{
 "metadata": {
  "name": "Task 2"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%pylab inline"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n",
        "Welcome to pylab, a matplotlib-based Python environment [backend: module://IPython.zmq.pylab.backend_inline].\n",
        "For more information, type 'help(pylab)'.\n"
       ]
      }
     ],
     "prompt_number": 1
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "from glob import glob\n",
      "from nipype.interfaces.dcm2nii import Dcm2nii\n",
      "from nipype.interfaces.fsl import BET\n",
      "\n",
      "import nipype.pipeline.engine as pe"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 2
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "convert = pe.Node(Dcm2nii(), name='convert_dicom')\n",
      "skull_stripper = pe.Node(BET(), name = 'skull_stripper')\n",
      "\n",
      "convert_flow = pe.Workflow(name = 'convert_and_strip')\n",
      "convert_flow.connect(convert, 'converted_files', skull_stripper, 'in_file')"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 3
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "fl = glob('/opt/data/NIPYPE_DATA/NKI.archive.1-5.007.LiteDICOM/3466763/session_1/MPRAGE_1/*.dcm')\n",
      "convert_flow.inputs.convert_dicom.source_names = fl[0] # or fl\n",
      "convert_flow.base_dir = '/mnt/mydir/'"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 4
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "convert_flow.run()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "120909-06:56:28,132 workflow INFO:\n",
        "\t ['check', 'execution', 'logging']\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "120909-06:56:28,136 workflow INFO:\n",
        "\t Running serially.\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "120909-06:56:28,138 workflow INFO:\n",
        "\t Executing node convert_dicom in dir: /mnt/mydir/convert_and_strip/convert_dicom\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "120909-06:56:28,151 workflow INFO:\n",
        "\t Running: dcm2nii -g n -n y -i n -o /mnt/mydir/convert_and_strip/convert_dicom -b config.ini /opt/data/NIPYPE_DATA/NKI.archive.1-5.007.LiteDICOM/3466763/session_1/MPRAGE_1/m000-s0155-defaced_MPRAGE.nii.dcm\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "120909-06:56:28,192 interface INFO:\n",
        "\t stdout 2012-09-09T06:56:28.191981:Chris Rorden's dcm2nii :: 2 November 2010 (Debian)\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "120909-06:56:28,194 interface INFO:\n",
        "\t stdout 2012-09-09T06:56:28.191981:reading preferences file /home/nipype_user/.dcm2nii/dcm2nii.ini\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "120909-06:56:28,195 interface INFO:\n",
        "\t stdout 2012-09-09T06:56:28.191981:reading preferences file config.ini\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "120909-06:56:28,196 interface INFO:\n",
        "\t stdout 2012-09-09T06:56:28.191981:Data will be exported to /mnt/mydir/convert_and_strip/convert_dicom/\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "120909-06:56:29,45 interface INFO:\n",
        "\t stdout 2012-09-09T06:56:29.044975:Validating 384 potential DICOM images.\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "120909-06:56:29,45 interface INFO:\n",
        "\t stdout 2012-09-09T06:56:29.044975:Found 192 DICOM images.\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "120909-06:56:29,46 interface INFO:\n",
        "\t stdout 2012-09-09T06:56:29.044975:Converting 192/192  1\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "120909-06:56:29,46 interface INFO:\n",
        "\t stdout 2012-09-09T06:56:29.044975:m000-s0001-defaced_MPRAGE.nii.dcm->18991230_010000MPRAGEs011a1001.nii\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "120909-06:56:29,47 interface INFO:\n",
        "\t stdout 2012-09-09T06:56:29.044975:Saving /mnt/mydir/convert_and_strip/convert_dicom/18991230_010000MPRAGEs011a1001.nii\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "120909-06:56:29,633 interface INFO:\n",
        "\t stdout 2012-09-09T06:56:29.633844:Reorienting as /mnt/mydir/convert_and_strip/convert_dicom/o18991230_010000MPRAGEs011a1001.nii\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "120909-06:56:29,634 interface INFO:\n",
        "\t stdout 2012-09-09T06:56:29.633844:Saving /mnt/mydir/convert_and_strip/convert_dicom/o18991230_010000MPRAGEs011a1001.nii\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "120909-06:56:29,635 interface INFO:\n",
        "\t stdout 2012-09-09T06:56:29.633844:Cropping NIfTI/Analyze image /mnt/mydir/convert_and_strip/convert_dicom/o18991230_010000MPRAGEs011a1001.nii\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "120909-06:56:29,668 interface INFO:\n",
        "\t stdout 2012-09-09T06:56:29.668688:Saving /mnt/mydir/convert_and_strip/convert_dicom/co18991230_010000MPRAGEs011a1001.nii\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "120909-06:56:29,711 workflow INFO:\n",
        "\t Executing node skull_stripper in dir: /mnt/mydir/convert_and_strip/skull_stripper\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "120909-06:56:29,718 workflow INFO:\n",
        "\t Running: bet /mnt/mydir/convert_and_strip/convert_dicom/18991230_010000MPRAGEs011a1001.nii /mnt/mydir/convert_and_strip/skull_stripper/18991230_010000MPRAGEs011a1001_brain.nii.gz\n"
       ]
      },
      {
       "output_type": "pyout",
       "prompt_number": 5,
       "text": [
        "<networkx.classes.digraph.DiGraph at 0x4553c90>"
       ]
      }
     ],
     "prompt_number": 5
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 5
    }
   ],
   "metadata": {}
  }
 ]
}