subcortex-visualization 0.1.2__py3-none-any.whl

subcortex_visualization/data/subcortex_aseg_both_ordering.csv

@@ -0,0 +1,27 @@
+region,face,plot_order,Hemisphere
+accumbens,lateral,1,L
+caudate,lateral,2,L
+thalamus,lateral,3,L
+hippocampus,lateral,4,L
+amygdala,lateral,5,L
+putamen,lateral,6,L
+putamen,medial,7,L
+pallidum,medial,8,L
+accumbens,medial,9,L
+caudate,medial,10,L
+thalamus,medial,11,L
+amygdala,medial,12,L
+hippocampus,medial,13,L
+accumbens,lateral,14,R
+caudate,lateral,15,R
+thalamus,lateral,16,R
+hippocampus,lateral,17,R
+amygdala,lateral,18,R
+putamen,lateral,19,R
+putamen,medial,20,R
+pallidum,medial,21,R
+accumbens,medial,22,R
+caudate,medial,23,R
+thalamus,medial,24,R
+amygdala,medial,25,R
+hippocampus,medial,26,R

subcortex_visualization/data/subcortical_aseg_paths_lookup.csv

@@ -0,0 +1,49 @@
+region,view,path_number,Hemisphere,Num_Hemi
+caudate,lateral,0,L,1
+putamen,lateral,1,L,1
+thalamus,lateral,2,L,1
+hippocampus,lateral,3,L,1
+amygdala,lateral,4,L,1
+putamen,medial,5,L,1
+caudate,medial,6,L,1
+accumbens,medial,7,L,1
+pallidum,medial,8,L,1
+thalamus,medial,9,L,1
+amygdala,medial,10,L,1
+hippocampus,medial,11,L,1
+caudate,lateral,0,R,1
+putamen,lateral,1,R,1
+thalamus,lateral,2,R,1
+hippocampus,lateral,3,R,1
+amygdala,lateral,4,R,1
+putamen,medial,5,R,1
+caudate,medial,6,R,1
+accumbens,medial,7,R,1
+pallidum,medial,8,R,1
+thalamus,medial,9,R,1
+amygdala,medial,10,R,1
+hippocampus,medial,11,R,1
+caudate,lateral,0,L,2
+putamen,lateral,1,L,2
+thalamus,lateral,2,L,2
+hippocampus,lateral,3,L,2
+amygdala,lateral,4,L,2
+putamen,medial,5,L,2
+caudate,medial,6,L,2
+accumbens,medial,7,L,2
+pallidum,medial,8,L,2
+thalamus,medial,9,L,2
+amygdala,medial,10,L,2
+hippocampus,medial,11,L,2
+caudate,lateral,12,R,2
+putamen,lateral,13,R,2
+thalamus,lateral,14,R,2
+hippocampus,lateral,15,R,2
+amygdala,lateral,16,R,2
+putamen,medial,17,R,2
+caudate,medial,18,R,2
+accumbens,medial,19,R,2
+pallidum,medial,20,R,2
+thalamus,medial,21,R,2
+amygdala,medial,22,R,2
+hippocampus,medial,23,R,2

subcortex_visualization/plotting.py

@@ -0,0 +1,371 @@
+# Necessary imports 
+import pandas as pd
+import numpy as np
+
+# SVG parsing
+import xml.etree.ElementTree as ET
+from svgpath2mpl import parse_path
+
+# matplotlib plotting
+import matplotlib
+import matplotlib.pyplot as plt
+import matplotlib.colors as mcolors
+from matplotlib.patches import PathPatch, Patch
+
+# Files 
+from importlib.resources import files
+
+def add_legend(ax, fig, atlas_ordering, ncols=4, value_column='value', cmap_colors=None, fill_title=None, cmap='plasma', norm=None):
+    """
+    Add a legend or colorbar to the plot based on the provided data.
+
+    Parameters
+    ----------
+    ax : matplotlib.axes.Axes
+        The axes object to which the legend or colorbar will be added.
+
+    fig : matplotlib.figure.Figure
+        The figure object containing the plot.
+
+    atlas_ordering : pandas.DataFrame
+        DataFrame containing the atlas ordering information.
+
+    value_column : str
+        The name of the column in `atlas_ordering` that contains the values to be visualized.
+
+    cmap_colors : list of str, optional
+        List of colors corresponding to the regions in the atlas.
+
+    fill_title : str, optional
+        Title for the legend or colorbar.
