workflow.ipynb

{
 "metadata": {
  "name": "workflow"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "heading",
     "level": 2,
     "metadata": {},
     "source": [
      "Workflow"
     ]
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "The big picture"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "We have data, we have some code we want to run on the data.\n",
      "\n",
      "What is the simplest possible way we could do this?\n",
      "\n",
      "What could go wrong?\n",
      "\n",
      "How could we help ourselves to reduce mistakes?"
     ]
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "Mistakes"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "> In my own experience, error is ubiquitous in scientific computing, and one needs to work very diligently and energetically to eliminate it. One needs a very clear idea of what has been done in order to know where to look for likely sources of error. I often cannot really be sure what a student or colleague has done from his/her own presentation, and in fact often his/her description does not agree with my own understanding of what has been done, once I look carefully at the scripts. Actually, I find that researchers quite generally forget what they have done and misrepresent their computations.\n",
      ">\n",
      "> Computing results are now being presented in a very loose, \u201cbreezy\u201d way\u2014in journal articles, in conferences, and in books. All too often one simply takes computations at face value. This is spectacularly against the evidence of my own experience. I would much rather that at talks and in referee reports, the possibility of such error were seriously examined.\n",
      ">\n",
      "> -- <cite>David L. Donoho. An invitation to reproducible computational research. Biostatistics Volume 11, Issue 3 Pp. 385-388</cite>\n"
     ]
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "The components"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "* The data tree - *data*\n",
      "* Code that is specific to this data tree - *scripts*\n",
      "* Notebooks explaining analysis - *notebooks*\n",
      "* Code that is more generally useful - *library code*"
     ]
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "Version control"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Is absolutely essential.\n",
      "\n",
      "No - seriously."
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "See the notebook \"roll your own CMS\""
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Install git"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Get the course notebooks and files"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%bash\n",
      "cd\n",
      "mkdir practical_fmri\n",
      "cd practical_fmri\n",
      "git clone git://github.com/practical-neuroimaging/pna-notebooks.git\n",
      "ls ~/practical_fmri/pna-notebooks"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Cloning into 'pna-notebooks'...\n",
        "Makefile\n",
        "README.md\n",
        "Using nipy transforms.ipynb\n",
        "awesome.py\n",
        "bold_QC_again.ipynb\n",
        "check_openfmri.py\n",
        "checkhash.py\n",
        "finding_outliers_reprise.ipynb\n",
        "images\n",
        "interpolation-padding.ipynb\n",
        "introduction_to_python.ipynb\n",
        "loading_images.ipynb\n",
        "more_awesome.py\n",
        "openfmri.py\n",
        "outlier_detect.ipynb\n",
        "outliers.py\n",
        "python_libraries.ipynb\n",
        "roll_your_own_cms.ipynb\n",
        "slice_timing.ipynb\n",
        "slice_timing_full.ipynb\n",
        "spline_interpolation.ipynb\n",
        "test_awesome_more.py\n",
        "test_checkhash.py\n",
        "test_openfmri.py\n",
        "test_outliers.py\n",
        "visualization.ipynb\n",
        "what_are_my_times.ipynb\n",
        "what_is_an_image.ipynb\n",
        "workflow.ipynb\n"
       ]
      }
     ],
     "prompt_number": 1
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "Getting started - data"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Assuming your downloaded data file is in ``~/Downloads``:\n",
      "   "
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%bash\n",
      "cd\n",
      "mkdir data\n",
      "cd data\n",
      "unzip ~/Downloads/ds105_trimmed.zip\n",
      "ls ds105"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Archive:  /Users/mb312/Downloads/ds105_trimmed.zip\n",
        " extracting: README.rst              \n",
        "   creating: ds105/\n",
        " extracting: ds105/license.txt       \n",
        "   creating: ds105/models/\n",
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        " extracting: ds105/models/model001/condition_key.txt  \n",
        " extracting: ds105/models/model001/task_contrasts.txt  \n",
        " extracting: ds105/README            \n",
        " extracting: ds105/references.txt    \n",
        " extracting: ds105/release_history.txt  \n",
        " extracting: ds105/scan_key.txt      \n",
        " extracting: ds105/study_key.txt     \n",
        "   creating: ds105/sub001/\n",
        "   creating: ds105/sub001/anatomy/\n",
        " extracting: ds105/sub001/anatomy/highres001.nii.gz  \n",
        " extracting: ds105/sub001/anatomy/highres001_brain.nii.gz  \n",
        " extracting: ds105/sub001/anatomy/highres001_brain_mask.nii.gz  \n",
        "   creating: ds105/sub001/behav/\n",
        "   creating: ds105/sub001/BOLD/\n",
        "   creating: ds105/sub001/BOLD/task001_run001/\n",
        " extracting: ds105/sub001/BOLD/task001_run001/bold.nii.gz  \n",
        "   creating: ds105/sub001/BOLD/task001_run002/\n",
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        " extracting: ds105/sub001/model/model001/onsets/task001_run003/cond001.txt  \n",
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        " extracting: ds105/sub001/model/model001/onsets/task001_run005/cond001.txt  \n",
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        " extracting: ds105/sub001/model/model001/onsets/task001_run005/cond008.txt  \n",
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        " extracting: ds105/sub001/model/model001/onsets/task001_run006/cond001.txt  \n",
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        " extracting: ds105/sub001/model/model001/onsets/task001_run006/cond008.txt  \n",
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        " extracting: ds105/sub001/model/model001/onsets/task001_run007/cond001.txt  \n",
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        " extracting: ds105/sub002/anatomy/highres001.nii.gz  \n",
        " extracting: ds105/sub002/anatomy/highres001_brain.nii.gz  \n",
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        " extracting: ds105/sub002/model/model001/onsets/task001_run002/cond006.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run002/cond007.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run002/cond008.txt  \n",
        "   creating: ds105/sub002/model/model001/onsets/task001_run003/\n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run003/cond001.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run003/cond002.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run003/cond003.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run003/cond004.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run003/cond005.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run003/cond006.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run003/cond007.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run003/cond008.txt  \n",
