nanslice.nanslicer module

A command-line tool for producing figures with slices through MR images. This is installed by PIP as nanslicer. Supports overlays, dual-coded overlays and colorbars. Dual-coding is described here

The minimum command-line call is:

nanslicer image.nii.gz output.png

To add a dual-coded overlay, call:

nanslicer structural.nii.gz output.png --overlay beta.nii.gz --overlay_alpha pval.nii.gz

There are a lot of command-line options to control the colormaps and scaling. Type nanviewer --help to see a full list. The number of slices can be controlled with the --slice_rows and --slice_cols arguments, or you can choose --three_axis. The --slice_axis and --slice_lims arguments specify the axis along which to slice, and where to start and stop along it (expressed as fractions), for example:

nanslicer structural.nii.gz --slice_axis x --slice_lims 0.25 0.75

If you have timeseries data as the base image, you can plot the same slice through each volume with --timeseries, or you can choose the volume in the timeseries to use with --volume N (the default is the first).

Controlling image quality is slightly complicated because there are two interpolation steps. First we have to sample the 3D volumes to produce 2D slices to arbitrary precision. Then, matplotlib has to sample those slices to plot them to the canvas. The first step is controlled by --samples N, which controls the number of points to sample in each direction of the slice, and --interp_order N, which controls the quality of the interpolation. The defaults are 128 and 1 (linear interpolation). Increase them to increase the quality. The matplotlib step is controlled by --interp METHOD, and can be any valid matplotlib` interpolation method. The default is ``hanning, for increased speed this can be changed to linear or none. From experience, it is the quality of the matplotlib step which is the dominant factor in figure quality, hence the defaults of fairly fast sampling in the slicing step but using Hanning sampling in the matplotlib step.


The main function that is called from the command line.


  • args – The command-line arguments. See module docstring or command-line help for a full list