{ "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", "> -- David L. Donoho. An invitation to reproducible computational research. Biostatistics Volume 11, Issue 3 Pp. 385-388\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", " creating: ds105/models/model001/\n", " 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", " extracting: ds105/sub001/BOLD/task001_run002/bold.nii.gz \n", " creating: ds105/sub001/BOLD/task001_run003/\n", " extracting: ds105/sub001/BOLD/task001_run003/bold.nii.gz \n", " creating: ds105/sub001/BOLD/task001_run004/\n", " extracting: ds105/sub001/BOLD/task001_run004/bold.nii.gz \n", " creating: ds105/sub001/BOLD/task001_run005/\n", " extracting: ds105/sub001/BOLD/task001_run005/bold.nii.gz \n", " creating: ds105/sub001/BOLD/task001_run006/\n", " extracting: ds105/sub001/BOLD/task001_run006/bold.nii.gz \n", " creating: ds105/sub001/BOLD/task001_run007/\n", " extracting: ds105/sub001/BOLD/task001_run007/bold.nii.gz \n", " creating: ds105/sub001/BOLD/task001_run008/\n", " extracting: ds105/sub001/BOLD/task001_run008/bold.nii.gz \n", " creating: ds105/sub001/BOLD/task001_run009/\n", " extracting: ds105/sub001/BOLD/task001_run009/bold.nii.gz \n", " creating: ds105/sub001/BOLD/task001_run010/\n", " extracting: ds105/sub001/BOLD/task001_run010/bold.nii.gz \n", " creating: ds105/sub001/BOLD/task001_run011/\n", " extracting: ds105/sub001/BOLD/task001_run011/bold.nii.gz \n", " creating: ds105/sub001/BOLD/task001_run012/\n", " extracting: ds105/sub001/BOLD/task001_run012/bold.nii.gz \n", " creating: ds105/sub001/model/\n", " creating: ds105/sub001/model/model001/\n", " creating: ds105/sub001/model/model001/onsets/\n", " creating: ds105/sub001/model/model001/onsets/task001_run001/\n", " extracting: 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ds105/sub001/model/model001/onsets/task001_run002/cond004.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run002/cond005.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run002/cond006.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run002/cond007.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run002/cond008.txt \n", " creating: ds105/sub001/model/model001/onsets/task001_run003/\n", " extracting: ds105/sub001/model/model001/onsets/task001_run003/cond001.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run003/cond002.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run003/cond003.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run003/cond004.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run003/cond005.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run003/cond006.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run003/cond007.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run003/cond008.txt \n", " creating: ds105/sub001/model/model001/onsets/task001_run004/\n", " extracting: ds105/sub001/model/model001/onsets/task001_run004/cond001.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run004/cond002.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run004/cond003.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run004/cond004.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run004/cond005.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run004/cond006.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run004/cond007.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run004/cond008.txt \n", " creating: ds105/sub001/model/model001/onsets/task001_run005/\n", " extracting: 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ds105/sub001/model/model001/onsets/task001_run006/cond004.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run006/cond005.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run006/cond006.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run006/cond007.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run006/cond008.txt \n", " creating: ds105/sub001/model/model001/onsets/task001_run007/\n", " extracting: ds105/sub001/model/model001/onsets/task001_run007/cond001.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run007/cond002.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run007/cond003.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run007/cond004.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run007/cond005.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run007/cond006.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run007/cond007.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run007/cond008.txt \n", " creating: ds105/sub001/model/model001/onsets/task001_run008/\n", " extracting: ds105/sub001/model/model001/onsets/task001_run008/cond001.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run008/cond002.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run008/cond003.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run008/cond004.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run008/cond005.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run008/cond006.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run008/cond007.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run008/cond008.txt \n", " creating: ds105/sub001/model/model001/onsets/task001_run009/\n", " extracting: ds105/sub001/model/model001/onsets/task001_run009/cond001.