MRtrix_y_inversion_test.ipynb

{
 "metadata": {
  "gist_id": "7642891",
  "name": ""
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "heading",
     "level": 1,
     "metadata": {},
     "source": [
      "Mrtrix y inversion test"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "FSL2mrtrix has an option to invert the bvecs in the y direction when converting from FSL format bvals + bvecs. This isn't part of the mrtrix documentation, which is concerned with processing directly from dicoms. Whether or not to use it appears to be a scanner specific thing. \n",
      "\n",
      "Here we run two mrtrix workflows and compare the outputs after inverting and not inverting the y vector.\n",
      "\n"
     ]
    },
    {
     "cell_type": "heading",
     "level": 2,
     "metadata": {},
     "source": [
      "Setup"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "from nipype.workflows.dmri.mrtrix import create_mrtrix_dti_pipeline as cmdp\n",
      "from os import mkdir, chdir, system\n",
      "\n",
      "\n",
      "test_subs = ['CBU100017', 'CBU100023', 'CBU10024']\n",
      "\n",
      "dwi_dir = '/media/sf_WINDOWS_C_DRIVE/Users/John/CloudStorage/Dropbox/dwi_dat_temp/raw_dat/cslb/dwi'\n",
      "out_dir = '/home/adminuser/mrtrix_y_inversion_test'\n",
      "system('mkdir ' + out_dir)\n",
      "\n",
      "chdir(out_dir)\n"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "ename": "OSError",
       "evalue": "[Errno 2] No such file or directory: '/home/adminuser/mrtrix_y_inversion_test'",
       "output_type": "pyerr",
       "traceback": [
        "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m\n\u001b[1;31mOSError\u001b[0m                                   Traceback (most recent call last)",
        "\u001b[1;32m<ipython-input-1-0905d9dedf18>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[0;32m      9\u001b[0m \u001b[0msystem\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m'mkdir '\u001b[0m \u001b[1;33m+\u001b[0m \u001b[0mout_dir\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m     10\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m---> 11\u001b[1;33m \u001b[0mchdir\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mout_dir\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
        "\u001b[1;31mOSError\u001b[0m: [Errno 2] No such file or directory: '/home/adminuser/mrtrix_y_inversion_test'"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "matplotlib not available. Can not plot matrix\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "/usr/local/lib/python2.7/site-packages/nipype-0.8.0-py2.7.egg/nipype/interfaces/cmtk/nbs.py:20: UserWarning: ConnectomeViewer not installed\n",
        "  warnings.warn('ConnectomeViewer not installed')\n",
        "/usr/local/lib/python2.7/site-packages/nipype-0.8.0-py2.7.egg/nipype/interfaces/mrtrix/convert.py:28: UserWarning: dipy not installed\n",
        "  warnings.warn('dipy not installed')\n",
        "/usr/local/lib/python2.7/site-packages/nipype-0.8.0-py2.7.egg/nipype/interfaces/dipy/tracks.py:17: UserWarning: dipy not installed\n",
        "  warnings.warn('dipy not installed')\n",
        "/usr/local/lib/python2.7/site-packages/nipype-0.8.0-py2.7.egg/nipype/interfaces/dipy/tensors.py:26: UserWarning: dipy not installed\n",
        "  warnings.warn('dipy not installed')\n"
       ]
      }
     ],
     "prompt_number": 1
    },
    {
     "cell_type": "heading",
     "level": 2,
     "metadata": {},
     "source": [
      "Workflow"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "\n",
      "wfs = {} # workflows\n",
      "for t in test_subs[0:1]:\n",
      "    \n",
      "  wfs[t] = cmdp('mrtrix_dti_%s' %t)\n",
      "        \n",
      "  wfs[t].inputs.inputnode.dwi = join(dwi_dir,t,'data.nii.gz')        \n",
      "  wfs[t].inputs.inputnode.bvals = join(dwi_dir, t, 'bvals') \n",
      "  wfs[t].inputs.inputnode.bvecs = join(dwi_dir, t, 'bvecs')\n",
      "\n",
      "  #wfs[t].iterables = [ ('fsl2mrtrix.invert_x', ['True', 'False'] ),\n",
      "  #                     ('fsl2mrtrix.invert_y', ['True', 'False'] ),    \n",
      "  #                     ('fsl2mrtrix.invert_z', ['True', 'False'] )  ]    \n",
      "  wfs[t].iterables = ('fsl2mrtrix.invert_y', ['True', 'False'])"
     ],
     "language": "python",
     "metadata": {},
     "outputs": []
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "wfs[t].run()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": []
    }
   ],
   "metadata": {}
  }
 ]
}

MRtrix_y_inversion_test_cslb.ipynb