subcortex-visualization 0.1.12__tar.gz → 1.1.0__tar.gz

{subcortex_visualization-0.1.12/subcortex_visualization.egg-info → subcortex_visualization-1.1.0}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: subcortex_visualization
-Version: 0.1.12
-Summary: A package to visualize subcortical brain data in two dimensions.
+Version: 1.1.0
+Summary: A package to visualize subcortical and cerebellar brain data in two dimensions.
 Author: Annie G. Bryant
 Author-email: "Annie G. Bryant" <anniegbryant@gmail.com>
 License: GNU General Public License v3 (GPLv3)
@@ -25,26 +25,25 @@ 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:
+[![DOI](https://zenodo.org/badge/965897997.svg)](https://doi.org/10.5281/zenodo.15385315)
 
-<img src="images/all_atlas_showcase.png" width="100%">
+This python package currently includes the following nine subcortical and cerebellar atlases for data visualization in two-dimensional vector graphics:
 
-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.
+<img src="docs-site/docs/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 and at the [project website](https://anniegbryant.github.io/subcortex_visualization/).
 
 ## 🙋‍♀️ 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).
+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) ([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%">
-
+<img src="docs-site/docs/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.
-
+Moreover, there is currently no other software available to visualize any of the other above subcortical, thalamic, or cerebellar atlases in two dimensions with real data, hence development here.
 
 ## 🖥️ Installation
 
@@ -69,14 +68,14 @@ This will install the `subcortex_visualization` package so you have access to th
 
 ### ❗️ 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:
+Running the code below 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%">
+<img src="docs-site/docs/images/example_aseg_subcortex_plot.png" width="80%">
 
