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Adding Jupytext Support to Notebooks #36

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Adding Jupytext Support to Notebooks #36

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a0cb6f4
Added jupytext metadata to all code/notebooks
samwalkow Oct 5, 2021
a4b3af0
Removed an error message
samwalkow Oct 5, 2021
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7 changes: 5 additions & 2 deletions code/01_preprocessing.ipynb
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Expand Up @@ -73,8 +73,11 @@
}
],
"metadata": {
"jupytext": {
"formats": "code///ipynb,_episodes///md"
},
"kernelspec": {
"display_name": "Python [default]",
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
Expand All @@ -88,7 +91,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.2"
"version": "3.7.3"
}
},
"nbformat": 4,
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6 changes: 5 additions & 1 deletion code/02-exploring_fmriprep.ipynb
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Expand Up @@ -9,6 +9,7 @@
"BIDS applications such as fMRIPREP output data into a full data structure with strong similarity to BIDS organization principals. In fact, there is a specification for derivatives (outputs derived from) BIDS datasets; although this is a current work in progress, details can be found in: [BIDS Derivatives](https://bids-specification.readthedocs.io/en/latest/06-extensions.html). \n",
"\n",
"In this tutorial, we'll explore the outputs generated by fMRIPREP and get a handle of how the data is organized from this preprocessing pipeline\n",
"\n",
"***"
]
},
Expand Down Expand Up @@ -360,6 +361,9 @@
}
],
"metadata": {
"jupytext": {
"formats": "code///ipynb,_episodes///md"
},
"kernelspec": {
"display_name": "Python 3",
"language": "python",
Expand All @@ -375,7 +379,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.0"
"version": "3.7.3"
}
},
"nbformat": 4,
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11 changes: 6 additions & 5 deletions code/02-exploring_fmriprep_solutions.ipynb
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Expand Up @@ -297,15 +297,16 @@
},
{
"cell_type": "markdown",
"metadata": {
"collapsed": true
},
"metadata": {},
"source": [
"Now that we have a handle on how fMRIPREP preprocessed data is organized and how we can pull this data. Let's start working with the actual data itself!"
]
}
],
"metadata": {
"jupytext": {
"formats": "code///ipynb,_episodes///md"
},
"kernelspec": {
"display_name": "Python 3",
"language": "python",
Expand All @@ -321,9 +322,9 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.0"
"version": "3.7.3"
}
},
"nbformat": 4,
"nbformat_minor": 2
"nbformat_minor": 4
}
5 changes: 4 additions & 1 deletion code/03-basic_image_manipulation.ipynb
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Expand Up @@ -333,6 +333,9 @@
}
],
"metadata": {
"jupytext": {
"formats": "code///ipynb,_episodes///md"
},
"kernelspec": {
"display_name": "Python 3",
"language": "python",
Expand All @@ -348,7 +351,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.0"
"version": "3.7.3"
}
},
"nbformat": 4,
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10 changes: 8 additions & 2 deletions code/03-basic_image_manipulation_solutions.ipynb
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Expand Up @@ -329,6 +329,12 @@
}
],
"metadata": {
"interpreter": {
"hash": "2fe2689612c0ab7397cf4462f922098fb75a2e15e2b422cd69da130ba4292710"
},
"jupytext": {
"formats": "code///ipynb,_episodes///md"
},
"kernelspec": {
"display_name": "Python 3",
"language": "python",
Expand All @@ -344,9 +350,9 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.0"
"version": "3.7.3"
}
},
"nbformat": 4,
"nbformat_minor": 2
"nbformat_minor": 4
}
5 changes: 4 additions & 1 deletion code/04-integrating_functional_data.ipynb
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Expand Up @@ -535,6 +535,9 @@
}
],
"metadata": {
"jupytext": {
"formats": "code///ipynb,_episodes///md"
},
"kernelspec": {
"display_name": "Python 3",