        "   creating: ds105/sub002/model/model001/onsets/task001_run004/\n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run004/cond001.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run004/cond002.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run004/cond003.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run004/cond004.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run004/cond005.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run004/cond006.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run004/cond007.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run004/cond008.txt  \n",
        "   creating: ds105/sub002/model/model001/onsets/task001_run005/\n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run005/cond001.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run005/cond002.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run005/cond003.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run005/cond004.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run005/cond005.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run005/cond006.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run005/cond007.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run005/cond008.txt  \n",
        "   creating: ds105/sub002/model/model001/onsets/task001_run006/\n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run006/cond001.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run006/cond002.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run006/cond003.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run006/cond004.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run006/cond005.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run006/cond006.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run006/cond007.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run006/cond008.txt  \n",
        "   creating: ds105/sub002/model/model001/onsets/task001_run007/\n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run007/cond001.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run007/cond002.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run007/cond003.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run007/cond004.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run007/cond005.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run007/cond006.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run007/cond007.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run007/cond008.txt  \n",
        "   creating: ds105/sub002/model/model001/onsets/task001_run008/\n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run008/cond001.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run008/cond002.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run008/cond003.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run008/cond004.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run008/cond005.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run008/cond006.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run008/cond007.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run008/cond008.txt  \n",
        "   creating: ds105/sub002/model/model001/onsets/task001_run009/\n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run009/cond001.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run009/cond002.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run009/cond003.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run009/cond004.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run009/cond005.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run009/cond006.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run009/cond007.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run009/cond008.txt  \n",
        "   creating: ds105/sub002/model/model001/onsets/task001_run010/\n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run010/cond001.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run010/cond002.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run010/cond003.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run010/cond004.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run010/cond005.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run010/cond006.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run010/cond007.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run010/cond008.txt  \n",
        "   creating: ds105/sub002/model/model001/onsets/task001_run011/\n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run011/cond001.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run011/cond002.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run011/cond003.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run011/cond004.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run011/cond005.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run011/cond006.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run011/cond007.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run011/cond008.txt  \n",
        "   creating: ds105/sub002/model/model001/onsets/task001_run012/\n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run012/cond001.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run012/cond002.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run012/cond003.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run012/cond004.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run012/cond005.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run012/cond006.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run012/cond007.txt  \n",
        " extracting: ds105/sub002/model/model001/onsets/task001_run012/cond008.txt  \n",
        "   creating: ds105/sub003/\n",
        "   creating: ds105/sub003/anatomy/\n",
        " extracting: ds105/sub003/anatomy/highres001.nii.gz  \n",
        " extracting: ds105/sub003/anatomy/highres001_brain.nii.gz  \n",
        " extracting: ds105/sub003/anatomy/highres001_brain_mask.nii.gz  \n",
        "   creating: ds105/sub003/behav/\n",
        "   creating: ds105/sub003/BOLD/\n",
        "   creating: ds105/sub003/BOLD/task001_run001/\n",
        " extracting: ds105/sub003/BOLD/task001_run001/bold.nii.gz  \n",
        "   creating: ds105/sub003/BOLD/task001_run002/\n",
        " extracting: ds105/sub003/BOLD/task001_run002/bold.nii.gz  \n",
        "   creating: ds105/sub003/BOLD/task001_run003/\n",
        " extracting: ds105/sub003/BOLD/task001_run003/bold.nii.gz  \n",
        "   creating: ds105/sub003/BOLD/task001_run004/\n",
        " extracting: ds105/sub003/BOLD/task001_run004/bold.nii.gz  \n",
        "   creating: ds105/sub003/BOLD/task001_run005/\n",
        " extracting: ds105/sub003/BOLD/task001_run005/bold.nii.gz  \n",
        "   creating: ds105/sub003/BOLD/task001_run006/\n",
        " extracting: ds105/sub003/BOLD/task001_run006/bold.nii.gz  \n",
        "   creating: ds105/sub003/BOLD/task001_run007/\n",
        " extracting: ds105/sub003/BOLD/task001_run007/bold.nii.gz  \n",
        "   creating: ds105/sub003/BOLD/task001_run008/\n",
        " extracting: ds105/sub003/BOLD/task001_run008/bold.nii.gz  \n",
        "   creating: ds105/sub003/BOLD/task001_run009/\n",
        " extracting: ds105/sub003/BOLD/task001_run009/bold.nii.gz  \n",
        "   creating: ds105/sub003/BOLD/task001_run010/\n",
        " extracting: ds105/sub003/BOLD/task001_run010/bold.nii.gz  \n",
        "   creating: ds105/sub003/BOLD/task001_run011/\n",
        " extracting: ds105/sub003/BOLD/task001_run011/bold.nii.gz  \n",
        "   creating: ds105/sub003/BOLD/task001_run012/\n",
        " extracting: ds105/sub003/BOLD/task001_run012/bold.nii.gz  \n",
        "   creating: ds105/sub003/model/\n",
