{
 "metadata": {
  "name": "",
  "signature": "sha256:ee13bff5f8afd89506a788a447196670da588a4ef80b3365606aabce6e8da1b7"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# - compatibility with Python 3\n",
      "from __future__ import print_function  # print('me') instead of print 'me'\n",
      "from __future__ import division  # 1/2 == 0.5, not 0"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 8
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# - show figures inside the notebook\n",
      "%matplotlib inline"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 9
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# - import common modules\n",
      "import numpy as np  # the Python array package\n",
      "import matplotlib.pyplot as plt  # the Python plotting package"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 10
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# - set gray colormap and nearest neighbor interpolation by default\n",
      "plt.rcParams['image.cmap'] = 'gray'\n",
      "plt.rcParams['image.interpolation'] = 'nearest'"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 11
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "## Introducing nipype"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "[Nipype](http://nipy.sourceforge.net/nipype) is a Python module that provides Python interfaces to many imaging tools, including SPM, AFNI and FSL."
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "We install it with the Python `pip` tool.\n",
      "\n",
      "In our case we need the current development version to give us the most recent SPM interfaces.\n",
      "\n",
      "We install like this (from your `cmd` or `Terminal.app` window):\n",
      "\n",
      "```\n",
      "pip install git+https://github.com/nipy/nipype.git\n",
      "```\n",
      "\n",
      "After this has run, check that you can import nipype with:"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "import nipype\n",
      "nipype.__version__"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 12,
       "text": [
        "'1.0.0dev'"
       ]
      }
     ],
     "prompt_number": 12
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "We are interested in the nipype `interfaces` sub-package.  Specifically, we want the interfaces to the `spm` routines:"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "from nipype.interfaces import spm"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 13
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Our first job is to make sure that nipype can run MATLAB.  Let's check with a test call:"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "import nipype.interfaces.matlab as nim\n",
      "mlab = nim.MatlabCommand()\n",
      "mlab.inputs.script = \"version\"  # get MATLAB version\n",
      "mlab.run()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "ename": "IOError",
       "evalue": "matlab could not be found on host shanghai.local\nInterface MatlabCommand failed to run. ",
       "output_type": "pyerr",
       "traceback": [
        "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m\n\u001b[0;31mIOError\u001b[0m                                   Traceback (most recent call last)",
        "\u001b[0;32m<ipython-input-14-e298d2a8617f>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      2\u001b[0m \u001b[0mmlab\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mnim\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mMatlabCommand\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      3\u001b[0m \u001b[0mmlab\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0minputs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mscript\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"version\"\u001b[0m  \u001b[0;31m# get MATLAB version\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 4\u001b[0;31m \u001b[0mmlab\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
        "\u001b[0;32m/Users/mb312/.virtualenvs/test/lib/python2.7/site-packages/nipype/interfaces/base.pyc\u001b[0m in \u001b[0;36mrun\u001b[0;34m(self, **inputs)\u001b[0m\n\u001b[1;32m   1001\u001b[0m                     \u001b[0mruntime\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0menviron\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'DISPLAY'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m':%s'\u001b[0m \u001b[0;34m%\u001b[0m \u001b[0mvdisplay_num\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1002\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1003\u001b[0;31m             \u001b[0mruntime\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_run_interface\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mruntime\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1004\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1005\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_redirect_x\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
        "\u001b[0;32m/Users/mb312/.virtualenvs/test/lib/python2.7/site-packages/nipype/interfaces/matlab.pyc\u001b[0m in \u001b[0;36m_run_interface\u001b[0;34m(self, runtime)\u001b[0m\n\u001b[1;32m    136\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0m_run_interface\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mruntime\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    137\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0minputs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mterminal_output\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'allatonce'\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 138\u001b[0;31m         \u001b[0mruntime\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msuper\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mMatlabCommand\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_run_interface\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mruntime\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    139\u001b[0m         \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    140\u001b[0m             \u001b[0;31m# Matlab can leave the terminal in a barbbled state\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