 
 ### 📚 Tutorial
@@ -96,7 +95,7 @@ To plot real data in the subcortex, your `subcortex_data` should be  a `pandas.D
 
 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)
+* `atlas`: The name of the subcortical, thalamic, or cerebellar segmentation atlas (default is 'aseg', all options listed below)
 * `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')
@@ -128,22 +127,48 @@ plot_subcortical_data(subcortex_data=example_continuous_data, atlas='aseg',
                       cmap=white_blue_red_cmap, midpoint=0)
 ```
 
-<img src="images/example_aseg_subcortex_normdist.png" width="80%">
+<img src="docs-site/docs/images/example_aseg_subcortex_normdist.png" width="80%">
+
+### Available atlases
+
+The following nine subcortical atlases are currently supported with more information at the [project website](https://anniegbryant.github.io/subcortex_visualization/atlas_info/): 
+
+* `aseg`: The `aseg` parcellation atlas from FreeSurfer
+* `Melbourne_S1`: The Melbourne Subcortex Atlas at granularity level S1, from [Tian et al. *Nature Neuroscience* (2020)](https://www.nature.com/articles/s41593-020-00711-6)
+* `Melbourne_S2`: The Melbourne Subcortex Atlas at granularity level S2, from [Tian et al. *Nature Neuroscience* (2020)](https://www.nature.com/articles/s41593-020-00711-6)
+* `Melbourne_S3`: The Melbourne Subcortex Atlas at granularity level S3, from [Tian et al. *Nature Neuroscience* (2020)](https://www.nature.com/articles/s41593-020-00711-6)
+* `Melbourne_S4`: The Melbourne Subcortex Atlas at granularity level S4, from [Tian et al. *Nature Neuroscience* (2020)](https://www.nature.com/articles/s41593-020-00711-6)
+* `AICHA`: The AICHA subcortex atlas, from [Joliot et al. *J Neurosci Methods* (2015)](https://pubmed.ncbi.nlm.nih.gov/26213217/).
+* `Brainnetome`: The Brainnetome subcortex atlas, from [Fan et al. *Cerebral Cortex* (2016)](https://pmc.ncbi.nlm.nih.gov/articles/PMC4961028/)
+* `Thalamus_Nuclei_HCP`: The thalamic nuclei atlas derived from HCP data, from [Najdenovska et al. *Scientific Data* (2018)](https://www.nature.com/articles/sdata2018270)
+* `SUIT`: The SUIT cerebellum atlas, from [Diedrichsen *Neuroimage* (2006)](https://doi.org/10.1016/j.neuroimage.2006.05.056)
 
 
 ## 💡 Want to generate your own mesh and/or parcellation?
 
-This package provides six subcortical atlases as a starting point.
+<img src="docs-site/docs/images/custom_vector_method.png" width="70%">
+
+This package provides nine subcortical, thalamic, and cerebellar 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 
+1. Rendering a series of triangulated surface meshes from your parcellation atlas (starting from a .nii.gz volume), using the [`surfice_atlas`](https://github.com/neurolabusc/surfice_atlas) software, both developed by [Chris Rorden's lab](https://github.com/rordenlab); 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!
+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 the development of this project!
+
+We're also very grateful for ongoing contributions from members of the GitHub community: 
+
+[![Contributors](https://contrib.rocks/image?repo=anniegbryant/subcortex_visualization)](https://github.com/anniegbryant/subcortex_visualization/graphs/contributors)
+
+## 🔗 Citing this package
+
+If you use this package in a scientific publication, blog post, etc., please cite the corresponding Zenodo release as follows:
+
+Annie G. Bryant. (2025). anniegbryant/subcortex_visualization: Initial Zenodo release (initial_release). Zenodo. https://doi.org/10.5281/zenodo.15385316
 
 ## ❓📧 Questions, comments, or suggestions always welcome!
 

{subcortex_visualization-0.1.12 → subcortex_visualization-1.1.0}/README.md

@@ -1,25 +1,24 @@
 # Subcortical data visualization in 2D
 
-This python package currently includes the following six subcortical atlases for data visualization in two-dimensional vector graphics:
+[![DOI](https://zenodo.org/badge/965897997.svg)](https://doi.org/10.5281/zenodo.15385315)
 
-<img src="images/all_atlas_showcase.png" width="100%">
+This python package currently includes the following nine subcortical and cerebellar atlases for data visualization in two-dimensional vector graphics:
 
-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.
+<img src="docs-site/docs/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 and at the [project website](https://anniegbryant.github.io/subcortex_visualization/).
 
 ## 🙋‍♀️ 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).
+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) ([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%">
-
+<img src="docs-site/docs/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.
-
+Moreover, there is currently no other software available to visualize any of the other above subcortical, thalamic, or cerebellar atlases in two dimensions with real data, hence development here.
 
 ## 🖥️ Installation
 
@@ -44,14 +43,14 @@ This will install the `subcortex_visualization` package so you have access to th
 
 ### ❗️ 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:
+Running the code below 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%">
+<img src="docs-site/docs/images/example_aseg_subcortex_plot.png" width="80%">
 
 
 ### 📚 Tutorial
@@ -71,7 +70,7 @@ To plot real data in the subcortex, your `subcortex_data` should be  a `pandas.D
 
 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)
+* `atlas`: The name of the subcortical, thalamic, or cerebellar segmentation atlas (default is 'aseg', all options listed below)
 * `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')
@@ -103,26 +102,52 @@ plot_subcortical_data(subcortex_data=example_continuous_data, atlas='aseg',
                       cmap=white_blue_red_cmap, midpoint=0)
 ```
 