+
+    cmap : str or matplotlib.colors.Colormap, optional
+        Colormap to use for the colorbar. Default is 'plasma'.
+
+    norm : matplotlib.colors.Normalize or matplotlib.colors.TwoSlopeNorm, optional
+        Normalization object for the colorbar. If None, a discrete legend is created.
+
+    Returns
+    -------
+    None (adds to the plot directly)
+        
+    """
+
+    if fill_title is None:
+        fill_title = "values"
+
+    if norm is None:
+        # Discrete legend
+        unique_regions = atlas_ordering[['region', value_column]].drop_duplicates()
+        legend_elements = [
+            Patch(facecolor=cmap_colors[row[value_column]], edgecolor='black', label=row['region'])
+            for _, row in unique_regions.iterrows()
+        ]
+        # Add legend to the plot
+        ax.legend(handles=legend_elements, loc='lower center',
+                    bbox_to_anchor=(0.5, -0.25), ncols=ncols, frameon=False,
+                    fontsize='medium', handleheight=1.2, handlelength=1.2,
+                    title=fill_title, 
+                    handletextpad=0.4)
+        fig.subplots_adjust(bottom=0.5)  # Reserve space for legend
+
+    else:
+        # Continuous colorbar
+        sm = plt.cm.ScalarMappable(cmap=cmap, norm=norm)
+        sm.set_array([])  # Only needed for compatibility
+        cbar = fig.colorbar(sm, ax=ax, orientation='horizontal', fraction=0.046, pad=0.04)
+        cbar.set_label(fill_title)
+
+def prep_data(atlas_ordering, value_column='value', subcortex_data=None, cmap=None, vmin=None, vmax=None, midpoint=None):
+    """ 
+    Prepare data for plotting by merging with subcortex_data and normalizing values.
+
+    Parameters
+    ----------
+    atlas_ordering : pandas.DataFrame
+        DataFrame containing the atlas ordering information.
+
+    value_column : str
+        The name of the column in `atlas_ordering` that contains the values to be visualized. Default is 'value'.
+
+    subcortex_data : pandas.DataFrame, optional
+        DataFrame with columns ['region', 'value', 'Hemisphere'].
+        If None, a default dataset is generated based on the selected hemisphere.
+        
+    cmap : str or matplotlib.colors.Colormap, optional
+        Colormap to use for the colorbar. Default is 'plasma'.
+
+    vmin : float, optional
+        Minimum value for colormap normalization. If None, the minimum of the input values is used.
+
+    vmax : float, optional
+        Maximum value for colormap normalization. If None, the maximum of the input values is used.
+
+    midpoint : float, optional
+        If provided, uses a diverging colormap centered around this value.
+
+    Returns
+    -------
+    atlas_ordering : pandas.DataFrame
+        DataFrame with merged and normalized values.
+
+    color_lookup : dict
+        Dictionary mapping region names to colors for discrete colormap.
+
+    cmap_colors : list of str
+        List of colors corresponding to the regions in the atlas.
+
+    norm : matplotlib.colors.Normalize or matplotlib.colors.TwoSlopeNorm
+        Normalization object for the colorbar. If None, a discrete legend is created.
+
+    Notes
+    -----
+    - The function handles both discrete and continuous colormaps based on the presence of subcortex_data.
+    - If subcortex_data is None, a discrete colormap is created based on the unique regions in atlas_ordering.
+    - If subcortex_data is provided, the values are normalized and a continuous colormap is created.
+    - The function returns the updated atlas_ordering DataFrame, color lookup dictionary, and colormap colors.
+
+    """
+
+    if subcortex_data is None:
+        # Assign discrete indices per region
+        unique_regions = atlas_ordering['region'].unique()
+        region_to_index = {region: idx for idx, region in enumerate(unique_regions)}
+        atlas_ordering[value_column] = atlas_ordering['region'].map(region_to_index)
+        
+        # Discrete colormap
+        num_regions = len(unique_regions)
+        cmap_colors = cmap(np.linspace(0, 1, num_regions))
+        color_lookup = {region: cmap_colors[i] for region, i in region_to_index.items()}
+
+        return atlas_ordering, color_lookup, cmap_colors
+    
+    else:
+        # Merge and normalize
+        atlas_ordering = atlas_ordering.merge(subcortex_data, on=['region', 'Hemisphere'], how='left')
+
+        fill_values = atlas_ordering[value_column].values
+
+        if midpoint is not None:
+            max_dev = np.nanmax(np.abs(fill_values - midpoint))
+            if vmin is None:
+                vmin = midpoint - max_dev
+            if vmax is None:
+                vmax = midpoint + max_dev
+            norm = mcolors.TwoSlopeNorm(vmin=vmin, vcenter=midpoint, vmax=vmax)
+        else:
+            if vmin is None:
+                vmin = np.nanmin(fill_values)
+            if vmax is None:
+                vmax = np.nanmax(fill_values)
+            norm = mcolors.Normalize(vmin=vmin, vmax=vmax)
+
+        return atlas_ordering, norm, vmin, vmax, midpoint
+
+def plot_helper(atlas_ordering, paths, value_column='value', hemisphere='L', subcortex_data=None, line_color='black', line_thickness=1.5,
+                color_lookup=None, cmap=None, norm=None):
+    """ 
+    
+    Helper function to plot the SVG paths with the specified colors and line properties.
