diff --git a/examples/glm_example_2.ipynb b/examples/glm_example_2.ipynb index 49238d7..fc5b3b5 100644 --- a/examples/glm_example_2.ipynb +++ b/examples/glm_example_2.ipynb @@ -2,16 +2,16 @@ "cells": [ { "cell_type": "code", - "execution_count": 6, + "execution_count": 1, "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "" + "" ] }, - "execution_count": 6, + "execution_count": 1, "metadata": {}, "output_type": "execute_result" } @@ -32,15 +32,22 @@ "xr.set_options(display_expand_data=False)" ] }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Define Parameters" + ] + }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 2, "metadata": {}, "outputs": [], "source": [ "# relative time in seconds for HRF extraction\n", - "HRFmin = -2\n", - "HRFmax = 15 \n", + "HRF_tmin = -2\n", + "HRF_tmax = 15 \n", "\n", "# remove first 20 seconds of data (motion artefacts)\n", "omsec = 20\n", @@ -51,16 +58,23 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 3, "metadata": {}, "outputs": [], "source": [ "DATADIR = \"/home/thomas/Dokumente/SHK/Data/RESTING_DATA\"" ] }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Load Data" + ] + }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 4, "metadata": {}, "outputs": [], "source": [ @@ -123,18 +137,28 @@ " data[sbj] = data[sbj].sel(time = amp.time >= omsec)\n" ] }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Select Example Subject" + ] + }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 5, "metadata": {}, "outputs": [], "source": [ - "sbj = 91" + "sbj = 91\n", + "conc = data[sbj].data_vars[\"conc\"]\n", + "stim = data[sbj].attrs[\"stim\"]\n", + "geo3d = data[sbj].data_vars[\"geo\"]" ] }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 6, "metadata": {}, "outputs": [ { @@ -526,29 +550,29 @@ " conc (time, chromo, channel) float64 [µM] -3.532 -0.5335 ... -3.638\n", " stim (time, condition) float64 0.0 0.0 0.0 0.0 ... 0.0 0.0 0.0 0.0\n", "Attributes:\n", - " stim: onset duration value trial_type\\n1 36.92 10.0 ...