Added jupytext metadata to all code/notebooks

Added jupytext metadata to all code/notebooks so they are paired to the _episode md files

code/01_preprocessing.ipynb

@@ -73,8 +73,11 @@
   }
  ],
  "metadata": {
+  "jupytext": {
+   "formats": "code///ipynb,_episodes///md"
+  },
   "kernelspec": {
-   "display_name": "Python [default]",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -88,7 +91,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.2"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,

code/02-exploring_fmriprep.ipynb

@@ -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",
     "***"
    ]
   },
@@ -360,6 +361,9 @@
   }
  ],
  "metadata": {
+  "jupytext": {
+   "formats": "code///ipynb,_episodes///md"
+  },
   "kernelspec": {
    "display_name": "Python 3",
    "language": "python",
@@ -375,7 +379,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.0"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,

code/02-exploring_fmriprep_solutions.ipynb

@@ -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",
@@ -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
 }

code/03-basic_image_manipulation.ipynb

@@ -333,6 +333,9 @@
   }
  ],
  "metadata": {
+  "jupytext": {
+   "formats": "code///ipynb,_episodes///md"
+  },
   "kernelspec": {
    "display_name": "Python 3",
    "language": "python",
@@ -348,7 +351,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.0"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,

code/03-basic_image_manipulation_solutions.ipynb

@@ -329,6 +329,12 @@
   }
  ],
  "metadata": {
+  "interpreter": {
+   "hash": "2fe2689612c0ab7397cf4462f922098fb75a2e15e2b422cd69da130ba4292710"
+  },
+  "jupytext": {
+   "formats": "code///ipynb,_episodes///md"
+  },
   "kernelspec": {
    "display_name": "Python 3",
    "language": "python",
@@ -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
 }

code/04-integrating_functional_data.ipynb

@@ -535,6 +535,9 @@
   }
  ],
  "metadata": {
+  "jupytext": {
+   "formats": "code///ipynb,_episodes///md"
+  },
   "kernelspec": {
    "display_name": "Python 3",
    "language": "python",
@@ -550,7 +553,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.0"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,

code/04-integrating_functional_data_solutions.ipynb

@@ -548,6 +548,9 @@
   }
  ],
  "metadata": {
+  "jupytext": {
+   "formats": "code///ipynb,_episodes///md"
+  },
   "kernelspec": {
    "display_name": "Python 3",
    "language": "python",
@@ -563,7 +566,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.0"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,

code/05_applying-a-parcellation.ipynb

@@ -230,6 +230,9 @@
  ],
  "metadata": {
   "anaconda-cloud": {},
+  "jupytext": {
+   "formats": "code///ipynb,_episodes///md"
+  },
   "kernelspec": {
    "display_name": "Python 3",
    "language": "python",
@@ -245,7 +248,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.0"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,

code/05_applying-a-parcellation_solutions.ipynb

@@ -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"
@@ -273,6 +273,9 @@
  ],
  "metadata": {
   "anaconda-cloud": {},
+  "jupytext": {
+   "formats": "code///ipynb,_episodes///md"
+  },
   "kernelspec": {
    "display_name": "Python 3",
    "language": "python",
@@ -288,7 +291,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.0"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,

code/06_data-cleaning-with-nilearn.ipynb

@@ -677,6 +677,9 @@
   }
  ],
  "metadata": {
+  "jupytext": {
+   "formats": "code///ipynb,_episodes///md"
+  },
   "kernelspec": {
    "display_name": "Python 3",
    "language": "python",
@@ -692,7 +695,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.0"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,

code/06_data-cleaning-with-nilearn_solutions.ipynb

@@ -712,6 +712,9 @@
   }
  ],
  "metadata": {
+  "jupytext": {
+   "formats": "code///ipynb,_episodes///md"
+  },
   "kernelspec": {
    "display_name": "Python 3",
    "language": "python",
@@ -727,7 +730,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.0"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,

code/07_functional-connectivity-analysis.ipynb

@@ -1068,6 +1068,9 @@
   }
  ],
  "metadata": {
+  "jupytext": {
+   "formats": "code///ipynb,_episodes///md"
+  },
   "kernelspec": {
    "display_name": "Python 3",
    "language": "python",
@@ -1083,7 +1086,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.0"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,

code/07_functional-connectivity-analysis_solutions.ipynb

@@ -78,7 +78,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -91,7 +91,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -102,9 +102,23 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
+   "execution_count": 8,
+   "metadata": {},
+   "outputs": [
+    {
+     "ename": "ValueError",
+     "evalue": "BIDS root does not exist: /Users/swalkow2/Documents/GitHub/SDC-BIDS-fMRI/data/ds000030/derivatives/fmriprep",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mValueError\u001b[0m                                Traceback (most recent call last)",
+      "\u001b[0;32m/var/folders/02/bsg_wyl53q1bq10qyh56b_q40000gp/T/ipykernel_2951/865981971.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0;31m#Use PyBIDS to parse BIDS data structure\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0mlayout\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mBIDSLayout\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfmriprep_dir\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalidate\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
+      "\u001b[0;32m~/Documents/GitHub/SDC-BIDS-fMRI/CDS-BIDS-fMRI/lib/python3.9/site-packages/bids/layout/layout.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, root, validate, absolute_paths, derivatives, config, sources, ignore, force_index, config_filename, regex_search, database_path, database_file, reset_database, index_metadata)\u001b[0m\n\u001b[1;32m    254\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    255\u001b[0m         \u001b[0;31m# Do basic BIDS validation on root directory\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 256\u001b[0;31m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_validate_root\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    257\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    258\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mignore\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/Documents/GitHub/SDC-BIDS-fMRI/CDS-BIDS-fMRI/lib/python3.9/site-packages/bids/layout/layout.py\u001b[0m in \u001b[0;36m_validate_root\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    484\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    485\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mexists\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mroot\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 486\u001b[0;31m             \u001b[0;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"BIDS root does not exist: %s\"\u001b[0m \u001b[0;34m%\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mroot\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    487\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    488\u001b[0m         \u001b[0mtarget\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mjoin\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mroot\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'dataset_description.json'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;31mValueError\u001b[0m: BIDS root does not exist: /Users/swalkow2/Documents/GitHub/SDC-BIDS-fMRI/data/ds000030/derivatives/fmriprep"
+     ]
+    }
+   ],
    "source": [
     "#Use PyBIDS to parse BIDS data structure\n",
     "layout = BIDSLayout(fmriprep_dir, validate=False)"
@@ -1017,6 +1031,12 @@
   }
  ],
  "metadata": {
+  "interpreter": {
+   "hash": "2fe2689612c0ab7397cf4462f922098fb75a2e15e2b422cd69da130ba4292710"
+  },
+  "jupytext": {
+   "formats": "code///ipynb,_episodes///md"
+  },
   "kernelspec": {
    "display_name": "Python 3",
    "language": "python",
@@ -1032,7 +1052,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.0"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,