+
+    Parameters
+    ----------
+    atlas_ordering : pandas.DataFrame
+        DataFrame containing the atlas ordering information.
+
+    paths : list of xml.etree.ElementTree.Element
+        List of SVG path elements to be plotted.
+    
+    value_column : str
+        The name of the column in `atlas_ordering` that contains the values to be visualized. Default is 'value'.
+
+    hemisphere : {'L', 'R', 'both'}, default='L'
+        Which hemisphere(s) to display. Use 'L' for left, 'R' for right, or 'both' for bilateral plots.
+
+    subcortex_data : pandas.DataFrame, optional
+        DataFrame with columns ['region', 'value', 'Hemisphere'].
+        If None, a default dataset is generated based on the selected hemisphere.
+
+    line_color : str, default='black'
+        Color of the outline around each subcortical region.
+
+    line_thickness : float, default=1.5
+        Thickness of the outline for each region (in mm)
+
+    color_lookup : dict, optional
+        Dictionary mapping region names to colors for discrete colormap.
+
+    cmap : str or matplotlib.colors.Colormap, optional
+        Colormap to use for the colorbar. Default is 'plasma'.
+
+    norm : matplotlib.colors.Normalize or matplotlib.colors.TwoSlopeNorm, optional
+        Normalization object for the colorbar. If None, a discrete legend is created.
+
+    Returns
+    -------
+    fig : matplotlib.figure.Figure
+        The generated figure object.
+
+    ax : matplotlib.axes.Axes
+        The axes object containing the plot.
+
+    """
+
+    # Start plotting
+    if hemisphere == 'both': 
+        fig, ax = plt.subplots(figsize=(17,6))
+    else:
+        fig, ax = plt.subplots(figsize=(8, 6))
+    patches = []
+
+    for _, row in atlas_ordering.iterrows():
+        this_region = row['region']
+        this_region_side = row['face']
+        this_region_hemi = row['Hemisphere']
+
+        # Determine color
+        if subcortex_data is None:
+            this_region_color = color_lookup[this_region]
+        else:
+            val = row[value_column]
+            this_region_color = cmap(norm(val)) if not pd.isnull(val) else "#cccccc"
+
+        # Match title to region
+        for path in paths:
+            for child in path:
+                if child.tag.endswith('title') and child.text == f"{this_region}_{this_region_side}_{this_region_hemi}":
+                    d = path.attrib['d']
+                    path_obj = parse_path(d)
+                    patch = PathPatch(path_obj, facecolor=this_region_color,
+                                      edgecolor=line_color, lw=line_thickness)
+                    ax.add_patch(patch)
+                    patches.append(patch)
+
+    ax.autoscale_view()
+    ax.set_aspect('equal')
+    ax.axis('off')
+    ax.invert_yaxis()
+
+    return fig, ax
+
+def plot_subcortical_data(subcortex_data=None, atlas='aseg', value_column='value',
+                          line_thickness=1.5, line_color='black',
+                          hemisphere='L', fill_title="values", cmap='viridis',
+                          vmin=None, vmax=None, midpoint=None, show_legend=True,
+                          show_figure=True):
+    
+    """
+    Visualize subcortical brain data on an SVG map using matplotlib.
+
+    Parameters
+    ----------
+    subcortex_data : pandas.DataFrame, optional
+        DataFrame with columns ['region', 'value', 'Hemisphere'].
+        If None, a default dataset is generated based on the selected hemisphere.
+
+    atlas : str, default='aseg'
+        The atlas used for the subcortical regions. Currently, two options are supported: 'aseg' and 'Tian_S1'.
+
+    value_column : str, default='value'
+        The name of the column in `subcortex_data` that contains the values to be visualized.