        "   creating: ds105/sub003/model/model001/\n",
        "   creating: ds105/sub003/model/model001/onsets/\n",
        "   creating: ds105/sub003/model/model001/onsets/task001_run001/\n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run001/cond001.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run001/cond002.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run001/cond003.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run001/cond004.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run001/cond005.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run001/cond006.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run001/cond007.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run001/cond008.txt  \n",
        "   creating: ds105/sub003/model/model001/onsets/task001_run002/\n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run002/cond001.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run002/cond002.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run002/cond003.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run002/cond004.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run002/cond005.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run002/cond006.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run002/cond007.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run002/cond008.txt  \n",
        "   creating: ds105/sub003/model/model001/onsets/task001_run003/\n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run003/cond001.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run003/cond002.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run003/cond003.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run003/cond004.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run003/cond005.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run003/cond006.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run003/cond007.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run003/cond008.txt  \n",
        "   creating: ds105/sub003/model/model001/onsets/task001_run004/\n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run004/cond001.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run004/cond002.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run004/cond003.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run004/cond004.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run004/cond005.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run004/cond006.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run004/cond007.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run004/cond008.txt  \n",
        "   creating: ds105/sub003/model/model001/onsets/task001_run005/\n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run005/cond001.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run005/cond002.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run005/cond003.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run005/cond004.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run005/cond005.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run005/cond006.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run005/cond007.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run005/cond008.txt  \n",
        "   creating: ds105/sub003/model/model001/onsets/task001_run006/\n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run006/cond001.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run006/cond002.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run006/cond003.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run006/cond004.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run006/cond005.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run006/cond006.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run006/cond007.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run006/cond008.txt  \n",
        "   creating: ds105/sub003/model/model001/onsets/task001_run007/\n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run007/cond001.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run007/cond002.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run007/cond003.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run007/cond004.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run007/cond005.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run007/cond006.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run007/cond007.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run007/cond008.txt  \n",
        "   creating: ds105/sub003/model/model001/onsets/task001_run008/\n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run008/cond001.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run008/cond002.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run008/cond003.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run008/cond004.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run008/cond005.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run008/cond006.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run008/cond007.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run008/cond008.txt  \n",
        "   creating: ds105/sub003/model/model001/onsets/task001_run009/\n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run009/cond001.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run009/cond002.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run009/cond003.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run009/cond004.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run009/cond005.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run009/cond006.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run009/cond007.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run009/cond008.txt  \n",
        "   creating: ds105/sub003/model/model001/onsets/task001_run010/\n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run010/cond001.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run010/cond002.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run010/cond003.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run010/cond004.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run010/cond005.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run010/cond006.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run010/cond007.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run010/cond008.txt  \n",
        "   creating: ds105/sub003/model/model001/onsets/task001_run011/\n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run011/cond001.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run011/cond002.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run011/cond003.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run011/cond004.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run011/cond005.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run011/cond006.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run011/cond007.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run011/cond008.txt  \n",
        "   creating: ds105/sub003/model/model001/onsets/task001_run012/\n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run012/cond001.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run012/cond002.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run012/cond003.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run012/cond004.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run012/cond005.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run012/cond006.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run012/cond007.txt  \n",
        " extracting: ds105/sub003/model/model001/onsets/task001_run012/cond008.txt  \n",
