This file contains functions to display a large picture of a bunch of brain slices, using pylab and pynifti. It can be used as a module, or a standalone program. In the later case, see the usage information at the __main__ below. TODO : add an option for non-contour mode and for grid+markers mode
Display many brains slices on a large matplotlib figure.
niTemplate : a nifti image defining the “template” size on which other images will be visually resampled, and the contour of which will be overlayed. An in-Talairach mask is ideal here. filenameStruct : a list of structural (or anything else) images filepaths, the view of which is to be drawn on the left part of the final image. They should lie in the same CS as the template. filenameBold : a list of BOLD (or anything else) images filepaths, to be drawn on the right, or None if not needed. They should also lie on the same coordinate system as the template views : a list of views needed (with : 0 or “axial”, 1 or “sagittal”, 2 or “coronal”) angles : a list of slices (respectively on each above-mentionned axes). Caveat : as those are related to the template image, be sure to update it when switching to a different templates.
Note : the implementation is slower than necessary as the same contour is computed many times