+
+    line_thickness : float, default=1.5
+        Thickness of the outline for each region.
+
+    line_color : str, default='black'
+        Color of the outline around each subcortical region.
+
+    hemisphere : {'L', 'R', 'both'}, default='L'
+        Which hemisphere(s) to display. Use 'L' for left, 'R' for right, or 'both' for bilateral plots.
+
+    fill_title : str, default="values"
+        Label for the colorbar indicating the meaning of the fill values.
+
+    cmap : str or matplotlib.colors.Colormap, default='viridis'
+        Colormap used to fill in the regions. Accepts a string name or a Colormap object.
+
+    vmin : float, optional
+        Minimum value for colormap normalization. If None, the minimum of the input values is used.
+
+    vmax : float, optional
+        Maximum value for colormap normalization. If None, the maximum of the input values is used.
+
+    midpoint : float, optional
+        If provided, uses a diverging colormap centered around this value.
+
+    show_legend : bool, default=True
+        If True, displays a legend or colorbar indicating the mapping of values to colors.
+
+    show_figure : bool, default=True
+        If True, displays the figure using `plt.show()`. If False, returns the matplotlib Figure object.
+
+    Returns
+    -------
+    matplotlib.figure.Figure or None
+        The generated figure, if `show_figure` is False. Otherwise, displays the plot and returns None.
+
+    Notes
+    -----
+    - The function loads SVG files and a lookup CSV bundled with the package, which can be found under `data/` directory.
+    - The input `subcortex_data` should align with regions defined in the lookup table.
+    """
+    
+    # Load SVG
+    svg_path = files("subcortex_visualization.data").joinpath(f"subcortex_{atlas}_{hemisphere}.svg")
+    tree = ET.parse(svg_path)
+    root = tree.getroot()
+
+    # Define SVG namespace
+    ns = {'svg': 'http://www.w3.org/2000/svg'}
+    ET.register_namespace('', ns['svg'])
+
+    # Find path elements
+    paths = root.findall('.//svg:path', ns)
+
+    # Load ordering file
+    atlas_ordering = pd.read_csv(files("subcortex_visualization.data").joinpath(f"subcortex_{atlas}_{hemisphere}_ordering.csv"))
+
+    # Handle colormap
+    if isinstance(cmap, str):
+        cmap = matplotlib.colormaps.get_cmap(cmap)
+
+    # Prepare data for plotting
+    if subcortex_data is None: 
+        atlas_ordering, color_lookup, cmap_colors = prep_data(atlas_ordering, value_column=value_column, subcortex_data=None, cmap=cmap)
+    else: 
+        atlas_ordering, norm, vmin, vmax, midpoint = prep_data(atlas_ordering, value_column=value_column, 
+                                                               subcortex_data=subcortex_data, 
+                                                               cmap=cmap, vmin=vmin, vmax=vmax, midpoint=midpoint)
+
+    # Let's get plottin
+    if subcortex_data is None:
+
+        fig, ax = plot_helper(atlas_ordering, paths, value_column=value_column, hemisphere=hemisphere,
+                              line_color=line_color, line_thickness=line_thickness,
+                              color_lookup=color_lookup)
+        
+    else:
+
+        fig, ax = plot_helper(atlas_ordering, paths, value_column=value_column, hemisphere=hemisphere,
+                              line_color=line_color, line_thickness=line_thickness,
+                              subcortex_data=subcortex_data, cmap=cmap, norm=norm)
+
+    # Add a legend if requested
+    if show_legend:
+
+        ncols = np.where(hemisphere == 'both', 8, 4)
+
+        # Call add_legend function to add the legend (discrete when subcortex_data is None) or colorbar (continuous when subcortex_data is not None)
+        if subcortex_data is None:
+            add_legend(ax=ax, fig=fig, value_column=value_column, atlas_ordering=atlas_ordering, 
+                       cmap_colors=cmap_colors, fill_title=fill_title, ncols=ncols)
+        else:
+            add_legend(ax=ax, fig=fig, value_column=value_column, atlas_ordering=atlas_ordering, 
+                       cmap=cmap, norm=norm, fill_title=fill_title)
+
+    plt.tight_layout()
+
+    if show_figure:
+        plt.show()
+    else:
+        return fig

subcortex_visualization-0.1.2.dist-info/METADATA

@@ -0,0 +1,153 @@
+Metadata-Version: 2.4
+Name: subcortex_visualization
+Version: 0.1.2
+Summary: A package to visualize subcortical brain data in two dimensions.