-<img src="images/example_aseg_subcortex_normdist.png" width="80%">
+<img src="docs-site/docs/images/example_aseg_subcortex_normdist.png" width="80%">
+
+### Available atlases
+
+The following nine subcortical atlases are currently supported with more information at the [project website](https://anniegbryant.github.io/subcortex_visualization/atlas_info/): 
+
+* `aseg`: The `aseg` parcellation atlas from FreeSurfer
+* `Melbourne_S1`: The Melbourne Subcortex Atlas at granularity level S1, from [Tian et al. *Nature Neuroscience* (2020)](https://www.nature.com/articles/s41593-020-00711-6)
+* `Melbourne_S2`: The Melbourne Subcortex Atlas at granularity level S2, from [Tian et al. *Nature Neuroscience* (2020)](https://www.nature.com/articles/s41593-020-00711-6)
+* `Melbourne_S3`: The Melbourne Subcortex Atlas at granularity level S3, from [Tian et al. *Nature Neuroscience* (2020)](https://www.nature.com/articles/s41593-020-00711-6)
+* `Melbourne_S4`: The Melbourne Subcortex Atlas at granularity level S4, from [Tian et al. *Nature Neuroscience* (2020)](https://www.nature.com/articles/s41593-020-00711-6)
+* `AICHA`: The AICHA subcortex atlas, from [Joliot et al. *J Neurosci Methods* (2015)](https://pubmed.ncbi.nlm.nih.gov/26213217/).
+* `Brainnetome`: The Brainnetome subcortex atlas, from [Fan et al. *Cerebral Cortex* (2016)](https://pmc.ncbi.nlm.nih.gov/articles/PMC4961028/)
+* `Thalamus_Nuclei_HCP`: The thalamic nuclei atlas derived from HCP data, from [Najdenovska et al. *Scientific Data* (2018)](https://www.nature.com/articles/sdata2018270)
+* `SUIT`: The SUIT cerebellum atlas, from [Diedrichsen *Neuroimage* (2006)](https://doi.org/10.1016/j.neuroimage.2006.05.056)
 
 
 ## 💡 Want to generate your own mesh and/or parcellation?
 
-This package provides six subcortical atlases as a starting point.
+<img src="docs-site/docs/images/custom_vector_method.png" width="70%">
+
+This package provides nine subcortical, thalamic, and cerebellar 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 
+1. Rendering a series of triangulated surface meshes from your parcellation atlas (starting from a .nii.gz volume), using the [`surfice_atlas`](https://github.com/neurolabusc/surfice_atlas) software, both developed by [Chris Rorden's lab](https://github.com/rordenlab); 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!
+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 the development of this project!
+
+We're also very grateful for ongoing contributions from members of the GitHub community: 
+
+[![Contributors](https://contrib.rocks/image?repo=anniegbryant/subcortex_visualization)](https://github.com/anniegbryant/subcortex_visualization/graphs/contributors)
+
+## 🔗 Citing this package
+
+If you use this package in a scientific publication, blog post, etc., please cite the corresponding Zenodo release as follows:
+
+Annie G. Bryant. (2025). anniegbryant/subcortex_visualization: Initial Zenodo release (initial_release). Zenodo. https://doi.org/10.5281/zenodo.15385316
 
 ## ❓📧 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.
+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-0.1.12 → subcortex_visualization-1.1.0}/pyproject.toml

@@ -4,11 +4,11 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "subcortex_visualization"
-version = "0.1.12"
+version = "1.1.0"
 authors = [
   { name="Annie G. Bryant", email="anniegbryant@gmail.com" },
 ]
-description = "A package to visualize subcortical brain data in two dimensions."
+description = "A package to visualize subcortical and cerebellar brain data in two dimensions."
 readme = "README.md"
 requires-python = ">=3.9"
 

subcortex_visualization-1.1.0/subcortex_visualization/data/AICHA_L_ordering.csv

@@ -0,0 +1,36 @@
+region,Hemisphere,seg_index,face,plot_order
+Thalamus-9,L,383,lateral,1
+Thalamus-7,L,379,lateral,2
+Caudate-1,L,347,lateral,3
+Caudate-3,L,351,lateral,4
+Amygdala-1,L,345,lateral,5
+Caudate-2,L,349,lateral,6
+Caudate-4,L,353,lateral,7
+Thalamus-6,L,377,lateral,8
+Thalamus-5,L,375,lateral,9
+Thalamus-2,L,369,lateral,10
+Caudate-5,L,355,lateral,11
+Caudate-6,L,357,lateral,12
+Caudate-7,L,359,lateral,13
+Putamen-2,L,363,lateral,14
+Putamen-3,L,365,lateral,15
+Putamen-3,L,365,medial,16
+Putamen-2,L,363,medial,17
+Pallidum-1,L,361,medial,18
+Thalamus-1,L,367,medial,19
+Thalamus-5,L,375,medial,20
+Thalamus-6,L,377,medial,21
+Thalamus-7,L,379,medial,22
+Thalamus-8,L,381,medial,23
+Thalamus-2,L,369,medial,24
+Thalamus-4,L,373,medial,25
+Caudate-5,L,355,medial,26
+Amygdala-1,L,345,medial,27
+Thalamus-9,L,383,medial,28
+Caudate-3,L,351,medial,29
+Caudate-4,L,353,medial,30
+Caudate-6,L,357,medial,31
+Caudate-7,L,359,medial,32
+Caudate-1,L,347,medial,33
+Caudate-2,L,349,medial,34
+Thalamus-3,L,371,medial,35

