neurodata/ndmg

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'flirt -in /Users/gkiar/Desktop/KKI2009_113_1_B0.nii -ref /Users/gkiar/Desktop/KKI2009_113_1_MPRAGE.nii -omat /Users/gkiar/Desktop/B0toMPRAGE.mat -cost mutualinfo -bins 256 -dof 12 -searchrx -180 180 -searchry -180 180 -searchrz -180 180'"
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import os.path as op\n",
    "b0 = \"/Users/gkiar/Desktop/KKI2009_113_1_B0.nii\"\n",
    "mprage = \"/Users/gkiar/Desktop/KKI2009_113_1_MPRAGE.nii\"\n",
    "mat1 = '/Users/gkiar/Desktop/B0toMPRAGE.mat'\n",
    "mat1\n",
    "cmd = 'flirt -in ' + b0 + ' -ref ' + mprage + ' -omat '+ mat1 +\" -cost mutualinfo -bins 256 -dof 12 -searchrx -180 180 -searchry -180 180 -searchrz -180 180\"\n",
    "cmd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "('', '')"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from subprocess import Popen, PIPE\n",
    "p = Popen(cmd, stdout=PIPE, stderr=PIPE, shell=True)\n",
    "p.communicate()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'flirt -in /Users/gkiar/Desktop/KKI2009_113_1_MPRAGE.nii -ref /Users/gkiar/Desktop/MNI152_T1_1mm.nii.gz -omat /Users/gkiar/Desktop/MPRAGEtoMNI.mat -cost mutualinfo -bins 256 -dof 12 -searchrx -180 180 -searchry -180 180 -searchrz -180 180'"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mni = \"/Users/gkiar/Desktop/MNI152_T1_1mm.nii.gz\"\n",
    "mat2 = '/Users/gkiar/Desktop/MPRAGEtoMNI.mat'\n",
    "mat2\n",
    "cmd = 'flirt -in ' + mprage + ' -ref ' + mni + ' -omat '+ mat2 +\" -cost mutualinfo -bins 256 -dof 12 -searchrx -180 180 -searchry -180 180 -searchrz -180 180\"\n",
    "cmd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "('', '')"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "p = Popen(cmd, stdout=PIPE, stderr=PIPE, shell=True)\n",
    "p.communicate()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'convert_xfm -omat /Users/gkiar/Desktop/B0toMNI.mat -concat /Users/gkiar/Desktop/MPRAGEtoMNI.mat /Users/gkiar/Desktop/B0toMPRAGE.mat'"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mat3 = '/Users/gkiar/Desktop/B0toMNI.mat'\n",
    "cmd = 'convert_xfm -omat '+ mat3 +' -concat '+ mat2 + ' ' + mat1\n",
    "cmd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "('', '')"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "p = Popen(cmd, stdout=PIPE, stderr=PIPE, shell=True)\n",
    "p.communicate()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'flirt -in /Users/gkiar/Desktop/KKI2009_113_1_DTI.nii -ref /Users/gkiar/Desktop/MNI152_T1_1mm.nii.gz -out /Users/gkiar/Desktop/KKI2009_113_1_DTI_reg.nii.gz -init /Users/gkiar/Desktop/B0toMNI.mat -interp trilinear -applyxfm'"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dwi = '/Users/gkiar/Desktop/KKI2009_113_1_DTI.nii'\n",
    "reg_dwi = '/Users/gkiar/Desktop/KKI2009_113_1_DTI_reg.nii.gz'\n",
    "cmd = 'flirt -in '+ dwi +' -ref '+ mni +' -out '+ reg_dwi +' -init '+ mat3 +' -interp trilinear -applyxfm'\n",
    "cmd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "('', '')"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "p = Popen(cmd, stdout=PIPE, stderr=PIPE, shell=True)\n",
    "p.communicate()"
   ]
  }
 ],
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