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enh: updated tutorial
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‎examples/nipype_tutorial.ipynb

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"# What is Nipype?\n",
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"\n",
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"<center>\n",
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"<img src=\"https://raw.github.com/satra/intro2nipype/master/images/nipype.png\" width=\"50%\" />\n",
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"<img src=\"https://raw.github.com/satra/intro2nipype/master/images/nipype.png\" width=\"40%\" />\n",
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"<br>\n",
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"created by: Arno Klein (www.mindboggle.info)\n",
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"Figure designed and created by: Arno Klein (www.mindboggle.info)\n",
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"</center>\n"
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]
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},
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"- part of an ecosystem"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {
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"slideshow": {
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"slide_type": "subslide"
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}
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},
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"source": [
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"# Python ecosystem\n",
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"<table width=\"1024px\">\n",
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"<tr>\n",
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"<td colspan=\"2\"><a href=\"http://ipython.org/\"><img src=\"http://ipython.org/_static/IPy_header.png\"></a></td>\n",
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"<td colspan=\"2\"><a href=\"http://nipy.org/\"><img src=\"http://nipy.org/_static/nipy-community-banner-gy.png\"></a></td>\n",
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"</tr>\n",
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"<tr>\n",
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"<td><a href=\"http://scipy.org/\"><img src=\"http://www.scipy.org/_static/images/tutorial.png\"></a></td>\n",
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"<td><a href=\"http://numpy.org/\"><img src=\"http://www.numpy.org/_static/numpy_logo.png\"></a></td>\n",
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"<td><a href=\"http://pymvpa.org/\"><img src=\"http://www.pymvpa.org/_static/pymvpa_logo.jpg\" width=\"256\"></a></td>\n",
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"<td><a href=\"http://scikit-learn.org/\"><img src=\"http://scikit-learn.org/stable/_static/scikit-learn-logo-small.png\"></a></td>\n",
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"</tr>\n",
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"<tr>\n",
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"<td><a href=\"http://networkx.github.io/\"><img src=\"https://raw.github.com/networkx/networkx/master/doc/source/static/art1.png\" width=\"256\"></a></td>\n",
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"<td><a href=\"http://matplotlib.org/\"><img src=\"http://matplotlib.org/_static/logo2.png\" width=\"256\"></a></td>\n",
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"<td><a href=\"http://code.enthought.com/projects/mayavi/\"><img src=\"http://code.enthought.com/img/mayavi-samp.png\" width=\"256\"></a></td>\n",
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"<td><a href=\"http://neuro.debian.net/\"><img src=\"http://neuro.debian.net/_static/button_w200.png\"></a></td>\n",
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"</tr>\n",
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"</table>\n"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {
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"source": [
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"#Software interfaces\n",
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"\n",
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"Currently supported (5-2-2013). `Click here for latest <http://www.mit.edu/~satra/nipype-nightly/documentation.html>`_\n",
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"\n",
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"- [AFNI](http://afni.nimh.nih.gov/afni)\n",
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"- [ANTS](http://www.picsl.upenn.edu/ANTS)\n",
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"- [BRAINS](http://www.psychiatry.uiowa.edu/mhcrc/IPLpages/BRAINS.htm)\n",
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"- [Camino](http://www.cs.ucl.ac.uk/research/medic/camino)\n",
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"- [Camino-TrackVis](http://www.nitrc.org/projects/camino-trackvis)\n",
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"- [ConnectomeViewerToolkit](http://www.connectomeviewer.org)\n",
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"- [dcm2nii](http://www.cabiatl.com/mricro/mricron/dcm2nii.html)\n",
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"- [Diffusion Toolkit](http://www.trackvis.org/dtk)\n",
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"- [FreeSurfer](http://freesurfer.net)\n",
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"- [FSL](http://www.fmrib.ox.ac.uk/fsl)\n",
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"- [MRtrx](http://www.brain.org.au/software/mrtrix/index.html)\n",
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"- [Nipy](http://nipy.org/nipy)\n",
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"- [Nitime](http://nipy.org/nitime)\n",
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"- [PyXNAT](http://github.com/pyxnat)\n",
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"- [Slicer](http://www.slicer.org)\n",
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"- [SPM](http://www.fil.ion.ucl.ac.uk/spm)\n",
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"Currently supported (5-2-2013). [Click here for latest](http://www.mit.edu/~satra/nipype-nightly/documentation.html)\n",
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"\n",
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"<style>\n",
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".rendered_html table{border:0px}\n",
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".rendered_html tr{border:0px}\n",
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".rendered_html td{border:0px}\n",
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"</style>\n",
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"\n",
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"<table>\n",
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"<tr>\n",
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"<td>\n",
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"<ul>\n",
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"<li><a href=\"http://afni.nimh.nih.gov/afni\">AFNI</a></li>\n",
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"<li><a href=\"http://www.picsl.upenn.edu/ANTS\">ANTS</a></li>\n",
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"<li><a href=\"http://www.psychiatry.uiowa.edu/mhcrc/IPLpages/BRAINS.htm\">BRAINS</a></li>\n",
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"<li><a href=\"http://www.cs.ucl.ac.uk/research/medic/camino\">Camino</a></li>\n",
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"<li><a href=\"http://www.nitrc.org/projects/camino-trackvis\">Camino-TrackVis</a></li>\n",
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"<li><a href=\"http://www.connectomeviewer.org\">ConnectomeViewerToolkit</a></li>\n",
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"<li><a href=\"http://www.cabiatl.com/mricro/mricron/dcm2nii.html\">dcm2nii</a></li>\n",
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"<li><a href=\"http://www.trackvis.org/dtk\">Diffusion Toolkit</a></li>\n",
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"</ul>\n",
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"</td>\n",
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"<td>\n",
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"<ul>\n",
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"<li><a href=\"http://freesurfer.net\">FreeSurfer</a></li>\n",
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"<li><a href=\"http://www.fmrib.ox.ac.uk/fsl\">FSL</a></li>\n",
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"<li><a href=\"http://www.brain.org.au/software/mrtrix/index.html\">MRtrx</a></li>\n",
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"<li><a href=\"http://nipy.org/nipy\">Nipy</a></li>\n",
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"<li><a href=\"http://nipy.org/nitime\">Nitime</a></li>\n",
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"<li><a href=\"http://github.com/pyxnat\">PyXNAT</a></li>\n",