        "   creating: ds105/sub004/\n",
        "   creating: ds105/sub004/anatomy/\n",
        " extracting: ds105/sub004/anatomy/highres001.nii.gz  \n",
        " extracting: ds105/sub004/anatomy/highres001_brain.nii.gz  \n",
        " extracting: ds105/sub004/anatomy/highres001_brain_mask.nii.gz  \n",
        "   creating: ds105/sub004/behav/\n",
        "   creating: ds105/sub004/BOLD/\n",
        "   creating: ds105/sub004/BOLD/task001_run001/\n",
        " extracting: ds105/sub004/BOLD/task001_run001/bold.nii.gz  \n",
        "   creating: ds105/sub004/BOLD/task001_run002/\n",
        " extracting: ds105/sub004/BOLD/task001_run002/bold.nii.gz  \n",
        "   creating: ds105/sub004/BOLD/task001_run003/\n",
        " extracting: ds105/sub004/BOLD/task001_run003/bold.nii.gz  \n",
        "   creating: ds105/sub004/BOLD/task001_run004/\n",
        " extracting: ds105/sub004/BOLD/task001_run004/bold.nii.gz  \n",
        "   creating: ds105/sub004/BOLD/task001_run005/\n",
        " extracting: ds105/sub004/BOLD/task001_run005/bold.nii.gz  \n",
        "   creating: ds105/sub004/BOLD/task001_run006/\n",
        " extracting: ds105/sub004/BOLD/task001_run006/bold.nii.gz  \n",
        "   creating: ds105/sub004/BOLD/task001_run007/\n",
        " extracting: ds105/sub004/BOLD/task001_run007/bold.nii.gz  \n",
        "   creating: ds105/sub004/BOLD/task001_run008/\n",
        " extracting: ds105/sub004/BOLD/task001_run008/bold.nii.gz  \n",
        "   creating: ds105/sub004/BOLD/task001_run009/\n",
        " extracting: ds105/sub004/BOLD/task001_run009/bold.nii.gz  \n",
        "   creating: ds105/sub004/BOLD/task001_run010/\n",
        " extracting: ds105/sub004/BOLD/task001_run010/bold.nii.gz  \n",
        "   creating: ds105/sub004/BOLD/task001_run011/\n",
        " extracting: ds105/sub004/BOLD/task001_run011/bold.nii.gz  \n",
        "   creating: ds105/sub004/BOLD/task001_run012/\n",
        " extracting: ds105/sub004/BOLD/task001_run012/bold.nii.gz  \n",
        "   creating: ds105/sub004/model/\n",
        "   creating: ds105/sub004/model/model001/\n",
        "   creating: ds105/sub004/model/model001/onsets/\n",
        "   creating: ds105/sub004/model/model001/onsets/task001_run001/\n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run001/cond001.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run001/cond002.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run001/cond003.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run001/cond004.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run001/cond005.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run001/cond006.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run001/cond007.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run001/cond008.txt  \n",
        "   creating: ds105/sub004/model/model001/onsets/task001_run002/\n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run002/cond001.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run002/cond002.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run002/cond003.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run002/cond004.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run002/cond005.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run002/cond006.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run002/cond007.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run002/cond008.txt  \n",
        "   creating: ds105/sub004/model/model001/onsets/task001_run003/\n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run003/cond001.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run003/cond002.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run003/cond003.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run003/cond004.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run003/cond005.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run003/cond006.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run003/cond007.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run003/cond008.txt  \n",
        "   creating: ds105/sub004/model/model001/onsets/task001_run004/\n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run004/cond001.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run004/cond002.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run004/cond003.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run004/cond004.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run004/cond005.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run004/cond006.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run004/cond007.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run004/cond008.txt  \n",
        "   creating: ds105/sub004/model/model001/onsets/task001_run005/\n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run005/cond001.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run005/cond002.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run005/cond003.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run005/cond004.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run005/cond005.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run005/cond006.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run005/cond007.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run005/cond008.txt  \n",
        "   creating: ds105/sub004/model/model001/onsets/task001_run006/\n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run006/cond001.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run006/cond002.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run006/cond003.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run006/cond004.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run006/cond005.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run006/cond006.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run006/cond007.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run006/cond008.txt  \n",
        "   creating: ds105/sub004/model/model001/onsets/task001_run007/\n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run007/cond001.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run007/cond002.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run007/cond003.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run007/cond004.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run007/cond005.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run007/cond006.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run007/cond007.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run007/cond008.txt  \n",
        "   creating: ds105/sub004/model/model001/onsets/task001_run008/\n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run008/cond001.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run008/cond002.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run008/cond003.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run008/cond004.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run008/cond005.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run008/cond006.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run008/cond007.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run008/cond008.txt  \n",
        "   creating: ds105/sub004/model/model001/onsets/task001_run009/\n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run009/cond001.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run009/cond002.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run009/cond003.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run009/cond004.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run009/cond005.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run009/cond006.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run009/cond007.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run009/cond008.txt  \n",
