{
  "nbformat_minor": 0, 
  "nbformat": 4, 
  "cells": [
    {
      "execution_count": null, 
      "cell_type": "code", 
      "source": [
        "%matplotlib inline"
      ], 
      "outputs": [], 
      "metadata": {
        "collapsed": false
      }
    }, 
    {
      "source": [
        "\n# Generate a left cerebellum volume source space\n\n\nGenerate a volume source space of the left cerebellum and plot its vertices\nrelative to the left cortical surface source space and the freesurfer\nsegmentation file.\n\n\n"
      ], 
      "cell_type": "markdown", 
      "metadata": {}
    }, 
    {
      "execution_count": null, 
      "cell_type": "code", 
      "source": [
        "# Author: Alan Leggitt <alan.leggitt@ucsf.edu>\n#\n# License: BSD (3-clause)\n\nimport numpy as np\nfrom scipy.spatial import ConvexHull\nfrom mayavi import mlab\nfrom mne import setup_source_space, setup_volume_source_space\nfrom mne.datasets import sample\n\nprint(__doc__)\n\ndata_path = sample.data_path()\nsubjects_dir = data_path + '/subjects'\nsubj = 'sample'\naseg_fname = subjects_dir + '/sample/mri/aseg.mgz'"
      ], 
      "outputs": [], 
      "metadata": {
        "collapsed": false
      }
    }, 
    {
      "source": [
        "Setup the source spaces\n\n"
      ], 
      "cell_type": "markdown", 
      "metadata": {}
    }, 
    {
      "execution_count": null, 
      "cell_type": "code", 
      "source": [
        "# setup a cortical surface source space and extract left hemisphere\nsurf = setup_source_space(subj, fname=None, subjects_dir=subjects_dir,\n                          add_dist=False)\nlh_surf = surf[0]\n\n# setup a volume source space of the left cerebellum cortex\nvolume_label = 'Left-Cerebellum-Cortex'\nsphere = (0, 0, 0, 120)\nlh_cereb = setup_volume_source_space(subj, mri=aseg_fname, sphere=sphere,\n                                     volume_label=volume_label,\n                                     subjects_dir=subjects_dir)"
      ], 
      "outputs": [], 
      "metadata": {
        "collapsed": false
      }
    }, 
    {
      "source": [
        "Plot the positions of each source space\n\n"
      ], 
      "cell_type": "markdown", 
      "metadata": {}
    }, 
    {
      "execution_count": null, 
      "cell_type": "code", 
      "source": [
        "# extract left cortical surface vertices, triangle faces, and surface normals\nx1, y1, z1 = lh_surf['rr'].T\nfaces = lh_surf['use_tris']\nnormals = lh_surf['nn']\n# normalize for mayavi\nnormals /= np.sum(normals * normals, axis=1)[:, np.newaxis]\n\n# extract left cerebellum cortex source positions\nx2, y2, z2 = lh_cereb[0]['rr'][lh_cereb[0]['inuse'].astype(bool)].T\n\n# open a 3d figure in mayavi\nmlab.figure(1, bgcolor=(0, 0, 0))\n\n# plot the left cortical surface\nmesh = mlab.pipeline.triangular_mesh_source(x1, y1, z1, faces)\nmesh.data.point_data.normals = normals\nmlab.pipeline.surface(mesh, color=3 * (0.7,))\n\n# plot the convex hull bounding the left cerebellum\nhull = ConvexHull(np.c_[x2, y2, z2])\nmlab.triangular_mesh(x2, y2, z2, hull.simplices, color=3 * (0.5,), opacity=0.3)\n\n# plot the left cerebellum sources\nmlab.points3d(x2, y2, z2, color=(1, 1, 0), scale_factor=0.001)\n\n# adjust view parameters\nmlab.view(173.78, 101.75, 0.30, np.array([-0.03, -0.01,  0.03]))\nmlab.roll(85)"
      ], 
      "outputs": [], 
      "metadata": {
        "collapsed": false
      }
    }, 
    {
      "source": [
        "Compare volume source locations to segmentation file in freeview\n\n"
      ], 
      "cell_type": "markdown", 
      "metadata": {}
    }, 
    {
      "execution_count": null, 
      "cell_type": "code", 
      "source": [
        "# Export source positions to nift file\nnii_fname = data_path + '/MEG/sample/mne_sample_lh-cerebellum-cortex.nii'\n\n# Combine the source spaces\nsrc = surf + lh_cereb\n\nsrc.export_volume(nii_fname, mri_resolution=True)\n\n# Uncomment the following lines to display source positions in freeview.\n'''\n# display image in freeview\nfrom mne.utils import run_subprocess\nmri_fname = subjects_dir + '/sample/mri/brain.mgz'\nrun_subprocess(['freeview', '-v', mri_fname, '-v',\n                '%s:colormap=lut:opacity=0.5' % aseg_fname, '-v',\n                '%s:colormap=jet:colorscale=0,2' % nii_fname, '-slice',\n                '157 75 105'])\n'''"
      ], 
      "outputs": [], 
      "metadata": {
        "collapsed": false
      }
    }
  ], 
  "metadata": {
    "kernelspec": {
      "display_name": "Python 2", 
      "name": "python2", 
      "language": "python"
    }, 
    "language_info": {
      "mimetype": "text/x-python", 
      "nbconvert_exporter": "python", 
      "name": "python", 
      "file_extension": ".py", 
      "version": "2.7.13", 
      "pygments_lexer": "ipython2", 
      "codemirror_mode": {
        "version": 2, 
        "name": "ipython"
      }
    }
  }
}