MNT update notebooks

Author: mvdoc

tutorials/notebooks/movies_3T/00_download_vim5.ipynb

@@ -15,7 +15,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "\n# Download the data set from CRCNS\n\n\nIn this script, we download the data set from CRCNS. A (free) account is\nrequired.\n\n.. Warning:: The data has not been publicly released yet on CRCNS, so this\n    notebook will not work ! You can download the data manually from `Google\n    Drive\n    <https://drive.google.com/drive/folders/1NuxO5_GHgDvjrL2FX5ohzAsvWpZuepIA?usp=sharing>`_,\n    or run the tutorials from `Colab\n    <https://colab.research.google.com/github/gallantlab/voxelwise_tutorials/blob/main/tutorials/notebooks/movies_3T/merged_for_colab.ipynb>`_\n\nCite this data set\n------------------\n\nThis tutorial is based on publicly available data `published on CRCNS\n<https://crcns.org/data-sets/vc/TBD>`_. If you publish any work using this data\nset, please cite the original publication [1]_, and the data set [2]_.\n"
+        "\n# Download the data set from CRCNS\n\nIn this script, we download the data set from CRCNS. A (free) account is\nrequired.\n\n.. Warning:: The data has not been publicly released yet on CRCNS, so this\n    notebook will not work ! You can download the data manually from `Google\n    Drive\n    <https://drive.google.com/drive/folders/1NuxO5_GHgDvjrL2FX5ohzAsvWpZuepIA?usp=sharing>`_,\n    or run the tutorials from `Colab\n    <https://colab.research.google.com/github/gallantlab/voxelwise_tutorials/blob/main/tutorials/notebooks/movies_3T/merged_for_colab.ipynb>`_\n\n## Cite this data set\n\nThis tutorial is based on publicly available data `published on CRCNS\n<https://crcns.org/data-sets/vc/TBD>`_. If you publish any work using this data\nset, please cite the original publication [1]_, and the data set [2]_.\n"
       ]
     },
     {
@@ -33,7 +33,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Download\n--------\n\n"
+        "## Download\n\n"
       ]
     },
     {
@@ -80,7 +80,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "References\n----------\n\n.. [1] Huth, A. G., Nishimoto, S., Vu, A. T., & Gallant, J. L. (2012). A\n    continuous semantic space describes the representation of thousands of\n    object and action categories across the human brain. Neuron, 76(6),\n    1210-1224.\n\n.. [2] Huth, A. G., Nishimoto, S., Vu, A. T., & Gallant, J. L. (2020):\n    Gallant Lab Natural Movie 3T fMRI Data. CRCNS.org.\n    http://dx.doi.org/10.6080/TBD\n\n"
+        "## References\n\n.. [1] Huth, A. G., Nishimoto, S., Vu, A. T., & Gallant, J. L. (2012). A\n    continuous semantic space describes the representation of thousands of\n    object and action categories across the human brain. Neuron, 76(6),\n    1210-1224.\n\n.. [2] Huth, A. G., Nishimoto, S., Vu, A. T., & Gallant, J. L. (2020):\n    Gallant Lab Natural Movie 3T fMRI Data. CRCNS.org.\n    http://dx.doi.org/10.6080/TBD\n\n"
       ]
     }
   ],
@@ -100,7 +100,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.3"
+      "version": "3.8.3"
     }
   },
   "nbformat": 4,

tutorials/notebooks/movies_3T/00_load_colab.ipynb

@@ -15,7 +15,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "\n# Setup Google Colab\n\n\nIn this script, we setup a Google Colab environment. This script will only work\nwhen run from `Google Colab <https://colab.research.google.com/>`_). You can\nskip it if you run the tutorials on your machine.\n"
+        "\n# Setup Google Colab\n\nIn this script, we setup a Google Colab environment. This script will only work\nwhen run from `Google Colab <https://colab.research.google.com/>`_). You can\nskip it if you run the tutorials on your machine.\n"
       ]
     },
     {
@@ -33,14 +33,14 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Change runtime to use a GPU\n---------------------------\n\nThis tutorial is much faster when a GPU is available to run the computations:\n\n(Menu) \"Runtime\" -> \"Change runtime type\" -> \"Hardware accelerator\" -> \"GPU\".\n\n"
+        "## Change runtime to use a GPU\n\nThis tutorial is much faster when a GPU is available to run the computations.\nIn Google Colab you can request access to a GPU by changing the runtime type. \nTo do so, click the following menu options in Google Colab: \n\n(Menu) \"Runtime\" -> \"Change runtime type\" -> \"Hardware accelerator\" -> \"GPU\".\n\n"
       ]
     },
     {
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Mount data with Google Drive\n----------------------------\n\nFirst, open the following Google Drive link:\nhttps://drive.google.com/drive/folders/1NuxO5_GHgDvjrL2FX5ohzAsvWpZuepIA\n\nThen, clic on the directory name (\"vim-5\"), and add a shortcut to your Drive\n(\"Add shortcut to Drive\").\n\nThen, mount Google Drive in Google Colab. To do so, run the following cell,\nand follow the instructions from Google to copy/paste the authorization code.\n\n"
+        "## Mount data with Google Drive\n\nFirst, open the following Google Drive link:\nhttps://drive.google.com/drive/folders/1NuxO5_GHgDvjrL2FX5ohzAsvWpZuepIA\n\nThen, click on the directory name (\"vim-5\"), and add a shortcut to your Drive\n(\"Add shortcut to Drive\"). Place the shortcut in the main directory of your\nGoogle Drive. Do not place it in another folder, or you will have to change \nthe code to update the location of the dataset.\n\nFinally, mount Google Drive in Google Colab. To do so, run the following cell,\nand follow the instructions from Google to copy/paste the authorization code.\n\n"
       ]
     },
     {
@@ -76,7 +76,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Then, tell the voxelwise_tutorials package where the data is.\n\n"
+        "Tell the voxelwise_tutorials package where the data is. (If you placed the\nshortcut in a different location than the main directory of your Google\nDrive, change this code to point to the correct location.)\n\n"
       ]
     },
     {
@@ -94,7 +94,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Install package helper\n----------------------\n\nFinally, install the tutorial helper package, by uncommenting and running\nthe install command.\n\n"
+        "## Install package helper\n\nFinally, install the tutorial helper package, by uncommenting and running\nthe install command.\n\n"
       ]
     },
     {
@@ -112,7 +112,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "When using Colab, the install of pycortex might fail to locate the default\npycortex filestore. You can fix it by uncommenting and running the following:\n\n"
+        "When using Colab, the install of pycortex might fail to locate the default\npycortex filestore. Uncomment and run the following line to fix it:\n\n"
       ]
     },
     {
@@ -130,7 +130,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "and changing the filestore path.\n\n"
+        "Now change the pycortex filestore path.\n\n"
       ]
     },
     {
@@ -143,6 +143,13 @@
       "source": [
         "import cortex\nfilestore = \"/content/pycortex/filestore/\"\ncortex.options.config['basic']['filestore'] = filestore\ncortex.options.config['webgl']['colormaps'] = \"/content/pycortex/filestore/colormaps\"\ncortex.database.db = cortex.database.Database(filestore)\ncortex.db = cortex.database.db\ncortex.utils.db = cortex.database.db\ncortex.dataset.braindata.db = cortex.database.db"
       ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "Your Google Colab environment is now set up for the voxelwise tutorials.\n\n"
+      ]
     }
   ],
   "metadata": {
@@ -161,7 +168,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.7.3"
+      "version": "3.8.3"
     }
   },
   "nbformat": 4,