        "   creating: ds105/sub004/model/model001/onsets/task001_run010/\n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run010/cond001.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run010/cond002.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run010/cond003.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run010/cond004.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run010/cond005.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run010/cond006.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run010/cond007.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run010/cond008.txt  \n",
        "   creating: ds105/sub004/model/model001/onsets/task001_run011/\n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run011/cond001.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run011/cond002.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run011/cond003.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run011/cond004.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run011/cond005.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run011/cond006.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run011/cond007.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run011/cond008.txt  \n",
        "   creating: ds105/sub004/model/model001/onsets/task001_run012/\n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run012/cond001.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run012/cond002.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run012/cond003.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run012/cond004.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run012/cond005.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run012/cond006.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run012/cond007.txt  \n",
        " extracting: ds105/sub004/model/model001/onsets/task001_run012/cond008.txt  \n",
        "   creating: ds105/sub005/\n",
        "   creating: ds105/sub005/anatomy/\n",
        " extracting: ds105/sub005/anatomy/highres001.nii.gz  \n",
        " extracting: ds105/sub005/anatomy/highres001_brain.nii.gz  \n",
        " extracting: ds105/sub005/anatomy/highres001_brain_mask.nii.gz  \n",
        "   creating: ds105/sub005/behav/\n",
        "   creating: ds105/sub005/BOLD/\n",
        "   creating: ds105/sub005/BOLD/task001_run001/\n",
        " extracting: ds105/sub005/BOLD/task001_run001/bold.nii.gz  \n",
        "   creating: ds105/sub005/BOLD/task001_run002/\n",
        " extracting: ds105/sub005/BOLD/task001_run002/bold.nii.gz  \n",
        "   creating: ds105/sub005/BOLD/task001_run003/\n",
        " extracting: ds105/sub005/BOLD/task001_run003/bold.nii.gz  \n",
        "   creating: ds105/sub005/BOLD/task001_run004/\n",
        " extracting: ds105/sub005/BOLD/task001_run004/bold.nii.gz  \n",
        "   creating: ds105/sub005/BOLD/task001_run005/\n",
        " extracting: ds105/sub005/BOLD/task001_run005/bold.nii.gz  \n",
        "   creating: ds105/sub005/BOLD/task001_run006/\n",
        " extracting: ds105/sub005/BOLD/task001_run006/bold.nii.gz  \n",
        "   creating: ds105/sub005/BOLD/task001_run007/\n",
        " extracting: ds105/sub005/BOLD/task001_run007/bold.nii.gz  \n",
        "   creating: ds105/sub005/BOLD/task001_run008/\n",
        " extracting: ds105/sub005/BOLD/task001_run008/bold.nii.gz  \n",
        "   creating: ds105/sub005/BOLD/task001_run009/\n",
        " extracting: ds105/sub005/BOLD/task001_run009/bold.nii.gz  \n",
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        " extracting: ds105/sub005/BOLD/task001_run010/bold.nii.gz  \n",
        "   creating: ds105/sub005/BOLD/task001_run011/\n",
        " extracting: ds105/sub005/BOLD/task001_run011/bold.nii.gz  \n",
        "   creating: ds105/sub005/model/\n",
        "   creating: ds105/sub005/model/model001/\n",
        "   creating: ds105/sub005/model/model001/onsets/\n",
        "   creating: ds105/sub005/model/model001/onsets/task001_run001/\n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run001/cond001.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run001/cond002.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run001/cond003.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run001/cond004.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run001/cond005.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run001/cond006.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run001/cond007.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run001/cond008.txt  \n",
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        " extracting: ds105/sub005/model/model001/onsets/task001_run002/cond001.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run002/cond002.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run002/cond003.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run002/cond004.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run002/cond005.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run002/cond006.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run002/cond007.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run002/cond008.txt  \n",
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        " extracting: ds105/sub005/model/model001/onsets/task001_run003/cond001.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run003/cond002.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run003/cond003.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run003/cond004.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run003/cond005.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run003/cond006.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run003/cond007.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run003/cond008.txt  \n",
        "   creating: ds105/sub005/model/model001/onsets/task001_run004/\n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run004/cond001.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run004/cond002.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run004/cond003.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run004/cond004.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run004/cond005.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run004/cond006.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run004/cond007.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run004/cond008.txt  \n",
        "   creating: ds105/sub005/model/model001/onsets/task001_run005/\n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run005/cond001.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run005/cond002.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run005/cond003.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run005/cond004.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run005/cond005.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run005/cond006.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run005/cond007.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run005/cond008.txt  \n",
        "   creating: ds105/sub005/model/model001/onsets/task001_run006/\n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run006/cond001.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run006/cond002.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run006/cond003.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run006/cond004.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run006/cond005.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run006/cond006.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run006/cond007.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run006/cond008.txt  \n",