"language": "python",
Expand All @@ -550,7 +553,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.0"
"version": "3.7.3"
}
},
"nbformat": 4,
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5 changes: 4 additions & 1 deletion code/04-integrating_functional_data_solutions.ipynb
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Expand Up @@ -548,6 +548,9 @@
}
],
"metadata": {
"jupytext": {
"formats": "code///ipynb,_episodes///md"
},
"kernelspec": {
"display_name": "Python 3",
"language": "python",
Expand All @@ -563,7 +566,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.0"
"version": "3.7.3"
}
},
"nbformat": 4,
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5 changes: 4 additions & 1 deletion code/05_applying-a-parcellation.ipynb
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Expand Up @@ -230,6 +230,9 @@
],
"metadata": {
"anaconda-cloud": {},
"jupytext": {
"formats": "code///ipynb,_episodes///md"
},
"kernelspec": {
"display_name": "Python 3",
"language": "python",
Expand All @@ -245,7 +248,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.0"
"version": "3.7.3"
}
},
"nbformat": 4,
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9 changes: 6 additions & 3 deletions code/05_applying-a-parcellation_solutions.ipynb
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Expand Up @@ -31,8 +31,8 @@
"outputs": [],
"source": [
"from nilearn import datasets\n",
"from nilearn import image as nimg\n",
"from nilearn import plotting as nplot\n",
"from nilearn import image as nimg\n",
"from nilearn import plotting as nplot\n",
"\n",
"#for inline visualization in jupyter notebook\n",
"%matplotlib inline"
Expand Down Expand Up @@ -273,6 +273,9 @@
],
"metadata": {
"anaconda-cloud": {},
"jupytext": {
"formats": "code///ipynb,_episodes///md"
},
"kernelspec": {
"display_name": "Python 3",
"language": "python",
Expand All @@ -288,7 +291,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.0"
"version": "3.7.3"
}
},
"nbformat": 4,
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5 changes: 4 additions & 1 deletion code/06_data-cleaning-with-nilearn.ipynb
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Expand Up @@ -677,6 +677,9 @@
}
],
"metadata": {
"jupytext": {
"formats": "code///ipynb,_episodes///md"
},
"kernelspec": {
"display_name": "Python 3",
"language": "python",
Expand All @@ -692,7 +695,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.0"
"version": "3.7.3"
}
},
"nbformat": 4,
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5 changes: 4 additions & 1 deletion code/06_data-cleaning-with-nilearn_solutions.ipynb
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Expand Up @@ -712,6 +712,9 @@
}
],
"metadata": {
"jupytext": {
"formats": "code///ipynb,_episodes///md"
},
"kernelspec": {
"display_name": "Python 3",
"language": "python",
Expand All @@ -727,7 +730,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.0"
"version": "3.7.3"
}
},
"nbformat": 4,
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5 changes: 4 additions & 1 deletion code/07_functional-connectivity-analysis.ipynb
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Expand Up @@ -1068,6 +1068,9 @@
}
],
"metadata": {
"jupytext": {
"formats": "code///ipynb,_episodes///md"
},
"kernelspec": {
"display_name": "Python 3",
"language": "python",
Expand All @@ -1083,7 +1086,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.0"
"version": "3.7.3"
}
},
"nbformat": 4,
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8 changes: 7 additions & 1 deletion code/07_functional-connectivity-analysis_solutions.ipynb
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Expand Up @@ -1017,6 +1017,12 @@
}
],
"metadata": {
"interpreter": {
"hash": "2fe2689612c0ab7397cf4462f922098fb75a2e15e2b422cd69da130ba4292710"
},
"jupytext": {
"formats": "code///ipynb,_episodes///md"
},
"kernelspec": {
"display_name": "Python 3",
"language": "python",
Expand All @@ -1032,7 +1038,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.0"
"version": "3.7.3"
}
},
"nbformat": 4,
Expand Down