diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
index 25937f8..a42c03a 100644
--- a/.github/workflows/deploy.yml
+++ b/.github/workflows/deploy.yml
@@ -48,7 +48,7 @@ jobs:
- name: Build HTML Assets
run: myst build --execute --html
- name: Upload artifact
- uses: actions/upload-pages-artifact@v1
+ uses: actions/upload-pages-artifact@v4
with:
path: './_build/html'
- name: Deploy to GitHub Pages
diff --git a/3 T2 Mapping/1 Monoexponential T2 Mapping/02-Signal modelling.md b/3 T2 Mapping/1 Monoexponential T2 Mapping/02-Signal modelling.md
index 8f922a2..6621ae7 100644
--- a/3 T2 Mapping/1 Monoexponential T2 Mapping/02-Signal modelling.md
+++ b/3 T2 Mapping/1 Monoexponential T2 Mapping/02-Signal modelling.md
@@ -24,10 +24,12 @@ where Mz(0-) is the longitudinal magnetization immediately preceding the 90 degr
Figure 3 shows transverse relaxation curves for T2 and T2* values for white matter and gray matter, using the relaxation times from Siemonsen et al. (2008).
+
:::{figure} #fig3p2cell
:label: t2Plot2
-Figure 3. Transverse relaxation decay curves for T2 and T2* values in white matter and gray matter. The T2 and T2* constants were taken from Siemonsen et al. (2008).
+Transverse relaxation decay curves for T2 and T2* values in white matter and gray matter. The T2 and T2* constants were taken from Siemonsen et al. (2008).
:::
+
In NMR physics, it has been shown that T2 relaxation times must be equal to or shorter than 2T1 (Levitt, 2008); however, it has been demonstrated that T2 can exceed T1 in very rare cases (Traficante, 1991). In living organisms however, T2 is always shorter than T1.
diff --git a/figures/3 T2 mapping/fig3p2.ipynb b/figures/3 T2 mapping/fig3p2.ipynb
new file mode 100644
index 0000000..0bf14eb
--- /dev/null
+++ b/figures/3 T2 mapping/fig3p2.ipynb
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+ "#636efa",
+ "#EF553B",
+ "#00cc96",
+ "#ab63fa",
+ "#FFA15A",
+ "#19d3f3",
+ "#FF6692",
+ "#B6E880",
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+ "font": {
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+ "geo": {
+ "bgcolor": "white",
+ "lakecolor": "white",
+ "landcolor": "#E5ECF6",
+ "showlakes": true,
+ "showland": true,
+ "subunitcolor": "white"
+ },
+ "hoverlabel": {
+ "align": "left"
+ },
+ "hovermode": "closest",
+ "mapbox": {
+ "style": "light"
+ },
+ "paper_bgcolor": "white",
+ "plot_bgcolor": "#E5ECF6",
+ "polar": {
+ "angularaxis": {
+ "gridcolor": "white",
+ "linecolor": "white",
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+ "bgcolor": "#E5ECF6",
+ "radialaxis": {
+ "gridcolor": "white",
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+ "scene": {
+ "xaxis": {
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+ "shapedefaults": {
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+ }
+ },
+ "ternary": {
+ "aaxis": {
+ "gridcolor": "white",
+ "linecolor": "white",
+ "ticks": ""
+ },
+ "baxis": {
+ "gridcolor": "white",
+ "linecolor": "white",
+ "ticks": ""
+ },
+ "bgcolor": "#E5ECF6",
+ "caxis": {
+ "gridcolor": "white",