        "   creating: ds105/sub005/model/model001/onsets/task001_run007/\n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run007/cond001.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run007/cond002.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run007/cond003.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run007/cond004.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run007/cond005.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run007/cond006.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run007/cond007.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run007/cond008.txt  \n",
        "   creating: ds105/sub005/model/model001/onsets/task001_run008/\n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run008/cond001.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run008/cond002.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run008/cond003.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run008/cond004.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run008/cond005.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run008/cond006.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run008/cond007.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run008/cond008.txt  \n",
        "   creating: ds105/sub005/model/model001/onsets/task001_run009/\n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run009/cond001.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run009/cond002.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run009/cond003.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run009/cond004.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run009/cond005.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run009/cond006.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run009/cond007.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run009/cond008.txt  \n",
        "   creating: ds105/sub005/model/model001/onsets/task001_run010/\n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run010/cond001.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run010/cond002.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run010/cond003.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run010/cond004.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run010/cond005.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run010/cond006.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run010/cond007.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run010/cond008.txt  \n",
        "   creating: ds105/sub005/model/model001/onsets/task001_run011/\n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run011/cond001.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run011/cond002.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run011/cond003.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run011/cond004.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run011/cond005.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run011/cond006.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run011/cond007.txt  \n",
        " extracting: ds105/sub005/model/model001/onsets/task001_run011/cond008.txt  \n",
        "   creating: ds105/sub006/\n",
        "   creating: ds105/sub006/anatomy/\n",
        " extracting: ds105/sub006/anatomy/highres001.nii.gz  \n",
        " extracting: ds105/sub006/anatomy/highres001_brain.nii.gz  \n",
        " extracting: ds105/sub006/anatomy/highres001_brain_mask.nii.gz  \n",
        "   creating: ds105/sub006/behav/\n",
        "   creating: ds105/sub006/BOLD/\n",
        "   creating: ds105/sub006/BOLD/task001_run001/\n",
        " extracting: ds105/sub006/BOLD/task001_run001/bold.nii.gz  \n",
        "   creating: ds105/sub006/BOLD/task001_run002/\n",
        " extracting: ds105/sub006/BOLD/task001_run002/bold.nii.gz  \n",
        "   creating: ds105/sub006/BOLD/task001_run003/\n",
        " extracting: ds105/sub006/BOLD/task001_run003/bold.nii.gz  \n",
        "   creating: ds105/sub006/BOLD/task001_run004/\n",
        " extracting: ds105/sub006/BOLD/task001_run004/bold.nii.gz  \n",
        "   creating: ds105/sub006/BOLD/task001_run005/\n",
        " extracting: ds105/sub006/BOLD/task001_run005/bold.nii.gz  \n",
        "   creating: ds105/sub006/BOLD/task001_run006/\n",
        " extracting: ds105/sub006/BOLD/task001_run006/bold.nii.gz  \n",
        "   creating: ds105/sub006/BOLD/task001_run007/\n",
        " extracting: ds105/sub006/BOLD/task001_run007/bold.nii.gz  \n",
        "   creating: ds105/sub006/BOLD/task001_run008/\n",
        " extracting: ds105/sub006/BOLD/task001_run008/bold.nii.gz  \n",
        "   creating: ds105/sub006/BOLD/task001_run009/\n",
        " extracting: ds105/sub006/BOLD/task001_run009/bold.nii.gz  \n",
        "   creating: ds105/sub006/BOLD/task001_run010/\n",
        " extracting: ds105/sub006/BOLD/task001_run010/bold.nii.gz  \n",
        "   creating: ds105/sub006/BOLD/task001_run011/\n",
        " extracting: ds105/sub006/BOLD/task001_run011/bold.nii.gz  \n",
        "   creating: ds105/sub006/BOLD/task001_run012/\n",
        " extracting: ds105/sub006/BOLD/task001_run012/bold.nii.gz  \n",
        "   creating: ds105/sub006/model/\n",
        "   creating: ds105/sub006/model/model001/\n",
        "   creating: ds105/sub006/model/model001/onsets/\n",
        "   creating: ds105/sub006/model/model001/onsets/task001_run001/\n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run001/cond001.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run001/cond002.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run001/cond003.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run001/cond004.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run001/cond005.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run001/cond006.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run001/cond007.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run001/cond008.txt  \n",
        "   creating: ds105/sub006/model/model001/onsets/task001_run002/\n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run002/cond001.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run002/cond002.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run002/cond003.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run002/cond004.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run002/cond005.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run002/cond006.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run002/cond007.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run002/cond008.txt  \n",
        "   creating: ds105/sub006/model/model001/onsets/task001_run003/\n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run003/cond001.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run003/cond002.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run003/cond003.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run003/cond004.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run003/cond005.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run003/cond006.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run003/cond007.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run003/cond008.txt  \n",
        "   creating: ds105/sub006/model/model001/onsets/task001_run004/\n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run004/cond001.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run004/cond002.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run004/cond003.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run004/cond004.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run004/cond005.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run004/cond006.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run004/cond007.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run004/cond008.txt  \n",
