nipy_tsdiffana1

positional arguments:

filename

4D image filename

optional arguments:

-h, --help

show this help message and exit

--out-file OUT_FILE

graphics file to write to instead of leaving image on screen

--write-results

if specified, write diagnostic images and analysis variables, plot to OUT_PATH. Mutually incompatible with OUT_FILE

--out-path OUT_PATH

path for output image files (default from FILENAME path

--out-fname-label OUT_FNAME_LABEL

mid part of output image / plot filenames

--time-axis TIME_AXIS

Image axis for time

--slice-axis SLICE_AXIS

Image axis for slice

nipy_tsdiffana runs the time series diference algorithm over a 4D image volume, often and FMRI volume.

It works in one of three modes:

* interactive : the time series difference plot appears on screen. This is the

default mode

* non-interactive, plot only : write time series difference plot to graphic

file. Use the "--out-file=<myfilename>" option to activate this mode

* non-interactive, write plot, images and variables : write plot to file, and

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).

Write-results option, generated files -------------------------------------

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]*.

The following images will be generated. <ext> is the input filename extension (e.g. '.nii'):

* "dv2_max_<label><ext>" : 3D image volume, where each slice S is slice from

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.

* "dv2_mean_<label><ext>" : the mean of all DV2 volumes DV2[0] .. DV[T-1]

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"

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 --out-path option, or the path of the input filename; <some_prefix> is one of the standard prefixes above, <label> is given by --out-label, 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, /some/path/dv2_max_fname.img`` etc.