+ "linecolor": "white",
+ "ticks": ""
+ }
+ },
+ "title": {
+ "x": 0.05
+ },
+ "xaxis": {
+ "automargin": true,
+ "gridcolor": "white",
+ "linecolor": "white",
+ "ticks": "",
+ "title": {
+ "standoff": 15
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+ "title": {
+ "standoff": 15
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+ "zerolinewidth": 2
+ }
+ }
+ },
+ "updatemenus": [
+ {
+ "buttons": [
+ {
+ "args": [
+ {
+ "visible": [
+ true,
+ true,
+ false,
+ false
+ ]
+ }
+ ],
+ "label": "T2",
+ "method": "update"
+ },
+ {
+ "args": [
+ {
+ "visible": [
+ false,
+ false,
+ true,
+ true
+ ]
+ }
+ ],
+ "label": "T2*",
+ "method": "update"
+ },
+ {
+ "args": [
+ {
+ "visible": [
+ true,
+ true,
+ true,
+ true
+ ]
+ }
+ ],
+ "label": "T2 and T2*",
+ "method": "update"
+ }
+ ],
+ "direction": "down",
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+ "color": "#000",
+ "family": "Times New Roman",
+ "size": 12
+ },
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+ "r": 10,
+ "t": 10
+ },
+ "showactive": true,
+ "x": 0.3,
+ "xanchor": "left",
+ "y": 1,
+ "yanchor": "top"
+ }
+ ],
+ "width": 600,
+ "xaxis": {
+ "linecolor": "black",
+ "linewidth": 2,
+ "showgrid": false
+ },
+ "yaxis": {
+ "linecolor": "black",
+ "linewidth": 2,
+ "range": [
+ 0,
+ 1
+ ],
+ "showgrid": false
+ }
+ }
+ }
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "#| label: fig3p2cell\n",
+ "\n",
+ "# Prepare Python environment\n",
+ "\n",
+ "import scipy.io as sio\n",
+ "from pathlib import Path\n",
+ "\n",
+ "data_dir = Path(\"../../data/03-T2\")\n",
+ "data_file = \"t2_and_t2star_curvs.mat\"\n",
+ "\n",
+ "#Load either archived or generated plot variables\n",
+ "mat_contents = sio.loadmat(data_dir / data_file)\n",
+ "\n",
+ "# Get the signals and parameters from Matlab\n",
+ "\n",
+ "# T2\n",
+ "T2_signal_WM = mat_contents['signal_WM_T2'][0]\n",
+ "T2_signal_GM = mat_contents['signal_GM_T2'][0]\n",
+ "\n",
+ "# T2*\n",
+ "T2star_signal_WM = mat_contents['signal_WM_T2star'][0]\n",
+ "T2star_signal_GM = mat_contents['signal_GM_T2star'][0]\n",
+ "\n",
+ "# TE \n",
+ "params = mat_contents['params']\n",
+ "TE = mat_contents['params']['TE'][0][0][0]\n",
+ "\n",
+ "## Plot\n",
+ "\n",
+ "import matplotlib.pyplot as plt\n",
+ "import chart_studio.plotly as py\n",
+ "import plotly.graph_objs as go\n",
+ "import numpy as np\n",
+ "from plotly.offline import iplot\n",
+ "\n",
+ "config={'showLink': False, 'displayModeBar': False}\n",
+ "\n",
+ "# T2 signals\n",
+ "\n",
+ "wm_T2 = go.Scatter(\n",
+ " x = TE,\n",
+ " y = T2_signal_WM,\n",
+ " name = 'T2 = 109.77 ms (White Matter)',\n",
+ " text = 'T2 = 109.77 ms (White Matter)',\n",
+ " hoverinfo = 'x+y+text',\n",
+ " line=dict(color='#1f77b4', dash='solid'),\n",
+ " visible = True\n",
+ ")\n",
+ "\n",
+ "gm_T2 = go.Scatter(\n",
+ " x = TE,\n",
+ " y = T2_signal_GM,\n",
+ " name = 'T2 = 96.07 ms (Gray Matter)',\n",
+ " text = 'T2 = 96.07 ms (Gray Matter)',\n",
+ " hoverinfo = 'x+y+text',\n",
+ " line=dict(color='#ff7f0e', dash='solid'),\n",
