fR<\fIlabel\fR>\fB.png\fR\ :
time series diagnostic plot
.RE
.P
The filenames for the outputs are of the form
.RI < out\-path > \fB/ < some_prefix >< label >< file\-ext >
where
.RI < out\-path >
is the path specified by the
.B \-\-out\-path
option, or the path of the input filename;
.RB < some_prefix >
are the standard prefixes above,
.RI < label >
is given by
.BR \-\-out\-label ,
or by the filename of the input image
(with path and extension removed), and
.RI < file\-ext >
is
.RB \(oq .png \(cq
for graphics,
or the extension of the input filename for volume images.
For example,
specifying only the input filename
.B /some/path/fname.img
will generate filenames of the form
.BR /some/path/components_fname.png ,
.B /some/path/max_fname.img
etc.
.SH OPTIONS
.SS "POSITIONAL ARGUMENTS"
.TP
.I filename
4D image filename
.SS "OPTIONAL ARGUMENTS"
.TP
.BR \-h ,\  \-\-help
Show a help message and exit
.TP
.B \-\-out\-path\ \fIOUT_PATH
Path for output image files
.TP
.B \-\-out\-fname\-label\ \fIOUT_FNAME_LABEL
Mid part of output image filenames
.TP
.B \-\-ncomponents\ \fINCOMPONENTS
Number of PCA components to write
.TP
.B \-\-time\-axis\ \fITIME_AXIS
Image axis for time
.TP
.B \-\-slice\-axis\ \fITSLICE_AXIS
Image axis for slice
.SH "SEE ALSO"
.BR nipy_3dto4d (1),
.BR nipy_4d_realign (1),
.BR nipy_4dto3d (1),
.BR nipy_tsdiffana (1)