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run009/cond002.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run009/cond003.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run009/cond004.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run009/cond005.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run009/cond006.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run009/cond007.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run009/cond008.txt \n", " creating: ds105/sub001/model/model001/onsets/task001_run010/\n", " extracting: ds105/sub001/model/model001/onsets/task001_run010/cond001.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run010/cond002.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run010/cond003.txt \n", " extracting: 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ds105/sub001/model/model001/onsets/task001_run011/cond007.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run011/cond008.txt \n", " creating: ds105/sub001/model/model001/onsets/task001_run012/\n", " extracting: ds105/sub001/model/model001/onsets/task001_run012/cond001.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run012/cond002.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run012/cond003.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run012/cond004.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run012/cond005.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run012/cond006.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run012/cond007.txt \n", " extracting: ds105/sub001/model/model001/onsets/task001_run012/cond008.txt \n", " creating: ds105/sub002/\n", " creating: ds105/sub002/anatomy/\n", " extracting: ds105/sub002/anatomy/highres001.nii.gz \n", " extracting: ds105/sub002/anatomy/highres001_brain.nii.gz \n", " extracting: ds105/sub002/anatomy/highres001_brain_mask.nii.gz \n", " creating: ds105/sub002/behav/\n", " creating: ds105/sub002/BOLD/\n", " creating: ds105/sub002/BOLD/task001_run001/\n", " extracting: ds105/sub002/BOLD/task001_run001/bold.nii.gz \n", " creating: ds105/sub002/BOLD/task001_run002/\n", " extracting: ds105/sub002/BOLD/task001_run002/bold.nii.gz \n", " creating: ds105/sub002/BOLD/task001_run003/\n", " extracting: ds105/sub002/BOLD/task001_run003/bold.nii.gz \n", " creating: ds105/sub002/BOLD/task001_run004/\n", " extracting: ds105/sub002/BOLD/task001_run004/bold.nii.gz \n", " creating: ds105/sub002/BOLD/task001_run005/\n", " extracting: ds105/sub002/BOLD/task001_run005/bold.nii.gz \n", " creating: ds105/sub002/BOLD/task001_run006/\n", " extracting: ds105/sub002/BOLD/task001_run006/bold.nii.gz \n", " creating: ds105/sub002/BOLD/task001_run007/\n", " extracting: ds105/sub002/BOLD/task001_run007/bold.nii.gz \n", " creating: ds105/sub002/BOLD/task001_run008/\n", " extracting: ds105/sub002/BOLD/task001_run008/bold.nii.gz \n", " creating: ds105/sub002/BOLD/task001_run009/\n", " extracting: ds105/sub002/BOLD/task001_run009/bold.nii.gz \n", " creating: ds105/sub002/BOLD/task001_run010/\n", " extracting: ds105/sub002/BOLD/task001_run010/bold.nii.gz \n", " creating: ds105/sub002/BOLD/task001_run011/\n", " extracting: ds105/sub002/BOLD/task001_run011/bold.nii.gz \n", " creating: ds105/sub002/BOLD/task001_run012/\n", " extracting: ds105/sub002/BOLD/task001_run012/bold.nii.gz \n", " creating: ds105/sub002/model/\n", " creating: ds105/sub002/model/model001/\n", " creating: ds105/sub002/model/model001/onsets/\n", " creating: ds105/sub002/model/model001/onsets/task001_run001/\n", " extracting: ds105/sub002/model/model001/onsets/task001_run001/cond001.txt \n", " extracting: ds105/sub002/model/model001/onsets/task001_run001/cond002.txt \n", " extracting: 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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", " creating: ds105/sub005/BOLD/task001_run010/\n", " 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", " creating: ds105/sub005/model/model001/onsets/task001_run002/\n", " 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", " creating: ds105/sub005/model/model001/onsets/task001_run003/\n", " 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:$PYTHONPATH" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 9 }, { "cell_type": "markdown", "metadata": {}, "source": [ "Here's what the same thing looks like in Windows Powershell. This sets PYTHONPATH for all future sessions:\n", "\n", "
\n",
      "$my_py_path = [Environment]::GetEnvironmentVariable(\"PYTHONPATH\",\"User\")\n",
      "$my_py_path += \";\" + $env:USERPROFILE + \"\\code\\datacheck\"\n",
      "[Environment]::SetEnvironmentVariable(\"PYTHONPATH\", $my_py_path, \"User\")\n",
      "
\n", "\n", "You'll need to quit Powershell and restart to set the setting in your shell." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Check the tests work" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!nosetests ~/code/datacheck" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "nose.config: INFO: Ignoring files matching ['^\\\\.', '^_', '^setup\\\\.py$']\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 \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 \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": {} } ] }