Ipython notebooks

matlab-example.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# This notebook uses the `matlab_kernel`.\n",
    "\n",
    "You can install this kernel from pypi by typing `pip install matlab_kernel`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1\n",
      "\n",
      "     2\n",
      "\n",
      "     3\n",
      "\n",
      "     4\n",
      "\n",
      "     5\n",
      "\n",
      "     6\n",
      "\n",
      "     7\n",
      "\n",
      "     8\n",
      "\n",
      "     9\n",
      "\n",
      "    10\n",
      "\n",
      "    11\n",
      "\n",
      "    12\n",
      "\n",
      "    13\n",
      "\n",
      "    14\n",
      "\n",
      "    15\n",
      "\n",
      "    16\n",
      "\n",
      "    17\n",
      "\n",
      "    18\n",
      "\n",
      "    19\n",
      "\n",
      "    20\n"
     ]
    }
   ],
   "source": [
    "% this is matlab code\n",
    "for i = 1:20\n",
    "    disp(i)\n",
    "end\n",
    "test = 'teststring';"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "command line works too\n"
     ]
    }
   ],
   "source": [
    "!echo \"command line works too\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "%plot native\n",
    "plot(1:500, 1:2:1000)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "this is a python string\n",
      "0\n",
      "1\n",
      "2\n",
      "3\n",
      "4\n"
     ]
    }
   ],
   "source": [
    "%%python\n",
    "print('this is a python string')\n",
    "for a in range(5):\n",
    "    print(a)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Let's try some rudimentary imaging analysis\n",
    "\n",
    "T1 from some random person:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "!fslview /Users/jan/Documents/prf-data/freesurfer/subjects/starling44_2/mri/T1.nii"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "And we can do the same in matlab:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "im = read_avw('/Users/jan/Documents/prf-data/freesurfer/subjects/starling44_2/mri/T1.nii');\n",
    "imshow(im(:, :, round(end/2))/255)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "ename": "ImportError",
     "evalue": "(\"No module named 'nipy'\",)",
     "output_type": "error",
     "traceback": [
      "  File \"/Library/anaconda/envs/py35/lib/python3.5/site-packages/metakernel/magics/python_magic.py\", line 19, in exec_code\n    exec(code, env)\n",
      "  File \"<string>\", line 1, in <module>\n"
     ]
    }
   ],
   "source": [
    "%%python\n",
    "from nipy.interfaces.fsl import utils\n",
    "smoother = Smooth()\n",
    "viewer.inputs.in_file = '/Users/jan/Documents/prf-data/freesurfer/subjects/starling44_2/mri/T1.nii'\n",
    "viewer.inputs.output_type = 'NIFTII_GZ'\n",
    "viewer.run()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "%plot -s 500,500"
   ]
  }
 ],
 "metadata": {
  "anaconda-cloud": {},
  "kernelspec": {
   "display_name": "Matlab",
   "language": "matlab",
   "name": "matlab"
  },
  "language_info": {
   "codemirror_mode": "octave",
   "file_extension": ".m",
   "help_links": [
    {
     "text": "MetaKernel Magics",
     "url": "https://github.com/calysto/metakernel/blob/master/metakernel/magics/README.md"
    }
   ],
   "mimetype": "text/x-octave",
   "name": "matlab",
   "version": "0.11.0"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 1
}

presentation.ipynb

python-example.ipynb

r-example.ipynb