+ " visible = True\n",
+ ")\n",
+ "\n",
+ "# T2* signals\n",
+ "\n",
+ "wm_T2star = go.Scatter(\n",
+ " x = TE,\n",
+ " y = T2star_signal_WM,\n",
+ " name = 'T2* = 67.63 ms (White Matter)',\n",
+ " text = 'T2* = 67.63 ms (White Matter)',\n",
+ " hoverinfo = 'x+y+text',\n",
+ " line=dict(color='#1f77b4', dash='dot'),\n",
+ " visible = False\n",
+ ")\n",
+ "\n",
+ "gm_T2star = go.Scatter(\n",
+ " x = TE,\n",
+ " y = T2star_signal_GM,\n",
+ " name = 'T2* = 48.48 ms (Gray Matter)',\n",
+ " text = 'T2* = 48.48 ms (Gray Matter)',\n",
+ " hoverinfo = 'x+y+text',\n",
+ " line=dict(color='#ff7f0e', dash='dot'),\n",
+ " visible = False\n",
+ ")\n",
+ "\n",
+ "data = [wm_T2, gm_T2, wm_T2star, gm_T2star]\n",
+ "\n",
+ "layout = go.Layout(\n",
+ " width=600,\n",
+ " height=375,\n",
+ " margin=go.layout.Margin(\n",
+ " l=100,\n",
+ " r=50,\n",
+ " b=60,\n",
+ " t=20,\n",
+ " ),\n",
+ " annotations=[\n",
+ " dict(\n",
+ " x=0.5004254919715793,\n",
+ " y=-0.175,\n",
+ " showarrow=False,\n",
+ " text='Echo Time – TE (ms)',\n",
+ " font=dict(\n",
+ " family='Times New Roman',\n",
+ " size=22\n",
+ " ),\n",
+ " xref='paper',\n",
+ " yref='paper'\n",
+ " ),\n",
+ " dict(\n",
+ " x=-0.15,\n",
+ " y=0.50,\n",
+ " showarrow=False,\n",
+ " text='Transverse Magnetization (Mxy)',\n",
+ " font=dict(\n",
+ " family='Times New Roman',\n",
+ " size=22\n",
+ " ),\n",
+ " textangle=-90,\n",
+ " xref='paper',\n",
+ " yref='paper'\n",
+ " ),\n",
+ " ],\n",
+ " xaxis=dict(\n",
+ " showgrid=False,\n",
+ " linecolor='black',\n",
+ " linewidth=2\n",
+ " ),\n",
+ " yaxis=dict(\n",
+ " showgrid=False,\n",
+ " linecolor='black',\n",
+ " linewidth=2,\n",
+ " range=[0, 1]\n",
+ " ),\n",
+ " legend=dict(\n",
+ " x=0.53,\n",
+ " y=0.97,\n",
+ " traceorder='normal',\n",
+ " font=dict(\n",
+ " family='Times New Roman',\n",
+ " size=12,\n",
+ " color='#000'\n",
+ " ),\n",
+ " bordercolor='#000000',\n",
+ " borderwidth=2\n",
+ " ),\n",
+ " updatemenus=[\n",
+ " dict(\n",
+ " buttons=list([\n",
+ " # Display T2\n",
+ " dict(\n",
+ " args=[{'visible': [True, True, False, False]}],\n",
+ " label='T2',\n",
+ " method='update'\n",
+ " ),\n",
+ " # Display T2*\n",
+ " dict(\n",
+ " args=[{'visible': [False, False, True, True]}],\n",
+ " label='T2*',\n",
+ " method='update'\n",
+ " ),\n",
+ " # Display both T2 and T2*\n",
+ " dict(\n",
+ " args=[{'visible': [True, True, True, True]}],\n",
+ " label='T2 and T2*',\n",
+ " method='update'\n",
+ " ),\n",
+ " ]),\n",
+ " direction='down',\n",
+ " pad={'r': 10, 't': 10},\n",
+ " showactive=True,\n",
+ " x=0.30,\n",
+ " xanchor='left',\n",
+ " y=1.0,\n",
+ " yanchor='top',\n",
+ " font=dict(\n",
+ " family='Times New Roman',\n",
+ " size=12,\n",
+ " color='#000'\n",
+ " )\n",
+ " ),\n",
+ " ]\n",
+ ") \n",
+ "\n",
+ "fig = dict(data=data, layout=layout)\n",
+ "\n",
+ "iplot(fig, filename = 'ir_fig_2.html', config = config)"
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "base",
+ "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": "3.12.2"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}