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"<li><a href=\"http://www.slicer.org\">Slicer</a></li>\n",
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"<li><a href=\"http://www.fil.ion.ucl.ac.uk/spm\">SPM</a></li>\n",
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"</ul>\n",
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"</td>\n",
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"</tr>\n",
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"</table>\n",
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"\n",
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"Most used/contributed policy!\n",
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"\n",
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"metadata": {
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"slideshow": {
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"slide_type": "subslide"
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}
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},
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"source": [
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"### Finding interface inputs and outputs and examples"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"metadata": {
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"slideshow": {
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"slide_type": "subslide"
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}
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},
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"source": [
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"### Creating a directory for running interfaces"
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]
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"metadata": {},
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"outputs": []
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},
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{
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"cell_type": "markdown",
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"metadata": {
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"slideshow": {
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"slide_type": "subslide"
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}
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},
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"source": [
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"## Other ways"
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]
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},
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{
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"cell_type": "code",
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"collapsed": false,
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"\n",
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" 'base_directory/container/parameterization/destloc/filename'\n",
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" \n",
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" destloc = string[[.[@]]string[[.[@]]string]] and\n",
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" destloc = [@]string[[.[@]]string[[.[@]]string]...] and\n",
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" destloc = realigned.@parameters --> 'realigned'\n",
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" destloc = realigned.parameters.@1 --> 'realigned/parameters'\n",
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" destloc = realigned.parameters.@2 --> 'realigned/parameters'\n",
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" filename comes from the input to the connect statement."
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]
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},
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"language": "python",
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"metadata": {
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"slideshow": {
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"slide_type": "subslide"
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"slide_type": "-"
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}
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},
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"outputs": []
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}
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},
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"source": [
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"# Or to other job managers\n",
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"### Or to other job managers\n",
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"\n",
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"```\n",
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" >>> connectedworkflow.run('PBS', plugin_args={'qsub_args': '-q many'})\n",
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" >>> connectedworkflow.run('SGE', plugin_args={'qsub_args': '-q many'})\n",
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" >>> connectedworkflow.run('LSF', plugin_args={'qsub_args': '-q many'})\n",
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" >>> connectedworkflow.run('Condor')\n",
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" >>> connectedworkflow.run('IPython')\n",
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"```\n",
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"- connectedworkflow.run('PBS', plugin_args={'qsub_args': '-q many'})\n",
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"- connectedworkflow.run('SGE', plugin_args={'qsub_args': '-q many'})\n",
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"- connectedworkflow.run('LSF', plugin_args={'qsub_args': '-q many'})\n",
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"- connectedworkflow.run('Condor')\n",
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"- connectedworkflow.run('IPython')\n",
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"\n",
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"### or submit graphs as a whole\n",
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"\n",
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"```\n",
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" >>> connectedworkflow.run('PBSGraph', plugin_args={'qsub_args': '-q many'})\n",
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" >>> connectedworkflow.run('SGEGraph', plugin_args={'qsub_args': '-q many'})\n",
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" >>> connectedworkflow.run('CondorDAGMan')\n",
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"```\n",
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"\n",
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"### Current Requirement: **shared filesystem**\n"
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"- connectedworkflow.run('PBSGraph', plugin_args={'qsub_args': '-q many'})\n",
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"- connectedworkflow.run('SGEGraph', plugin_args={'qsub_args': '-q many'})\n",
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"- connectedworkflow.run('CondorDAGMan')\n",
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"\n",
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"### Current Requirement: **SHARED FILESYSTEM**"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"metadata": {
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"slideshow": {
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"slide_type": "subslide"
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}
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},
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"source": [
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"### You can also set node specific plugin arguments"
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]
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"```\n",
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" >>> node.plugin_args = {'qsub_args': '-l nodes=1:ppn=3', 'overwrite': True}\n",
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"```"
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"\n",
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"- node.plugin_args = {'qsub_args': '-l nodes=1:ppn=3', 'overwrite': True}\n"
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]
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},
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{
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"cell_type": "code",
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"collapsed": false,
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"input": [
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"from os.path import abspath as opap\n",
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"\n",
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"from nipype.interfaces.io import XNATSource\n",
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"from nipype.pipeline.engine import Node, Workflow\n",
