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