1-3 notebooks for reposring part 1

analysis/AEPs/preprocessing.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 20,
    "id": "86c86cb2",
    "metadata": {},
    "outputs": [],
@@ -24,7 +24,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 21,
    "id": "33fca2bf",
    "metadata": {},
    "outputs": [
@@ -60,7 +60,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 22,
    "id": "55c1c0a6",
    "metadata": {},
    "outputs": [],
@@ -479,7 +479,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 23,
    "id": "5d823efb",
    "metadata": {},
    "outputs": [],
@@ -509,22 +509,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 24,
    "id": "58094149",
    "metadata": {},
    "outputs": [],
    "source": [
     "selected_sessions = [\n",
     "'009266_hippoSIT_2023-04-17_17-04-17',  # ch17, 20 + 55 correction, 5067 events\n",
-    "#'009266_hippoSIT_2023-04-18_10-10-37',  # ch17, 10 + 55 correction, 5682 events\n",
-    "#'009266_hippoSIT_2023-04-18_17-03-10',  # ch17, 6 + 55 correction, 5494 events\n",
-    "#'009266_hippoSIT_2023-04-19_10-33-51',  # ch17, 4 + 55 correction, 6424 events\n",
-    "#'009266_hippoSIT_2023-04-20_08-57-39',  # ch1, 1 + 55 correction, 6424 events\n",
-    "#'009266_hippoSIT_2023-04-24_16-56-55',  # ch17, 5 + 55* correction, 6165 events, frequency\n",
-    "#'009266_hippoSIT_2023-04-26_08-20-17',  # ch17, 12 + 55* correction, 6095 events, duration\n",
-    "#'009266_hippoSIT_2023-05-02_12-22-14',  # ch20, 10 + 55 correction, 5976 events, frequency\n",
-    "#'009266_hippoSIT_2023-05-04_09-11-06',  # ch17, 5 + 55* correction, 4487 events, coma session with baseline AEPs\n",
-    "#'009266_hippoSIT_2023-05-04_19-47-15',  # ch20, 2 + 55 correction, 5678 events, frequency\n",
+    "'009266_hippoSIT_2023-04-18_10-10-37',  # ch17, 10 + 55 correction, 5682 events\n",
+    "'009266_hippoSIT_2023-04-18_17-03-10',  # ch17, 6 + 55 correction, 5494 events\n",
+    "'009266_hippoSIT_2023-04-19_10-33-51',  # ch17, 4 + 55 correction, 6424 events\n",
+    "'009266_hippoSIT_2023-04-20_08-57-39',  # ch1, 1 + 55 correction, 6424 events\n",
+    "'009266_hippoSIT_2023-04-24_16-56-55',  # ch17, 5 + 55* correction, 6165 events, frequency\n",
+    "'009266_hippoSIT_2023-04-26_08-20-17',  # ch17, 12 + 55* correction, 6095 events, duration\n",
+    "'009266_hippoSIT_2023-05-02_12-22-14',  # ch20, 10 + 55 correction, 5976 events, frequency\n",
+    "'009266_hippoSIT_2023-05-04_09-11-06',  # ch17, 5 + 55* correction, 4487 events, coma session with baseline AEPs\n",
+    "'009266_hippoSIT_2023-05-04_19-47-15',  # ch20, 2 + 55 correction, 5678 events, frequency\n",
     "\n",
     "# old PPC data\n",
     "#'008229_hippoSIT_2022-05-17_21-44-43', #0 # chs: 0, 31, 54, 56\n",
@@ -555,7 +555,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 25,
    "id": "f2edd36e",
    "metadata": {},
    "outputs": [
@@ -563,7 +563,16 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Session 009266_hippoSIT_2023-04-17_17-04-17 done\n"
+      "Session 009266_hippoSIT_2023-04-17_17-04-17 done\n",
+      "Session 009266_hippoSIT_2023-04-18_10-10-37 done\n",
+      "Session 009266_hippoSIT_2023-04-18_17-03-10 done\n",
+      "Session 009266_hippoSIT_2023-04-19_10-33-51 done\n",
+      "Session 009266_hippoSIT_2023-04-20_08-57-39 done\n",
+      "Session 009266_hippoSIT_2023-04-24_16-56-55 done\n",
+      "Session 009266_hippoSIT_2023-04-26_08-20-17 done\n",
+      "Session 009266_hippoSIT_2023-05-02_12-22-14 done\n",
+      "Session 009266_hippoSIT_2023-05-04_09-11-06 done\n",
+      "Session 009266_hippoSIT_2023-05-04_19-47-15 done\n"
      ]
     }
    ],

reporting/State-dependent neural dynamics in the gerbil Auditory Cortex/01 - Dynamics of Auditory Evoked Responses.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 97,
+   "execution_count": 123,
    "id": "7dbf62e3",
    "metadata": {},
    "outputs": [],
@@ -29,7 +29,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 124,
    "id": "220a45cd",
    "metadata": {},
    "outputs": [
@@ -112,7 +112,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 72,
+   "execution_count": 125,
    "id": "2ccab1dd",
    "metadata": {},
    "outputs": [],
@@ -146,7 +146,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 73,
+   "execution_count": 126,
    "id": "a54d07da",
    "metadata": {},
    "outputs": [],
@@ -167,7 +167,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 74,
+   "execution_count": 127,
    "id": "3400d646",
    "metadata": {},
    "outputs": [
@@ -177,7 +177,7 @@
        "((5067, 200), (73, 5))"
       ]
      },
-     "execution_count": 74,
+     "execution_count": 127,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -278,7 +278,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 54,
+   "execution_count": 128,
    "id": "ddbdc8ae",
    "metadata": {
     "scrolled": true

reporting/State-dependent neural dynamics in the gerbil Auditory Cortex/03 - Evoked responses are driven by neuronal population activity.ipynb

@@ -1,116 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "id": "415b1905",
-   "metadata": {},
-   "source": [
-    "## State separation based on AEP metrics "
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "id": "f5666b26",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# just show low / high AEP metric state (red / gray?)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "df99ba10",
-   "metadata": {},
-   "source": [
-    "## On-responses are modulated by P1 state"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 4,
-   "id": "3fd32391",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# show example neurons and population statistics\n",
-    "# maybe compute strength of the ON response for each neuron and correlate with P1"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "1c0d058f",
-   "metadata": {},
-   "source": [
-    "## Off responses are ? modulated by N1 state"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 5,
-   "id": "c8c86dd4",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# maybe? check"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "2210ad95",
-   "metadata": {},
-   "source": [
-    "## Early responses are modulated by P2 state"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 6,
-   "id": "8cbda6e1",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# same"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "401a9289",
-   "metadata": {},
-   "source": [
-    "## Late responses are modulated by P3 state"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 7,
-   "id": "3d112a37",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# same"
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.10"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}

reporting/State-dependent neural dynamics in the gerbil Auditory Cortex/04 - Dynamics of the mismatch response depending on the AEP states.ipynb

@@ -1,88 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "id": "57a6fc24",
-   "metadata": {},
-   "source": [
-    "## Mismatch response (MMR) as a measure of stimulus change"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 2,
-   "id": "08a235ca",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# introduce MMR"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "675fcd2e",
-   "metadata": {},
-   "source": [
-    "## MMR response depending on P1, N1, P2 and P3 states"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "id": "033b6507",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# show examples for individual session\n",
-    "# compute across sessions?"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "af381ac6",
-   "metadata": {},
-   "source": [
-    "## Behavioral relevance of the MMR for performance in SIT"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 4,
-   "id": "4de99e39",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# compute..."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "d287fdfa",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.10"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}