neuromaps plugin

Authors: Le Thuy Duong Nguyen, Raymundo Cassani

This tutorial introduces our approach for a user-friendly implementation of neuromaps into Brainstorm.

Introduction

The neuromaps plugin in Brainstorm integrates curated annotations and tools from neuromaps to further expand the accessibility and inclusivity of brain-mapping tools, as part of an Open Science initiative. Our goal is to extend these pioneering tools, which were offered exclusively in Python, to the Brainstorm MATLAB environment to provide researchers access to cutting-edge research without any prior computer programming experience, in an intuitive point-and-click user environment. As technological and data sharing advances have increasingly moved neuroscience research towards integrative questions rooted in data science, we believe that Open Science is most impactful when everyone is provided with equal access to the newest and greatest resources in the field.

The present tutorial will demonstrate the plugin’s functionality within the Brainstorm interface; for a detailed breakdown of the algorithm, please refer to the neuromaps plugin Github.

For this first iteration, we focused on the neurotransmitter receptors and transporters. Thirty different maps from the neuromaps toolbox were selected, covering nine different neurotransmitter systems: dopamine, norepinephrine, serotonin, acetylcholine, glutamate, GABA, histamine, cannabinoid, and opioid. These maps are sourced from open-access repositories, addressing the need for a comprehensive tool that integrates standardized analytic workflows for both surface and volumetric data.

Key Features

• Two different coordinate systems:

  • FsAverage for surface maps- the default system used by the FreeSurfer software (164k vertices per hemisphere).

  • The most common surface coordinate system is FreeSurfer fsaverage, which is obtained by spherical alignment of 40 participants (Fischl et al., 1999a, 1999b). As a surface template, FsAverage offers excellent representation of the cortical surface's intrinsic topological structure as well as multi-scale summary statistics of cortical geometry. It also has an inflated form, which facilitates data visualization.

  • MNI152 for volumetric maps- 152 normative MRI scans developed by the Montreal Neurological Institute (to be added soon).

• Flexible framework designed to accommodate future expansions and updates.

• Repository of precomputed annotations sourced from the published literature for both volumetric and surface systems, ensuring accessibility and ease of use.

• All the information for these maps, including the appropriate citations to use can be found in this spreadsheet.

• To obtain the surfaces, the original maps offered in MNI152 space were transformed to FsAverage using the registration fusion framework proposed in neuromaps (Buckner et al., 2011; Wu et al., 2018).

• Correlation processes that account for spatial autocorrelation

Installing and running the neuromaps plugin

Importing the brain annotations

Accessing annotation parameters

Statistical analyses for significance testing

Possible uses

Summary

Acknowledgements

• All credit for the conception of the original neuromaps algorithm is due to Ross D. Markello, Justine Y. Hansen, Zhen-Qi Liu, Vincent Bazinet, Golia Shafiei, Laura E. Suárez, Nadia Blostein, Jakob Seidlitz, Sylvain Baillet, Theodore D. Satterthwaite, M. Mallar Chakravarty, Armin Raznahan & Bratislav Misic. The appropriate citation for neuromaps is as follows:

• Markello, R.D., Hansen, J.Y., Liu, ZQ. et al. neuromaps: structural and functional interpretation of brain maps. Nat Methods 19, 1472–1479 (2022).

• If you used any of the included maps, please also cite the original papers that publish the data. References for each map can be found in this spreadsheet.

• If you used the surface maps which were transformed using the registration fusion framework, please also cite:

• Wu, J. et al. Accurate nonlinear mapping between MNI volumetric and FreeSurfer surface coordinate systems. Hum. Brain Mapp. 39, 3793–3808 (2018).

Contributing

We welcome contributions from the community to help improve and expand the functionality of the neuromaps plugin. Feel free to submit pull requests on the Github repository, report issues, or provide suggestions below! Your feedback is invaluable in ensuring a user-friendly experience for researchers worldwide. We believe that Open Science is most impactful when the countless everyone is provided with equal access to the newest and greatest resources in the field.