        "\u001b[0;32m/Users/mb312/.virtualenvs/test/lib/python2.7/site-packages/nipype/interfaces/base.pyc\u001b[0m in \u001b[0;36m_run_interface\u001b[0;34m(self, runtime, correct_return_codes)\u001b[0m\n\u001b[1;32m   1445\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mexist_val\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1446\u001b[0m             raise IOError(\"%s could not be found on host %s\" %\n\u001b[0;32m-> 1447\u001b[0;31m                           (self.cmd.split()[0], runtime.hostname))\n\u001b[0m\u001b[1;32m   1448\u001b[0m         \u001b[0msetattr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mruntime\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'command_path'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcmd_path\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1449\u001b[0m         setattr(runtime, 'dependencies', get_dependencies(executable_name,\n",
        "\u001b[0;31mIOError\u001b[0m: matlab could not be found on host shanghai.local\nInterface MatlabCommand failed to run. "
       ]
      }
     ],
     "prompt_number": 14
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "If `nipype` does not have the right command to start MATLAB, this will fail with an error.  We can set the command to start MATLAB like this:"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "nim.MatlabCommand.set_default_matlab_cmd('/Applications/MATLAB_R2014a.app/bin/matlab')"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 15
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Check this is working by running the same code as previously:"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "mlab = nim.MatlabCommand()\n",
      "mlab.inputs.script = \"version\"  # get MATLAB version\n",
      "mlab.run()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 16,
       "text": [
        "<nipype.interfaces.base.InterfaceResult at 0x1074df8d0>"
       ]
      }
     ],
     "prompt_number": 16
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Next we need to make sure that nipype has SPM on the MATLAB path when it is running MATLAB.  Try running this command to get the SPM version?"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "mlab = nim.MatlabCommand()\n",
      "mlab.inputs.script = \"spm ver\"  # get SPM version\n",
      "mlab.run()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "ename": "RuntimeError",
       "evalue": "Command:\n/Applications/MATLAB_R2014a.app/bin/matlab -nodesktop -nosplash -singleCompThread -r \"addpath('/Users/mb312/dev_trees/pna2015/day12');pyscript;exit\"\nStandard output:\n\n                            < M A T L A B (R) >\n                  Copyright 1984-2014 The MathWorks, Inc.\n                     R2014a (8.3.0.532) 64-bit (maci64)\n                             February 11, 2014\n\n[\bWarning: Name is nonexistent or not a directory: /Users/mb312/matlab/m2html]\b \n[\bWarning: Duplicate directory name: /Users/mb312/matlab]\b \n[\bWarning: Name is nonexistent or not a directory: /Users/mb312/matlab/m2html]\b \n[\bWarning: Duplicate directory name: /Users/mb312/matlab]\b \n \nTo get started, type one of these: helpwin, helpdesk, or demo.\nFor product information, visit www.mathworks.com.\n \nExecuting pyscript at 14-May-2015 18:59:57:\n----------------------------------------------------------------------------------------------------\nMATLAB Version: 8.3.0.532 (R2014a)\nMATLAB License Number: 731130\nOperating System: Mac OS X  Version: 10.9.5 Build: 13F1077 \nJava Version: Java 1.7.0_11-b21 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode\n----------------------------------------------------------------------------------------------------\nMATLAB                                                Version 8.3        (R2014a)\nImage Processing Toolbox                              Version 9.0        (R2014a)\nMATLAB Compiler                                       Version 5.1        (R2014a)\nSignal Processing Toolbox                             Version 6.21       (R2014a)\nStatistics Toolbox                                    Version 9.0        (R2014a)\nWavelet Toolbox                                       Version 4.13       (R2014a)\n\nStandard error:\nMATLAB code threw an exception:\nUndefined function 'spm' for input arguments of type 'char'.\nFile:/Users/mb312/dev_trees/pna2015/day12/pyscript.m\nName:pyscript\nLine:3\n\nReturn code: 0\nInterface MatlabCommand failed to run. ",
       "output_type": "pyerr",
       "traceback": [
        "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m\n\u001b[0;31mRuntimeError\u001b[0m                              Traceback (most recent call last)",
        "\u001b[0;32m<ipython-input-17-024eb141edae>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0mmlab\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mnim\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mMatlabCommand\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      2\u001b[0m \u001b[0mmlab\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0minputs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mscript\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"spm ver\"\u001b[0m  \u001b[0;31m# get SPM version\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0mmlab\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
        "\u001b[0;32m/Users/mb312/.virtualenvs/test/lib/python2.7/site-packages/nipype/interfaces/base.pyc\u001b[0m in \u001b[0;36mrun\u001b[0;34m(self, **inputs)\u001b[0m\n\u001b[1;32m   1001\u001b[0m                     \u001b[0mruntime\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0menviron\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'DISPLAY'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m':%s'\u001b[0m \u001b[0;34m%\u001b[0m \u001b[0mvdisplay_num\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1002\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1003\u001b[0;31m             \u001b[0mruntime\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_run_interface\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mruntime\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1004\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1005\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_redirect_x\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
