This allows plotting an MRI interactively

interactive_mri.py

import numpy as np
import matplotlib.pyplot as plt
from nilearn.plotting.img_plotting import _load_anat
fname = '/home/jrking/nilearn_data/haxby2001/subj1/anat.nii.gz'


class MRI_viewer():
    def __init__(self, fname):
        # setup figure
        fig, axes = plt.subplots(1, 3)
        self.fig = fig
        self.axes = axes
        # setup mri
        anat_img, black_bg, anat_vmin, anat_vmax = _load_anat(fname)
        self.anat_img = anat_img
        ny, nx, nz = np.shape(anat_img.dataobj)
        self.x = 50
        self.y = 50
        self.z = 50
        self.ims = [[], [], []]
        self.sagittal = axes[0].matshow(anat_img.dataobj[self.y, :, :].T,
                                        extent=[0, nx, 0, nz],
                                        aspect='auto', origin='lower',
                                        cmap='gray')
        self.coronal = axes[1].matshow(anat_img.dataobj[:, self.x, :].T,
                                       extent=[0, ny, 0, nx],
                                       aspect='auto', origin='lower',
                                       cmap='gray')
        self.axial = axes[2].matshow(anat_img.dataobj[:, :, self.z].T,
                                     extent=[0, ny, 0, ny],
                                     aspect='auto', origin='lower',
                                     cmap='gray')
        # setup cursor
        self.lh = dict()
        self.lv = dict()
        for view, ax in zip(['sagittal', 'coronal', 'axial'], axes):
            self.lv[view] = ax.axvline(color='r', zorder=20)
            self.lh[view] = ax.axhline(color='r', zorder=20)

        # interaction
        fig.canvas.callbacks.connect('motion_notify_event', self.on_move)
        fig.canvas.callbacks.connect('button_press_event', self.on_click)

    def get_xyz(self, event):
        if event.inaxes is None:
            return
        ax = np.where(event.inaxes == self.axes)[0][0]
        view = ['sagittal', 'coronal', 'axial'][ax]
        print event.xdata, event.ydata, view

        if view == 'sagittal':
            self.x = int(np.floor(event.xdata))
            self.z = int(np.floor(event.ydata))
        elif view == 'coronal':
            self.y = int(np.floor(event.xdata))
            self.z = int(np.floor(event.ydata))
        elif view == 'axial':
            self.y = int(np.floor(event.xdata))
            self.x = int(np.floor(event.ydata))
        print(self.x, self.y, self.z)

    def on_click(self, event):
        self.get_xyz(event)
        self.sagittal.set_data(self.anat_img.dataobj[self.y, :, :].T)
        self.coronal.set_data(self.anat_img.dataobj[:, self.x, :].T)
        self.axial.set_data(self.anat_img.dataobj[:, :, self.z].T)
        self.lv['sagittal'].set_xdata(self.x)
        self.lh['sagittal'].set_ydata(self.z)
        self.lv['coronal'].set_xdata(self.y)
        self.lh['coronal'].set_ydata(self.z)
        self.lv['axial'].set_xdata(self.y)
        self.lh['axial'].set_ydata(self.x)
        plt.draw()

    def on_move(self, event):
        pass

cursor = MRI_viewer(fname)
plt.show()