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JThoennissen committed Jul 14, 2023
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4 changes: 2 additions & 2 deletions .zenodo.json
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}
],
"license": "Apache-2.0",
"title": "voluba-mriwarp: Integration of whole brain MRI scans into EBRAINS atlases",
"description": "voluba-mriwarp is a desktop application that integrates whole brain T1-weighted MRI scans into the anatomical context of the Julich Brain Atlas. It incorporates all required components like skull stripping, registration to MNI ICBM 152 2009c Nonlinear Asymmetric space, and detailed analysis with the siibra toolsuite. The corresponding functionalities are provided via open-source tools like HD-BET, ANTs and siibra-python. voluba-mriwarp is primarily designed for Windows 10 but can also be executed on Linux.\nWarping brain data to a standardized space like MNI152 enables anchoring of whole brain MRI scans to atlas volumes like BigBrain. However, reasonable registration requires various steps that need optimization effort. voluba-mriwarp aims to simplify this workflow. With this application, you avoid installing multiple tools and tweaking parameters for a proper registration result. Instead, voluba-mriwarp is an easy-to-install and easy-to-use tool combining all necessary steps into one pipeline.\nvoluba-mriwarp applies a set of predefined parameters to remove the skull and warp the input brain scan to MNI152 space. You can utilize the warping results in voluba-mriwarp to interactively assign brain regions to a point in the input space. Select a location in the displayed brain of a subject to perform a probabilistic assignment using Julich-Brain Cytoarchitectonic Maps 2.9. Hence, you can estimate the probability of a brain region occurring at the selected point. To explore even more information about a cytoarchitectonic area, you can access siibra-explorer through the application.",
"title": "voluba-mriwarp: Integration of whole-brain MRI scans into multilevel brain atlases",
"description": "voluba-mriwarp is a desktop application that integrates whole-brain T1-weighted MRI scans into the anatomical context of the EBRAINS Human Brain Atlas. It incorporates all required components like skull stripping, registration to MNI ICBM 152 2009c Nonlinear Asymmetric space, and detailed analysis with the siibra toolsuite. The corresponding functionalities are provided via open-source tools like HD-BET, ANTs and siibra-python. voluba-mriwarp is primarily designed for Windows 10 but can also be executed on Linux.\nWarping brain data to a standardized space like MNI152 enables anchoring of whole-brain MRI scans to atlas volumes and therefore facilitates analysis in a detailed anatomical context. However, reasonable registration requires various steps that need optimization effort. _voluba-mriwarp_ aims to simplify this workflow. With this application, you avoid installing multiple tools and tweaking parameters for a proper registration result. Instead, _voluba-mriwarp_ is an easy-to-install and easy-to-use tool combining all necessary steps into one pipeline.\napplies a set of predefined parameters to remove the skull and warp the input brain scan to MNI152 space. You can utilize the warping results in _voluba-mriwarp_ to interactively analyze points by making a probabilistic assignment of coordinates in the input space to brain regions of the EBRAINS Human Brain Atlas. To get an overview of more information about a brain region, you can access siibra-explorer through the application. For further analysis, _voluba-mriwarp_ offers to export the anatomical assignments together with linked multimodal data features like receptor densities, cell distributions or brain connectivity.",
"keywords": [
"neuroimaging",
"skull stripping",
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14 changes: 6 additions & 8 deletions README.md
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voluba (**Volu**metric **B**rain **A**nchoring) offers tools to connect volumetric imaging data to multilevel atlases and in this way makes it accessible for analysis with the siibra toolsuite.

_voluba-mriwarp_ is a desktop application that integrates whole brain T1-weighted MRI scans into the anatomical context of the [Julich Brain Atlas](https://julich-brain-atlas.de/). It incorporates all required components like skull stripping, registration to [MNI ICBM 152 2009c Nonlinear Asymmetric space](https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009), and detailed analysis with the siibra toolsuite. The corresponding functionalities are provided via open-source tools like [HD-BET](https://github.com/MIC-DKFZ/HD-BET)[^1], [ANTs](http://stnava.github.io/ANTs/) and [siibra-python](https://github.com/FZJ-INM1-BDA/siibra-python). _voluba-mriwarp_ is primarily designed for Windows 10 but can also be executed on Linux.