subcortex_visualization-1.1.0/subcortex_visualization/data/AICHA_R_ordering.csv

@@ -0,0 +1,36 @@
+region,Hemisphere,seg_index,face,plot_order
+Thalamus-9,R,384,lateral,1
+Thalamus-7,R,380,lateral,2
+Caudate-1,R,348,lateral,3
+Caudate-3,R,352,lateral,4
+Amygdala-1,R,346,lateral,5
+Caudate-2,R,350,lateral,6
+Caudate-4,R,354,lateral,7
+Thalamus-6,R,378,lateral,8
+Thalamus-5,R,376,lateral,9
+Thalamus-2,R,370,lateral,10
+Caudate-5,R,356,lateral,11
+Caudate-6,R,358,lateral,12
+Caudate-7,R,360,lateral,13
+Putamen-2,R,364,lateral,14
+Putamen-3,R,366,lateral,15
+Putamen-3,R,366,medial,16
+Putamen-2,R,364,medial,17
+Pallidum-1,R,362,medial,18
+Thalamus-1,R,368,medial,19
+Thalamus-5,R,376,medial,20
+Thalamus-6,R,378,medial,21
+Thalamus-7,R,380,medial,22
+Thalamus-8,R,382,medial,23
+Thalamus-2,R,370,medial,24
+Thalamus-4,R,374,medial,25
+Caudate-5,R,356,medial,26
+Amygdala-1,R,346,medial,27
+Thalamus-9,R,384,medial,28
+Caudate-3,R,352,medial,29
+Caudate-4,R,354,medial,30
+Caudate-6,R,358,medial,31
+Caudate-7,R,360,medial,32
+Caudate-1,R,348,medial,33
+Caudate-2,R,350,medial,34
+Thalamus-3,R,372,medial,35

subcortex_visualization-1.1.0/subcortex_visualization/data/AICHA_both_ordering.csv