        "\u001b[0;32m/Users/mb312/.virtualenvs/test/lib/python2.7/site-packages/nipype/interfaces/matlab.pyc\u001b[0m in \u001b[0;36m_run_interface\u001b[0;34m(self, runtime)\u001b[0m\n\u001b[1;32m    144\u001b[0m             \u001b[0;32mpass\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    145\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0;34m'MATLAB code threw an exception'\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mruntime\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstderr\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 146\u001b[0;31m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mraise_exception\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mruntime\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    147\u001b[0m         \u001b[0;32mreturn\u001b[0m \u001b[0mruntime\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    148\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
        "\u001b[0;32m/Users/mb312/.virtualenvs/test/lib/python2.7/site-packages/nipype/interfaces/base.pyc\u001b[0m in \u001b[0;36mraise_exception\u001b[0;34m(self, runtime)\u001b[0m\n\u001b[1;32m   1381\u001b[0m         \u001b[0mmessage\u001b[0m \u001b[0;34m+=\u001b[0m \u001b[0;34m\"Standard error:\\n\"\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0mruntime\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstderr\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0;34m\"\\n\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1382\u001b[0m         \u001b[0mmessage\u001b[0m \u001b[0;34m+=\u001b[0m \u001b[0;34m\"Return code: \"\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mruntime\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mreturncode\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1383\u001b[0;31m         \u001b[0;32mraise\u001b[0m \u001b[0mRuntimeError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmessage\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1384\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1385\u001b[0m     \u001b[0;34m@\u001b[0m\u001b[0mclassmethod\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
        "\u001b[0;31mRuntimeError\u001b[0m: Command:\n/Applications/MATLAB_R2014a.app/bin/matlab -nodesktop -nosplash -singleCompThread -r \"addpath('/Users/mb312/dev_trees/pna2015/day12');pyscript;exit\"\nStandard output:\n\n                            < M A T L A B (R) >\n                  Copyright 1984-2014 The MathWorks, Inc.\n                     R2014a (8.3.0.532) 64-bit (maci64)\n                             February 11, 2014\n\n[\bWarning: Name is nonexistent or not a directory: /Users/mb312/matlab/m2html]\b \n[\bWarning: Duplicate directory name: /Users/mb312/matlab]\b \n[\bWarning: Name is nonexistent or not a directory: /Users/mb312/matlab/m2html]\b \n[\bWarning: Duplicate directory name: /Users/mb312/matlab]\b \n \nTo get started, type one of these: helpwin, helpdesk, or demo.\nFor product information, visit www.mathworks.com.\n \nExecuting pyscript at 14-May-2015 18:59:57:\n----------------------------------------------------------------------------------------------------\nMATLAB Version: 8.3.0.532 (R2014a)\nMATLAB License Number: 731130\nOperating System: Mac OS X  Version: 10.9.5 Build: 13F1077 \nJava Version: Java 1.7.0_11-b21 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode\n----------------------------------------------------------------------------------------------------\nMATLAB                                                Version 8.3        (R2014a)\nImage Processing Toolbox                              Version 9.0        (R2014a)\nMATLAB Compiler                                       Version 5.1        (R2014a)\nSignal Processing Toolbox                             Version 6.21       (R2014a)\nStatistics Toolbox                                    Version 9.0        (R2014a)\nWavelet Toolbox                                       Version 4.13       (R2014a)\n\nStandard error:\nMATLAB code threw an exception:\nUndefined function 'spm' for input arguments of type 'char'.\nFile:/Users/mb312/dev_trees/pna2015/day12/pyscript.m\nName:pyscript\nLine:3\n\nReturn code: 0\nInterface MatlabCommand failed to run. "
       ]
      }
     ],
     "prompt_number": 17
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "If this does not work, you may not have SPM set up on your MATLAB path by default.  You can add SPM to the path like this:"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "nim.MatlabCommand.set_default_paths('/Users/mb312/spm')"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 18
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Now try running the `spm ver` command again:"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "mlab = nim.MatlabCommand()\n",
      "mlab.inputs.script = \"spm ver\"  # get SPM version\n",
      "mlab.run()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 19,
       "text": [
        "<nipype.interfaces.base.InterfaceResult at 0x107458e10>"
       ]
      }
     ],
     "prompt_number": 19
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "We are going to put the setup we need into a Python file we can import from any script that we write that uses nipype.\n",
      "\n",
      "Change directory to your `pna_code` directory:\n",
      "\n",
      "```\n",
      "cd ~/pna_code\n",
      "```\n",
      "\n",
      "In this directory, make a new file called `nipype_settings.py` with contents like this:\n",
      "\n",
      "```\n",
      "\"\"\" Defaults for using nipype\n",
      "\"\"\"\n",
      "import nipype.interfaces.matlab as nim\n",
      "# If you needed to set the default matlab command above\n",
      "nim.MatlabCommand.set_default_matlab_cmd('/Applications/MATLAB_R2014a.app/bin/matlab')\n",
      "# If you needed to set the SPM path above\n",
      "nim.MatlabCommand.set_default_paths('/Users/mb312/spm')\n",
      "```"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Finally, open `cmd` or `Terminal.app` in this current directory, and do the following:\n",
      "\n",
      "```\n",
      "ipython\n",
      "```\n",
      "\n",
      "This starts the IPython console.  Next, at the IPython prompt, type these lines:\n",
      "\n",
      "```\n",
      "import nipype_settings\n",
      "import nipype.interfaces.matlab as nim\n",
      "mlab = nim.MatlabCommand()\n",
      "mlab.inputs.script = \"spm ver\"  # get SPM version\n",
      "mlab.run()\n",
      "```\n",
      "\n",
      "These should run without error.  Call us over for help if you did get an error."
     ]
    }
   ],
   "metadata": {}
  }
 ]
}