+Author: Annie G. Bryant
+Author-email: "Annie G. Bryant" <anniegbryant@gmail.com>
+License: GNU General Public License v3 (GPLv3)
+Project-URL: Homepage, https://github.com/anniegbryant/subcortex_visualization
+Project-URL: Issues, https://github.com/anniegbryant/subcortex_visualization/issues
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Development Status :: 1 - Planning
+Classifier: Operating System :: OS Independent
+Classifier: Intended Audience :: Science/Research
+Classifier: Environment :: Console
+Classifier: Environment :: Other Environment
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Dynamic: author
+Dynamic: license-file
+
+# Subcortical data visualization in 2D
+
+This python package currently includes the following six subcortical atlases for data visualization in two-dimensional vector graphics:
+
+<img src="images/all_atlas_showcase.png" width="100%">
+
+More information about these atlases, including the process of rendering the surfaces and tracing the outlines for each, can be found in the [`atlas_info/`](https://github.com/anniegbryant/subcortex_visualization/tree/main/atlas_info) directory.
+
+
+## 🙋‍♀️ Motivation
+
+This Python package was created to generate two-dimensional subcortex images in the style of the popular [`ggseg` package](https://github.com/ggseg/ggseg) in R.
+We based our vector graphic outlines on the three-dimensional subcortical meshes either (1) provided as part of the [ENIGMA toolbox](https://github.com/MICA-MNI/ENIGMA) for the aseg atlas or (2) meshes generated in-house using rendering software from [Chris Rorden's lab](https://github.com/neurolabusc) (either [nii2mesh](https://github.com/neurolabusc/nii2mesh) or [Surf Ice](https://github.com/neurolabusc/surf-ice); check out [`custom_segmentation_pipeline/`](https://github.com/anniegbryant/subcortex_visualization/tree/main/custom_segmentation_pipeline) for more information).
+
+The below graphic summarizes the transformation from 3D volumetric meshes to 2D surfaces, starting from the ENIGMA toolbox ('aseg' atlas, left) or a custom-rendered mesh from the [Melbourne Subcortex Atlas](https://github.com/yetianmed/subcortex/tree/master) as published in [Tian et al. (2020)]()https://www.nature.com/articles/s41593-020-00711-6 -- ('S1' granularity level, right).
+
+<img src="images/aseg_and_Melbourne_S1_3D_to_2D_schematic.png" width="90%">
+
+
+While `ggseg` offers subcortical plotting with the `aseg` atlas, it is [not currently possible](https://github.com/ggseg/ggseg/issues/104) to show data from all seven subcortical regions (accumbens, amygdala, caudate, hippocampus, pallidum, putamen, thalamus) in the same figure.
+Moreover, there is currently no other software available to visualize any of the other above subcortical/thalamic atlases in 2D with real data, hence development here.
+
+
+## 🖥️ Installation
+
+The package can be installed from GitHub in two ways.
+First, you can install directly with pip from the [PyPI repository](https://pypi.org/project/subcortex-visualization/):
+
+```bash
+pip install subcortex-visualization
+```
+
+If you would like to make your own modifications before installing, you can also clone this repository first and then install from your local version:
+
+```bash
+git clone https://github.com/anniegbryant/subcortex_visualization.git
+cd subcortex_visualization
+pip install .
+```
+
+This will install the `subcortex_visualization` package so you have access to the `plot_subcortical_data` function and associated data.
+
+## 👨‍💻 Usage
+
+### ❗️ Quick start
+
+Running the below code will produce an image of the left subcortex in the aseg atlas (the default), each region colored by its index, with the plasma color scheme:
+
+```python
+plot_subcortical_data(hemisphere='L', cmap='plasma', 
+                      fill_title = "Subcortical region index")
+```
+
+<img src="images/example_aseg_subcortex_plot.png" width="80%">
+
+
+### 📚 Tutorial
+
+For a guide that goes through all the functionality and atlases available in this package, we compiled a simple walkthrough tutorial in [tutorial.ipynb](https://github.com/anniegbryant/subcortex_visualization/blob/main/tutorial.ipynb).