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"from nipype.interfaces.fsl import BET\n",
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"\n",
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"subject_id = 'xnat_S00001'\n",
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"\n",
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"dg = Node(XNATSource(infields=['subject_id'],\n",
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" outfields=['struct'],\n",
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" config='/Users/satra/xnat_configs/nitrc_ir_config'),\n",
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" name='xnatsource')\n",
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"dg.inputs.query_template = ('/projects/fcon_1000/subjects/%s/experiments/xnat_E00001'\n",
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" '/scans/%s/resources/NIfTI/files')\n",
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"dg.inputs.query_template_args['struct'] = [['subject_id', 'anat_mprage_anonymized']]\n",
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"dg.inputs.subject_id = 'xnat_S00001'\n",
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"dg.inputs.subject_id = subject_id\n",
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"\n",
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"bet = Node(BET(), name='skull_stripper')\n",
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"\n",
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"wf = Workflow(name='testxnat')\n",
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"wf.base_dir = opap('xnattest')\n",
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"wf.connect(dg, 'struct', bet, 'in_file')\n",
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"wf.run()"
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"wf.connect(dg, 'struct', bet, 'in_file')"
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],
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"language": "python",
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"metadata": {},
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"outputs": []
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},
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{
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"cell_type": "code",
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"collapsed": false,
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"input": [
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"from nipype.interfaces.io import XNATSink\n",
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"\n",
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"ds = Node(XNATSink(config='/Users/satra/xnat_configs/central_config'),\n",
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" name='xnatsink')\n",
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"ds.inputs.project_id = 'NPTEST'\n",
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"ds.inputs.subject_id = 'NPTEST_xnat_S00001'\n",
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"ds.inputs.experiment_id = 'test_xnat'\n",
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"ds.inputs.reconstruction_id = 'bet'\n",
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"ds.inputs.share = True\n",
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"wf.connect(bet, 'out_file', ds, 'brain')"
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],
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"language": "python",
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"metadata": {
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"slideshow": {
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"slide_type": "skip"
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}
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},
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"outputs": []
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},
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{
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"cell_type": "code",
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"collapsed": false,
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"input": [
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"wf.run()"
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],
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"language": "python",
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"metadata": {
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"slideshow": {
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"slide_type": "subslide"
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}
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},
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"outputs": []
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},
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"cell_type": "markdown",
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"metadata": {
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"metadata": {
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"slideshow": {
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"slide_type": "subslide"
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}
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},
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"source": [
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"Configurations can also be set at the node level."
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"wf.run()"
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],
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"language": "python",
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"metadata": {},
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"metadata": {
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"slideshow": {
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"slide_type": "subslide"
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}
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},
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"outputs": []
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{
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"metadata": {},
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"outputs": []
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},
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{
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"cell_type": "markdown",
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"metadata": {
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"slideshow": {
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"slide_type": "slide"
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}
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},
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"source": [
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"# Summary\n",
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"\n",
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"\n",
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"- This tutorial covers the concepts of Nipype\n",
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"\n",
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" 1. Installing and testing the installation \n",
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" 2. Working with interfaces\n",
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" 3. Using Nipype caching\n",
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" 4. Creating Nodes, MapNodes and Workflows\n",
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" 5. Getting and saving data\n",
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" 6. Using Iterables\n",
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" 7. Function nodes\n",
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" 8. Distributed computation\n",
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" 9. Connecting to databases\n",
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" 10. Execution configuration options\n",
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"\n",
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"- It will allow you to reuse and debug the various workflows available in Nipype, BIPS and CPAC\n",
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"- Please contribute new interfaces and workflows!"
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]
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},
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{
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"cell_type": "code",
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"collapsed": false,
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"metadata": {}
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}
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]
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}
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}

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