{
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    {
      "cell_type": "markdown",
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      "source": [
        "\n\n# Generate a left cerebellum volume source space\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"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "# Author: Alan Leggitt <alan.leggitt@ucsf.edu>\n#\n# License: BSD-3-Clause\n# Copyright the MNE-Python contributors."
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "import mne\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\"\nsubject = \"sample\"\naseg_fname = subjects_dir / \"sample\" / \"mri\" / \"aseg.mgz\""
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Setup the source spaces\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "# setup a cortical surface source space and extract left hemisphere\nsurf = setup_source_space(subject, subjects_dir=subjects_dir, 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, 0.12)\nlh_cereb = setup_volume_source_space(\n    subject,\n    mri=aseg_fname,\n    sphere=sphere,\n    volume_label=volume_label,\n    subjects_dir=subjects_dir,\n    sphere_units=\"m\",\n)\n\n# Combine the source spaces\nsrc = surf + lh_cereb"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Plot the positions of each source space\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "fig = mne.viz.plot_alignment(\n    subject=subject,\n    subjects_dir=subjects_dir,\n    surfaces=\"white\",\n    coord_frame=\"mri\",\n    src=src,\n)\nmne.viz.set_3d_view(\n    fig, azimuth=180, elevation=90, distance=0.30, focalpoint=(-0.03, -0.01, 0.03)\n)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "You can export source positions to a NIfTI file::\n\n    >>> nii_fname = 'mne_sample_lh-cerebellum-cortex.nii'\n    >>> src.export_volume(nii_fname, mri_resolution=True)\n\nAnd display source positions in freeview::\n\n   >>> from mne.utils import run_subprocess\n   >>> mri_fname = subjects_dir / \"sample\" / \"mri\" / \"brain.mgz\"\n   >>> run_subprocess([\"freeview\", \"-v\", str(mri_fname), \"-v\",\n                       f\"{aseg_fname}:colormap=lut:opacity=0.5\",\n                       \"-v\", f\"{nii_fname}:colormap=jet:colorscale=0,2\",\n                       \"--slice\", \"157\", \"75\", \"105\"])\n\n"
      ]
    }
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