@@ -0,0 +1,71 @@
+region,Hemisphere,seg_index,face,plot_order
+Thalamus-9,L,383,lateral,1
+Thalamus-7,L,379,lateral,2
+Caudate-1,L,347,lateral,3
+Caudate-3,L,351,lateral,4
+Amygdala-1,L,345,lateral,5
+Caudate-2,L,349,lateral,6
+Caudate-4,L,353,lateral,7
+Thalamus-6,L,377,lateral,8
+Thalamus-5,L,375,lateral,9
+Thalamus-2,L,369,lateral,10
+Caudate-5,L,355,lateral,11
+Caudate-6,L,357,lateral,12
+Caudate-7,L,359,lateral,13
+Putamen-2,L,363,lateral,14
+Putamen-3,L,365,lateral,15
+Putamen-3,L,365,medial,16
+Putamen-2,L,363,medial,17
+Pallidum-1,L,361,medial,18
+Thalamus-1,L,367,medial,19
+Thalamus-5,L,375,medial,20
+Thalamus-6,L,377,medial,21
+Thalamus-7,L,379,medial,22
+Thalamus-8,L,381,medial,23
+Thalamus-2,L,369,medial,24
+Thalamus-4,L,373,medial,25
+Caudate-5,L,355,medial,26
+Amygdala-1,L,345,medial,27
+Thalamus-9,L,383,medial,28
+Caudate-3,L,351,medial,29
+Caudate-4,L,353,medial,30
+Caudate-6,L,357,medial,31
+Caudate-7,L,359,medial,32
+Caudate-1,L,347,medial,33
+Caudate-2,L,349,medial,34
+Thalamus-3,L,371,medial,35
+Thalamus-9,R,384,lateral,36
+Thalamus-7,R,380,lateral,37
+Caudate-1,R,348,lateral,38
+Caudate-3,R,352,lateral,39
+Amygdala-1,R,346,lateral,40
+Caudate-2,R,350,lateral,41
+Caudate-4,R,354,lateral,42
+Thalamus-6,R,378,lateral,43
+Thalamus-5,R,376,lateral,44
+Thalamus-2,R,370,lateral,45
+Caudate-5,R,356,lateral,46
+Caudate-6,R,358,lateral,47
+Caudate-7,R,360,lateral,48
+Putamen-2,R,364,lateral,49
+Putamen-3,R,366,lateral,50
+Putamen-3,R,366,medial,51
+Putamen-2,R,364,medial,52
+Pallidum-1,R,362,medial,53
+Thalamus-1,R,368,medial,54
+Thalamus-5,R,376,medial,55
+Thalamus-6,R,378,medial,56
+Thalamus-7,R,380,medial,57
+Thalamus-8,R,382,medial,58
+Thalamus-2,R,370,medial,59
+Thalamus-4,R,374,medial,60
+Caudate-5,R,356,medial,61
+Amygdala-1,R,346,medial,62
+Thalamus-9,R,384,medial,63
+Caudate-3,R,352,medial,64
+Caudate-4,R,354,medial,65
+Caudate-6,R,358,medial,66
+Caudate-7,R,360,medial,67
+Caudate-1,R,348,medial,68
+Caudate-2,R,350,medial,69
+Thalamus-3,R,372,medial,70

subcortex_visualization-1.1.0/subcortex_visualization/data/Brainnetome_L_ordering.csv

@@ -0,0 +1,33 @@
+region,Hemisphere,seg_index,face,plot_order
+dCa,L,227,lateral,1
+mAmyg,L,211,lateral,2
+rHipp,L,215,lateral,3
+lAmyg,L,213,lateral,4
+cHipp,L,217,lateral,5
+cTtha,L,243,lateral,6
+Otha,L,241,lateral,7
+mPMtha,L,233,lateral,8
+PPtha,L,239,lateral,9
+lPFtha,L,245,lateral,10
+Stha,L,235,lateral,11
+rTtha,L,237,lateral,12
+vCa,L,219,lateral,13
+NAC,L,223,lateral,14
+vmPu,L,225,lateral,15
+GP,L,221,lateral,16
+cHipp,L,217,lateral,17
+dlPu,L,229,lateral,18
+cHipp,L,217,medial,19
+rHipp,L,215,medial,20
+vmPu,L,225,medial,21
+Otha,L,241,medial,22
+PPtha,L,239,medial,23
+cTtha,L,243,medial,24
+dCa,L,227,medial,25
+vCa,L,219,medial,26
+NAC,L,223,medial,27
+GP,L,221,medial,28
+lPFtha,L,245,medial,29
+mPFtha,L,231,medial,30
+rTtha,L,237,medial,31
+mAmyg,L,211,medial,32

subcortex_visualization-1.1.0/subcortex_visualization/data/Brainnetome_R_ordering.csv