+To plot real data in the subcortex, your `subcortex_data` should be  a `pandas.DataFrame` structured as follows (here we've just assigned an integer index to each region):
+
+| region        | value         | Hemisphere  |
+| :--- | :---: | :---: |
+| accumbens | 0 | L |
+| amygdala | 1 | L |
+| caudate | 2 | L |
+| hippocampus | 3 | L |
+| pallidum | 4 | L |
+| putamen | 5 | L |
+| thalamus | 6 | L |
+
+Briefly, all functionality is contained within the `plot_subcortical_data` function, which takes in the following arguments: 
+* `subcortex_data`: The three-column dataframe in a format as shown above; this is optional, if left out the plot will just color each region by its index
+* `atlas`: The name of the subcortical segmentation atlas (default is 'aseg', which is currently the only supported atlas)
+* `value_column`: The name of the column in your `subcortex_data` to plot, defaults to 'value'
+* `line_thickness`: How thick the lines around each subcortical region should be drawn, in mm (default is 1.5)
+* `line_color`: What color the lines around each subcortical region should be (default is 'black')
+* `hemisphere`: Which hemisphere ('L' or 'R') the `subcortex_data` is from; can also be 'both' (default is 'L')
+* `fill_title`: Name to add to legend (default is 'values')
+* `cmap`: name of colormap (e.g., 'plasma' or 'viridis') or a `matplotlib.colors.Colormap` (default is 'viridis')
+* `vmin`: Min fill value; this is optional, and you would only want to use this to manually constrain the fill range to match another figure
+* `vmax`: Max fill value; this is optional, and you would only want to use this to manually constrain the fill range to match another figure
+* `midpoint`: Midpoint value to enforce for fill range; this is optional
+
+Here's an example plotting both hemispheres, with data randomly sampled from a normal distribution, setting a color range from blue (low) to red (high) with white at the center (midpoint=0):
+
+```python
+import matplotlib.colors as mcolors
+import numpy as np
+
+np.random.seed(127)
+
+example_continuous_data_L = pd.DataFrame({"region": ["accumbens", "amygdala", "caudate", "hippocampus", "pallidum", "putamen", "thalamus"],
+                                          "value": np.random.normal(0, 1, 7)}).assign(Hemisphere = "L")
+example_continuous_data_R = pd.DataFrame({"region": ["accumbens", "amygdala", "caudate", "hippocampus", "pallidum", "putamen", "thalamus"],
+                                            "value": np.random.normal(0, 1, 7)}).assign(Hemisphere = "R")
+example_continuous_data = pd.concat([example_continuous_data_L, example_continuous_data_R], axis=0)
+
+white_blue_red_cmap = mcolors.LinearSegmentedColormap.from_list("BlueWhiteRed", ["blue", "white", "red"])
+
+plot_subcortical_data(subcortex_data=example_continuous_data, atlas='aseg',
+                      hemisphere='both', fill_title = "Normal distribution sample",
+                      cmap=white_blue_red_cmap, midpoint=0)
+```
+
+<img src="images/example_aseg_subcortex_normdist.png" width="80%">
+
+
+## 💡 Want to generate your own mesh and/or parcellation?
+
+This package provides six subcortical atlases as a starting point.
+The workflow can readily be extended to your favorite segmentation atlas, though! 
+We have a dedicated folder for a custom segmentation pipeline that will walk you through the two key steps:  
+1. Rendering a series of triangulated surface meshes from your parcellation atlas (starting from a .nii.gz volume), using either the [`nii2mesh`](https://github.com/neurolabusc/nii2mesh) or [`surfice_atlas`](https://github.com/neurolabusc/surfice_atlas) software, both developed by Chris Rorden; and 
+2. Tracing the outline of each region in the rendered mesh in vector graphic editing software (we use Inkscape in the tutorial as a powerful and free option), to yield a two-dimensional image of your atlas in scalable vector graphic (.svg) format.
+
+Check out the walkthrough in the [`custom_segmentation_pipeline/`](https://github.com/anniegbryant/subcortex_visualization/tree/main/custom_segmentation_pipeline) folder for more information on how to render your own volumetric segmentation with an interactive mesh and convert to a two-dimensional vector graphic that can be integrated with this package.
+
+## 🙏 Acknowledgments
+
+Thank you very much to [Chris Rorden](https://github.com/rordenlab), [Ye Tian](https://github.com/yetianmed), and [Sid Chopra](https://github.com/sidchop) for their suggestions and continued development of open tools for neuroimaging visualization that enabled development of this project!
+
+## ❓📧 Questions, comments, or suggestions always welcome!
+
+Please feel free to ask questions, report bugs, or share suggestions by creating an issue or by emailing me (Annie) at ([anniegbryant@gmail.com](mailto:anniegbryant@gmail.com)) 😊
+
+As an [open-source tool](https://opensource.guide/how-to-contribute/), pull requests are always welcome from the community, too.
