.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.12.
.TH NIPY_TSDIFFANA "1" "January 2020" "nipy_tsdiffana 0.4.2" "User Commands"
.SH NAME
nipy_tsdiffana \- Analyze, plot time series difference metrics
.SH DESCRIPTION
usage: nipy_tsdiffana [\-h] [\-\-out\-file OUT_FILE] [\-\-write\-results]
.TP
[\-\-out\-path OUT_PATH]
[\-\-out\-fname\-label OUT_FNAME_LABEL]
[\-\-time\-axis TIME_AXIS] [\-\-slice\-axis SLICE_AXIS]
filename
.IP
Analyze, plot time series difference metrics
.SS "positional arguments:"
.TP
filename
4D image filename
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-out\-file\fR OUT_FILE
graphics file to write to instead of leaving image on
screen
.TP
\fB\-\-write\-results\fR
if specified, write diagnostic images and analysis
variables, plot to OUT_PATH. Mutually incompatible
with OUT_FILE
.TP
\fB\-\-out\-path\fR OUT_PATH
path for output image files (default from FILENAME
path
.TP
\fB\-\-out\-fname\-label\fR OUT_FNAME_LABEL
mid part of output image / plot filenames
.TP
\fB\-\-time\-axis\fR TIME_AXIS
Image axis for time
.TP
\fB\-\-slice\-axis\fR SLICE_AXIS
Image axis for slice
.PP
nipy_tsdiffana runs the time series diference algorithm over a 4D
image volume, often and FMRI volume.
.PP
It works in one of three modes:
.PP
* interactive : the time series difference plot appears on screen.  This is the
.IP
default mode
.PP
* non\-interactive, plot only : write time series difference plot to graphic
.IP
file. Use the "\-\-out\-file=<myfilename>" option to activate this mode
.PP
* non\-interactive, write plot, images and variables : write plot to file, and
.IP
write generated diagnostic images and variables to files as well. Use the
"\-\-write\-results" flag to activate this option. The generated filenames come
from the results of the "\-\-out\-path" and "\-\-out\-fname\-label" options (see
help).
.PP
Write\-results option, generated files
\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
.PP
When doing the time point analysis, we will make a difference volume between
each time point and the next time point in the series.  If we have T volumes
then there will be (T\-1) difference volumes. Call the vector of difference
volumes DV and the first difference volume DV[0].  So DV[0] results from
subtraction of the second volume in the 4D input image from the first volume in
the 4D input image.  The element\-wise squared values from DV[0] is *DV2[0]*.
.PP
The following images will be generated. <ext> is the input filename extension
(e.g. '.nii'):
.PP
* "dv2_max_<label><ext>" : 3D image volume, where each slice S is slice from
.IP
all of DV2[0] (slice S) throudh DV2[T\-1] (slice S) that has the maximum
summed squared values.  This volume gives an idea of the worst (highest
difference) slices across the whole time series.
.PP
* "dv2_mean_<label><ext>" : the mean of all DV2 volumes DV2[0] .. DV[T\-1]
.TP
across the volume (time) dimension.
Higher voxel values in this volume mean
.IP
that time\-point to time point differences tended to be high in this voxel.
.PP
We also write the mean signal at each time point, and the mean squared
difference between each slice in time, as variables to a 'npz' file named
"tsdiff_<label>.npz"
.PP
The filenames for the outputs are of the form
<out\-path>/<some_prefix><label><file\-ext> where <out\-path> is the path
specified by the \fB\-\-out\-path\fR option, or the path of the input filename;
<some_prefix> is one of the standard prefixes above, <label> is given by
\fB\-\-out\-label\fR, or by the filename of the input image (with path and extension
removed), and <file\-ext> is '.png' for graphics, or the extension of the input
filename for volume images.  For example, specifying only the input filename
``/some/path/fname.img`` will generate filenames of the form
``/some/path/tsdiff_fname.png, \fI\,/some/path/dv2_max_fname\/\fP.img`` etc.