@@ -0,0 +1,33 @@
+region,Hemisphere,seg_index,face,plot_order
+dCa,R,228,lateral,1
+mAmyg,R,212,lateral,2
+rHipp,R,216,lateral,3
+lAmyg,R,214,lateral,4
+cHipp,R,218,lateral,5
+cTtha,R,244,lateral,6
+Otha,R,242,lateral,7
+mPMtha,R,234,lateral,8
+PPtha,R,240,lateral,9
+lPFtha,R,246,lateral,10
+Stha,R,236,lateral,11
+rTtha,R,238,lateral,12
+vCa,R,220,lateral,13
+NAC,R,224,lateral,14
+vmPu,R,226,lateral,15
+GP,R,222,lateral,16
+cHipp,R,218,lateral,17
+dlPu,R,230,lateral,18
+cHipp,R,218,medial,19
+rHipp,R,216,medial,20
+vmPu,R,226,medial,21
+Otha,R,242,medial,22
+PPtha,R,240,medial,23
+cTtha,R,244,medial,24
+dCa,R,228,medial,25
+vCa,R,220,medial,26
+NAC,R,224,medial,27
+GP,R,222,medial,28
+lPFtha,R,246,medial,29
+mPFtha,R,232,medial,30
+rTtha,R,238,medial,31
+mAmyg,R,212,medial,32

subcortex_visualization-1.1.0/subcortex_visualization/data/Brainnetome_both_ordering.csv

@@ -0,0 +1,65 @@
+region,Hemisphere,seg_index,face,plot_order
+dCa,L,227,lateral,1
+mAmyg,L,211,lateral,2
+rHipp,L,215,lateral,3
+lAmyg,L,213,lateral,4
+cHipp,L,217,lateral,5
+cTtha,L,243,lateral,6
+Otha,L,241,lateral,7
+mPMtha,L,233,lateral,8
+PPtha,L,239,lateral,9
+lPFtha,L,245,lateral,10
+Stha,L,235,lateral,11
+rTtha,L,237,lateral,12
+vCa,L,219,lateral,13
+NAC,L,223,lateral,14
+vmPu,L,225,lateral,15
+GP,L,221,lateral,16
+cHipp,L,217,lateral,17
+dlPu,L,229,lateral,18
+cHipp,L,217,medial,19
+rHipp,L,215,medial,20
+vmPu,L,225,medial,21
+Otha,L,241,medial,22
+PPtha,L,239,medial,23
+cTtha,L,243,medial,24
+dCa,L,227,medial,25
+vCa,L,219,medial,26
+NAC,L,223,medial,27
+GP,L,221,medial,28
+lPFtha,L,245,medial,29
+mPFtha,L,231,medial,30
+rTtha,L,237,medial,31
+mAmyg,L,211,medial,32
+dCa,R,228,lateral,33
+mAmyg,R,212,lateral,34
+rHipp,R,216,lateral,35
+lAmyg,R,214,lateral,36
+cHipp,R,218,lateral,37
+cTtha,R,244,lateral,38
+Otha,R,242,lateral,39
+mPMtha,R,234,lateral,40
+PPtha,R,240,lateral,41
+lPFtha,R,246,lateral,42
+Stha,R,236,lateral,43
+rTtha,R,238,lateral,44
+vCa,R,220,lateral,45
+NAC,R,224,lateral,46
+vmPu,R,226,lateral,47
+GP,R,222,lateral,48
+cHipp,R,218,lateral,49
+dlPu,R,230,lateral,50
+cHipp,R,218,medial,51
+rHipp,R,216,medial,52
+vmPu,R,226,medial,53
+Otha,R,242,medial,54
+PPtha,R,240,medial,55
+cTtha,R,244,medial,56
+dCa,R,228,medial,57
+vCa,R,220,medial,58
+NAC,R,224,medial,59
+GP,R,222,medial,60
+lPFtha,R,246,medial,61
+mPFtha,R,232,medial,62
+rTtha,R,238,medial,63
+mAmyg,R,212,medial,64

subcortex_visualization-1.1.0/subcortex_visualization/data/Melbourne_S1_L_ordering.csv

@@ -0,0 +1,16 @@
+region,Hemisphere,seg_index,face,plot_order
+putamen,L,15,medial,1
+pallidum,L,13,medial,2
+accumbens,L,14,medial,3
+caudate,L,16,medial,4
+thalamus_anterior,L,12,medial,5
+amygdala,L,10,medial,6
+hippocampus,L,9,medial,7
+thalamus_posterior,L,11,medial,8
+accumbens,L,14,lateral,9
+caudate,L,16,lateral,10
+thalamus_anterior,L,12,lateral,11
+thalamus_posterior,L,11,lateral,12
+hippocampus,L,9,lateral,13
+amygdala,L,10,lateral,14
+putamen,L,15,lateral,15

subcortex_visualization-1.1.0/subcortex_visualization/data/Melbourne_S1_R_ordering.csv

