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misc.plot.mri

Module: misc.plot.mri

Basic (f)MRI plotting with ability to interactively perform thresholding

mvpa.misc.plot.mri.plotMRI(background=None, background_mask=None, cmap_bg='gray', overlay=None, overlay_mask=None, cmap_overlay='autumn', vlim=(0.0, None), vlim_type=None, do_stretch_colors=False, add_info=True, add_hist=True, add_colorbar=True, fig=None, interactive=None, nrows=None, ncolumns=None)

Very basic plotting of 3D data with interactive thresholding.

Background/overlay could be nifti files names or NiftiImage objects, or 3D ndarrays. if no mask provided, only non-0 elements are plotted

Parameters:

• do_stretch_colors (bool) – Stratch color range to the data (not just to visible data)
• vlim – 2 element tuple of low/upper bounds of values to plot
• vlim_type (None or ‘symneg_z’) – If not None, then vlim would be treated accordingly: symneg_z z-score values of symmetric normal around 0, estimated by symmetrizing negative part of the distribution, which often could be assumed when total distribution is a mixture of by-chance performance normal around 0, and some other in the positive tail
• ncolumns (int or None) – Explicit starting number of columns into which position the slice renderings. If None, square arrangement would be used
• nrows (int or None) – Explicit starting number of rows into which position the slice renderings. If None, square arrangement would be used
• add_hist (bool or tuple (int, int)) – If True, add histogram and position automagically. If a tuple – use as (row, column)
• add_info (bool or tuple (int, int)) – If True, add information and position automagically. If a tuple – use as (row, column).

Available colormaps are presented nicely on

http://www.scipy.org/Cookbook/Matplotlib/Show_colormaps

TODO:

• Make interface more attractive/usable
• allow multiple overlays... or just unify for them all to be just a list of entries
• handle cases properly when there is only one - background/overlay