Warping brain data to a standardized space like MNI152 enables anchoring of whole brain MRI scans to atlas volumes like [BigBrain](https://julich-brain-atlas.de/atlas/bigbrain). However, reasonable registration requires various steps that need optimization effort. _voluba-mriwarp_ aims to simplify this workflow. With this application, you avoid installing multiple tools and tweaking parameters for a proper registration result. Instead, _voluba-mriwarp_ is an easy-to-install and easy-to-use tool combining all necessary steps into one pipeline.
_voluba-mriwarp_ is a desktop application that integrates whole-brain T1-weighted MRI scans into the anatomical context of the [EBRAINS Human Brain Atlas](https://www.ebrains.eu/tools/human-brain-atlas). It incorporates all required components like skull stripping, registration to [MNI ICBM 152 2009c Nonlinear Asymmetric space](https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009), and detailed analysis with the siibra toolsuite. The corresponding functionalities are provided via open-source tools like [HD-BET](https://github.com/MIC-DKFZ/HD-BET)[^1], [ANTs](http://stnava.github.io/ANTs/) and [siibra-python](https://github.com/FZJ-INM1-BDA/siibra-python). _voluba-mriwarp_ is primarily designed for Windows 10 but can also be executed on Linux.

> We designed _voluba-mriwarp_ as a desktop application. Therefore, **the input MRI dataset will not be uploaded to any online services**. It remains only on your local computer.
_voluba-mriwarp_ applies a set of predefined parameters to remove the skull and warp the input brain scan to MNI152 space. You can utilize the warping results in _voluba-mriwarp_ to interactively assign brain regions to a point in the input space. Select a location in the displayed brain of a subject to perform a probabilistic assignment using Julich-Brain Cytoarchitectonic Maps 2.9. Hence, you can estimate the probability of a brain region occurring at the selected point. To explore even more information about a cytoarchitectonic area, you can access [siibra-explorer](https://atlases.ebrains.eu/viewer/human) through the application.
Warping brain data to a standardized space like MNI152 enables anchoring of whole-brain MRI scans to atlas volumes and therefore facilitates analysis in a detailed anatomical context. However, reasonable registration requires various steps that need optimization effort. _voluba-mriwarp_ aims to simplify this workflow. With this application, you avoid installing multiple tools and tweaking parameters for a proper registration result. Instead, _voluba-mriwarp_ is an easy-to-install and easy-to-use tool combining all necessary steps into one pipeline.

_voluba-mriwarp_ applies a set of predefined parameters to remove the skull and warp the input brain scan to MNI152 space. You can utilize the warping results in _voluba-mriwarp_ to interactively analyze points by making a probabilistic assignment of coordinates in the input space to brain regions of the [EBRAINS Human Brain Atlas](https://www.ebrains.eu/tools/human-brain-atlas). To get an overview of more information about a brain region, you can access [siibra-explorer](https://atlases.ebrains.eu/viewer/human) through the application. For further analysis, _voluba-mriwarp_ offers to export the anatomical assignments together with linked multimodal data features like receptor densities, cell distributions or brain connectivity.

![image](docs/images/teaser.png)
![image](docs/images/teaser2.png)

## Getting Started

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#### Requirements

* Python 3.8 or higher
* [ANTs](https://github.com/ANTsX/ANTs/wiki/Compiling-ANTs-on-Linux-and-Mac-OS)
* [ANTs Eotapinoma](https://github.com/ANTsX/ANTs/releases/tag/v2.4.4)

#### Install voluba-mriwarp

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## Acknowledgments

This software code is funded from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 945539 (Human Brain Project SGA3).

![image](./data/hbp_ebrains_color_dark.png)

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