@@ -0,0 +1,16 @@
+region,face,plot_order,Hemisphere,seg_index
+putamen,medial,1,R,7
+pallidum,medial,2,R,5
+accumbens,medial,3,R,6
+caudate,medial,4,R,8
+thalamus_anterior,medial,5,R,4
+amygdala,medial,6,R,2
+hippocampus,medial,7,R,1
+thalamus_posterior,medial,8,R,3
+accumbens,lateral,9,R,6
+caudate,lateral,10,R,8
+thalamus_anterior,lateral,11,R,4
+thalamus_posterior,lateral,12,R,3
+hippocampus,lateral,13,R,1
+amygdala,lateral,14,R,2
+putamen,lateral,15,R,7

subcortex_visualization-1.1.0/subcortex_visualization/data/Melbourne_S1_both_ordering.csv

@@ -0,0 +1,31 @@
+region,Hemisphere,seg_index,face,plot_order
+putamen,L,15,medial,1
+pallidum,L,13,medial,2
+accumbens,L,14,medial,3
+caudate,L,16,medial,4
+thalamus_anterior,L,12,medial,5
+amygdala,L,10,medial,6
+hippocampus,L,9,medial,7
+thalamus_posterior,L,11,medial,8
+accumbens,L,14,lateral,9
+caudate,L,16,lateral,10
+thalamus_anterior,L,12,lateral,11
+thalamus_posterior,L,11,lateral,12
+hippocampus,L,9,lateral,13
+amygdala,L,10,lateral,14
+putamen,L,15,lateral,15
+putamen,R,7,medial,16
+pallidum,R,5,medial,17
+accumbens,R,6,medial,18
+caudate,R,8,medial,19
+thalamus_anterior,R,4,medial,20
+amygdala,R,2,medial,21
+hippocampus,R,1,medial,22
+thalamus_posterior,R,3,medial,23
+accumbens,R,6,lateral,24
+caudate,R,8,lateral,25
+thalamus_anterior,R,4,lateral,26
+thalamus_posterior,R,3,lateral,27
+hippocampus,R,1,lateral,28
+amygdala,R,2,lateral,29
+putamen,R,7,lateral,30

subcortex_visualization-1.1.0/subcortex_visualization/data/Melbourne_S2_L_ordering.csv

@@ -0,0 +1,30 @@
+region,Hemisphere,seg_index,face,plot_order
+putamen_posterior,L,30,medial,1
+putamen_anterior,L,29,medial,2
+accumbens_core,L,26,medial,3
+accumbens_shell,L,25,medial,4
+caudate_anterior,L,31,medial,5
+caudate_posterior,L,32,medial,6
+pallidum_posterior,L,27,medial,7
+pallidum_anterior,L,28,medial,8
+amygdala_lateral,L,19,medial,9
+amygdala_medial,L,20,medial,10
+hippocampus_posterior,L,18,medial,11
+hippocampus_anterior,L,17,medial,12
+thalamus_DP,L,21,medial,13
+thalamus_VP,L,22,medial,14
+thalamus_DA,L,24,medial,15
+thalamus_VA,L,23,medial,16
+thalamus_VA,L,23,lateral,17
+thalamus_DA,L,24,lateral,18
+thalamus_DP,L,21,lateral,19
+thalamus_VP,L,22,lateral,20
+hippocampus_posterior,L,18,lateral,21
+hippocampus_anterior,L,17,lateral,22
+amygdala_medial,L,20,lateral,23
+amygdala_lateral,L,19,lateral,24
+caudate_posterior,L,32,lateral,25
+caudate_anterior,L,31,lateral,26
+accumbens_core,L,26,lateral,27
+putamen_anterior,L,47,lateral,28
+putamen_posterior,L,30,lateral,29