        "   creating: ds105/sub006/model/model001/onsets/task001_run005/\n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run005/cond001.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run005/cond002.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run005/cond003.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run005/cond004.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run005/cond005.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run005/cond006.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run005/cond007.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run005/cond008.txt  \n",
        "   creating: ds105/sub006/model/model001/onsets/task001_run006/\n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run006/cond001.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run006/cond002.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run006/cond003.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run006/cond004.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run006/cond005.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run006/cond006.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run006/cond007.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run006/cond008.txt  \n",
        "   creating: ds105/sub006/model/model001/onsets/task001_run007/\n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run007/cond001.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run007/cond002.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run007/cond003.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run007/cond004.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run007/cond005.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run007/cond006.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run007/cond007.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run007/cond008.txt  \n",
        "   creating: ds105/sub006/model/model001/onsets/task001_run008/\n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run008/cond001.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run008/cond002.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run008/cond003.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run008/cond004.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run008/cond005.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run008/cond006.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run008/cond007.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run008/cond008.txt  \n",
        "   creating: ds105/sub006/model/model001/onsets/task001_run009/\n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run009/cond001.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run009/cond002.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run009/cond003.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run009/cond004.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run009/cond005.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run009/cond006.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run009/cond007.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run009/cond008.txt  \n",
        "   creating: ds105/sub006/model/model001/onsets/task001_run010/\n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run010/cond001.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run010/cond002.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run010/cond003.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run010/cond004.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run010/cond005.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run010/cond006.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run010/cond007.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run010/cond008.txt  \n",
        "   creating: ds105/sub006/model/model001/onsets/task001_run011/\n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run011/cond001.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run011/cond002.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run011/cond003.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run011/cond004.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run011/cond005.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run011/cond006.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run011/cond007.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run011/cond008.txt  \n",
        "   creating: ds105/sub006/model/model001/onsets/task001_run012/\n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run012/cond001.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run012/cond002.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run012/cond003.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run012/cond004.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run012/cond005.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run012/cond006.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run012/cond007.txt  \n",
        " extracting: ds105/sub006/model/model001/onsets/task001_run012/cond008.txt  \n",
        " extracting: ds105/task_key.txt      \n",
        "README\n",
        "license.txt\n",
        "models\n",
        "references.txt\n",
        "release_history.txt\n",
        "scan_key.txt\n",
        "study_key.txt\n",
        "sub001\n",
        "sub002\n",
        "sub003\n",
        "sub004\n",
        "sub005\n",
        "sub006\n",
        "task_key.txt\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stderr",
       "text": [
        "mkdir: data: File exists\n"
       ]
      }
     ],
     "prompt_number": 1
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "Getting started - library code"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Our library code we want to keep in a separate place from the code specific to our project; maybe someone wants it?  Maybe we want to use it ourselves in another analysis not tied to this one."
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Here I'm going to use a very basic code organization, just a single directory for the code and the tests.  More on this later, but for now:"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%bash\n",
      "cd\n",
      "mkdir code\n",
      "cd code\n",
      "mkdir datacheck"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 7
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!cp ~/practical_fmri/pna-notebooks/checkhash.py ~/code/datacheck\n",
      "!cp ~/practical_fmri/pna-notebooks/test_checkhash.py ~/code/datacheck"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 8
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "We need to tell Python where to find these scripts:"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%bash\n",
      "# On OSX, Linux\n",
      "export PYTHONPATH=~/code/datacheck:$PYTHONPATH"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 9
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Here's what the same thing looks like in Windows Powershell.  This sets PYTHONPATH for all future sessions:\n",
      "\n",
      "<pre>\n",
      "$my_py_path = [Environment]::GetEnvironmentVariable(\"PYTHONPATH\",\"User\")\n",
      "$my_py_path += \";\" + $env:USERPROFILE + \"\\code\\datacheck\"\n",
      "[Environment]::SetEnvironmentVariable(\"PYTHONPATH\", $my_py_path, \"User\")\n",
      "</pre>\n",
      "\n",
      "You'll need to quit Powershell and restart to set the setting in your shell."
