MRtrix_y_inversion_test.ipynb

MRtrix_y_inversion_test_cslb.ipynb

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  {
   "cells": [
    {
     "cell_type": "heading",
     "level": 1,
     "metadata": {},
     "source": [
      "Mrtrix y inversion test - CSLB system"
     ]
    },
    {
     "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",
      "test_subs = ['CBU100017', 'CBU100023', 'CBU10024']\n",
      "\n",
      "#dwi_dir = '/work/imaging5/DTI/CBU_DTI/raw_data/DTI_sequence_64D_2A'\n",
      "out_dir = '/work/imaging5/DTI/CBU_DTI/mrtrix_invert_y_test'\n",
      "dwi_dir = out_dir\n",
      "\n",
      "system('mkdir ' + out_dir)\n",
      "\n",
      "chdir(out_dir)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 2
    },
    {
     "cell_type": "heading",
     "level": 2,
     "metadata": {},
     "source": [
      "Workflow"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "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')        \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'])\n",
      "        \n",
      "  wfs[t].inputs.bet.output_type = 'NIFTI'\n",
      "  wfs[t].inputs.CSDstreamtrack.desired_number_of_tracks = 1        \n",
      "        \n",
      "  wfs[t].run()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 3
    }
   ],
   "metadata": {}
  }
 ]
}