+If you create your own custom vector graphic for your segmentation atlas of choice, feel free to create a pull request to incorporate and be acknowledged.

subcortex_visualization-0.1.2.dist-info/RECORD

@@ -0,0 +1,45 @@
+subcortex_visualization/__init__.py,sha256=jpAXYluGVENlJnvKDzL7RO3zeyCqp_ECl2fE8SnoEPU,43
+subcortex_visualization/plotting.py,sha256=XO6jcdRubkNGnHZoeKwmVrxQE_M0gIZwLFo8P2Lz5Uk,14233
+subcortex_visualization/data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+subcortex_visualization/data/subcortex_AICHA_L.svg,sha256=WMwgtZUqfhLW-2lUfhFEBND3ESJXxlew94vtfQhl6VY,135504
+subcortex_visualization/data/subcortex_AICHA_L_ordering.csv,sha256=thW6QuSAKNiI6uijz9ZpINIDrgFPiWGUF7k_UQUb_2s,864
+subcortex_visualization/data/subcortex_AICHA_R.svg,sha256=htwTJHWolkxlC89Se5HzEngh5w60ACGnZEAHf6EygM8,134310
+subcortex_visualization/data/subcortex_AICHA_R_ordering.csv,sha256=AJ9EcX5lFGMawkYEqPxP9rMdUx0NlCyWVhl4vbDFsb8,864
+subcortex_visualization/data/subcortex_AICHA_both.svg,sha256=_Urr7-XER4k50Qfj_8UKG-CWUnsCglNKBFfQhBPXmxM,271481
+subcortex_visualization/data/subcortex_AICHA_both_ordering.csv,sha256=RFcJx7dR_ekfBPgaXYumKFjCvQRthAygqtauPJemugE,1705
+subcortex_visualization/data/subcortex_Brainnetome_L.svg,sha256=PT7HnG3PKuAmMOrPwIULAvnh8x5aOTNHKymYkiw-JvY,115635
+subcortex_visualization/data/subcortex_Brainnetome_L_ordering.csv,sha256=UuVYc4lebice0PWKJbrL5WPNPZP2Rtk9OWAME6vWYcs,633
+subcortex_visualization/data/subcortex_Brainnetome_R.svg,sha256=xtDsm1x3C93NUD2pFuS-uHxIFjSZs1zzKrxZW1GO40M,120348
+subcortex_visualization/data/subcortex_Brainnetome_R_ordering.csv,sha256=gVp6eVJzhPzTfb3iI9vIBJQL5Apz9o0p6aCyYZheVls,633
+subcortex_visualization/data/subcortex_Brainnetome_both.svg,sha256=QR8r5FBq4b021XyWbcYd1V-EBofPkj0OjGBPT0cP284,233730
+subcortex_visualization/data/subcortex_Brainnetome_both_ordering.csv,sha256=EkhB1MiNYWU7w4Eg2EB0w2mPL7YtxZeZ3UtCJjz7znM,1239
+subcortex_visualization/data/subcortex_Melbourne_S1_L.svg,sha256=IH9bCCzqALsoigtT8j9t44ZINwp4dxhoBqurIgjKBuE,60411
+subcortex_visualization/data/subcortex_Melbourne_S1_L_ordering.csv,sha256=IvV_eOT3B_t6-Mzwx_AnsSfL5cOJ87-GGbxnKXkfYd8,406
+subcortex_visualization/data/subcortex_Melbourne_S1_R.svg,sha256=VTS7YZC2twcvWrTwCLBMNNRDeZzEfmkjZW0JY2dmZmU,60502
+subcortex_visualization/data/subcortex_Melbourne_S1_R_ordering.csv,sha256=kRbdHZGYiP_sejTQ0XP3Ntl232PSiXgkztw3_SxkmHk,406
+subcortex_visualization/data/subcortex_Melbourne_S1_both.svg,sha256=QS8sq_1clx48CxwcfDwHUyAXAVYP14WRAQhX-T4zhA8,114974
+subcortex_visualization/data/subcortex_Melbourne_S1_both_ordering.csv,sha256=3FkpewwtWo3aeZT-8soDzbfrLvAcIuO6NoK6HOLqkR8,785
+subcortex_visualization/data/subcortex_Melbourne_S2_L.svg,sha256=uVd8nGv1odY6P5GSrQA16FC4BLOUt_VGVAOfyY2VeeE,89813