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Check the tests work"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!nosetests ~/code/datacheck"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "nose.config: INFO: Ignoring files matching ['^\\\\.', '^_', '^setup\\\\.py$']\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "test_checkhash.test_check_store_hash ... ok\r\n",
        "\r\n",
        "----------------------------------------------------------------------\r\n",
        "Ran 1 test in 0.781s\r\n",
        "\r\n",
        "OK\r\n"
       ]
      }
     ],
     "prompt_number": 10
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "We want these under version control!"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%bash\n",
      "cd ~/code/datacheck\n",
      "git init\n",
      "git add *.py\n",
      "git commit -m \"Initial import of library code\""
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Initialized empty Git repository in /Users/mb312/code/datacheck/.git/\n",
        "[master (root-commit) b0dcf9f] Initial import of library code\n",
        " 2 files changed, 97 insertions(+)\n",
        " create mode 100644 checkhash.py\n",
        " create mode 100644 test_checkhash.py\n"
       ]
      }
     ],
     "prompt_number": 11
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "Getting started - scripts, notebooks"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%bash\n",
      "cd\n",
      "mkdir projects\n",
      "cd projects\n",
      "mkdir haxby2001\n",
      "cd haxby2001\n",
      "mkdir scripts\n",
      "mkdir notebooks"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 12
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!ls ~/projects/haxby2001"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\u001b[34mnotebooks\u001b[m\u001b[m \u001b[34mscripts\u001b[m\u001b[m\r\n"
       ]
      }
     ],
     "prompt_number": 13
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Copy some analysis-specific files into the scripts directory"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%bash\n",
      "cp ~/practical_fmri/pna-notebooks/openfmri.py ~/projects/haxby2001/scripts\n",
      "cp ~/practical_fmri/pna-notebooks/test_openfmri.py ~/projects/haxby2001/scripts\n",
      "cp ~/practical_fmri/pna-notebooks/check_openfmri.py ~/projects/haxby2001/scripts"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 14
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "We want these under version control!"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%bash\n",
      "cd ~/projects/haxby2001\n",
      "git init\n",
      "git add .\n",
      "git commit -m \"Initial import of scripts\""
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Initialized empty Git repository in /Users/mb312/projects/haxby2001/.git/\n",
        "[master (root-commit) 7764dbe] Initial import of scripts\n",
        " 3 files changed, 147 insertions(+)\n",
        " create mode 100755 scripts/check_openfmri.py\n",
        " create mode 100644 scripts/openfmri.py\n",
        " create mode 100644 scripts/test_openfmri.py\n"
       ]
      }
     ],
     "prompt_number": 15
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "No - never use ``git commit -m`` - it's bad.  I did it because this I wanted this to run as a script, rather than a command line; thats really the only use for this."
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "%%bash\n",
      "cd ~/projects/haxby2001\n",
      "git log"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "commit 7764dbe22acc138b39d2a5345d8cd1ec8901126e\n",
        "Author: Matthew Brett <matthew.brett@gmail.com>\n",
        "Date:   Fri May 3 09:50:19 2013 -0700\n",
        "\n",
        "    Initial import of scripts\n"
       ]
      }
     ],
     "prompt_number": 16
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Check the tests are working:"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!nosetests ~/projects/haxby2001/scripts"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "nose.config: INFO: Ignoring files matching ['^\\\\.', '^_', '^setup\\\\.py$']\r\n",
        "nose.selector: INFO: /Users/mb312/projects/haxby2001/scripts/check_openfmri.py is executable; skipped\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "test_openfmri.test_big_picture ... "
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "ok\r\n"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\r\n",
        "----------------------------------------------------------------------\r\n",
        "Ran 1 test in 1.951s\r\n",
        "\r\n",
        "OK\r\n"
       ]
      }
     ],
     "prompt_number": 17
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": [
      "Running a script over the data"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "!python ~/projects/haxby2001/scripts/check_openfmri.py /home/mb312/data/ds105"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Traceback (most recent call last):\r\n",
        "  File \"/Users/mb312/projects/haxby2001/scripts/check_openfmri.py\", line 3, in <module>\r\n",
        "    from checkhash import check_store_hash\r\n",
        "ImportError: No module named checkhash\r\n"
       ]
      }
     ],
     "prompt_number": 18
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "What did I do wrong here?"
     ]
    }
   ],
   "metadata": {}
  }
 ]
}