+subcortex_visualization/data/subcortex_Melbourne_S2_L_ordering.csv,sha256=RvHVj5WRV7dPBZkK_yPe3mJevulfjusu0xgH06--V5Q,888
+subcortex_visualization/data/subcortex_Melbourne_S2_R.svg,sha256=dLixnb0DHtXpj-X1akrXUyZSZL12yJWG2RF6qQ6mbYk,89315
+subcortex_visualization/data/subcortex_Melbourne_S2_R_ordering.csv,sha256=rz65wZE0Ki2b2iimodQ2A0nuDax-0HxgaIt9sXIlPqs,888
+subcortex_visualization/data/subcortex_Melbourne_S2_both.svg,sha256=-1zr5Ph2XC8_vebQ5m_0Lva1BAZyRJ3pxtJ3u8eJexU,173552
+subcortex_visualization/data/subcortex_Melbourne_S2_both_ordering.csv,sha256=biljYiz-fzwDwu3_tJQQOv1McoaOf0m8KOweMahxJNY,1749
+subcortex_visualization/data/subcortex_Thalamus_Nuclei_HCP_L.svg,sha256=RLOQqwcQoDkU6dU6Go_hAH39FxcQffPpnsKPC6gKpbo,36283
+subcortex_visualization/data/subcortex_Thalamus_Nuclei_HCP_L_ordering.csv,sha256=PJR6NNGyFtF9lRpJV0Ce-Pr-_U3fAIiOUQRngJ0zfj4,438
+subcortex_visualization/data/subcortex_Thalamus_Nuclei_HCP_R.svg,sha256=yMecggCGAN6Pgn0-3uUUy_YQ5wFotOgUVwxnJwlvrYQ,36344
+subcortex_visualization/data/subcortex_Thalamus_Nuclei_HCP_R_ordering.csv,sha256=qX2AFXQkwFmyU2xWlbTZLG_kpjHkd_MI3L4CiT51SFI,438
+subcortex_visualization/data/subcortex_Thalamus_Nuclei_HCP_both.svg,sha256=E6-oBTZ57Yh3czKfPBsr9KFNpuUXx1MCVf4O7IFW4nc,70473
+subcortex_visualization/data/subcortex_Thalamus_Nuclei_HCP_both_ordering.csv,sha256=8Ny_CPquekB7UE2hFGXY3gS9amY6Q7mNnI2G9RC11LE,849
+subcortex_visualization/data/subcortex_aseg_L.svg,sha256=LlG_-FSaTVY26mM3v8isexFAhzRBs09i4XsqCqGPYr4,50932
+subcortex_visualization/data/subcortex_aseg_L_ordering.csv,sha256=TGCJ2mXcgoP_X6iKIqkyYYa2ONfOQ65qb-mluRn3TOE,323
+subcortex_visualization/data/subcortex_aseg_R.svg,sha256=oqSCRJ1SvxNp58FYkejo7vT0WBp6MXIQF_8Xy6aTYks,50803
+subcortex_visualization/data/subcortex_aseg_R_ordering.csv,sha256=LS87Sm74mtnhmm_mFNXJXm-o0JUvvDC_PkYFh2Gw1aQ,323
+subcortex_visualization/data/subcortex_aseg_both.svg,sha256=PtHnjcch-xRg__1gH-8vKkVihhvP0U52R7wprkERyMs,96336
+subcortex_visualization/data/subcortex_aseg_both_ordering.csv,sha256=v0ylkZQXleNsRPB6uzS9VcuxI86UmkCL_VdogkKoTeI,619
+subcortex_visualization/data/subcortical_aseg_paths_lookup.csv,sha256=MQWisa4WyuYc0-h2o-GNVnW09RYGHDhOfnE6ySohgaM,1197
+subcortex_visualization-0.1.2.dist-info/licenses/LICENSE.txt,sha256=XimfHe3DgLiY7Sd9GPyH3u_SjNfg0IF3QvCNBAYC6Rc,35137
+subcortex_visualization-0.1.2.dist-info/METADATA,sha256=jqC5aZZEwtZzgnwygqBiCvB8O89vg79QgEwACUH0tQU,9661
+subcortex_visualization-0.1.2.dist-info/WHEEL,sha256=GHB6lJx2juba1wDgXDNlMTyM13ckjBMKf-OnwgKOCtA,91
+subcortex_visualization-0.1.2.dist-info/top_level.txt,sha256=NrC151UjYD1USCUAj_JFSZN6prg-WqbJWlP5CoC4r4E,24
+subcortex_visualization-0.1.2.dist-info/RECORD,,

subcortex_visualization-0.1.2.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (80.3.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+