Biology subjects

Pinho, A. L.

Publications and source records attributed to Pinho, A. L..

3 recordsLinked to original sources

bioRxiv2026

SUITPy: A Python-based toolbox for the analysis of cerebellar functional and anatomical imaging data across the human lifespan

The human cerebellum plays a central role in motor, emotional, and cognitive functions, and is implicated in many brain disorders. To improve the analysis of functional and anatomical imaging from the cerebellum, we introduce SUITPy, an improved and fully revised Python implementation of the widely used SUIT toolbox. For this new version, we developed a U-Net based model to automatically isolate the cerebellum from adjacent cortical tissue, which achieves higher fidelity than existing algorithms. The isolation works robustly without manual corrections for imaging data across the lifespan. We show that isolation and subsequent normalization to a cerebellum-only template lead to a more precise alignment of cerebellar structures across participants compared to normalization using a whole-brain template. We also show the utility of the cerebellar mask to prevent contamination of cerebellar functional data from surrounding cortical structures. The toolbox also provides functionality for visualizing cerebellar data on a flatmap, along with a range of anatomical and functional cerebellar atlases, thereby offering an essential tool that enables accurate cerebellar analysis across the lifespan.

neuroscience↗

bioRxiv2024

A network correspondence toolbox for quantitative evaluation of novel neuroimaging results

Decades of neuroscience research has shown that macroscale brain dynamics can be reliably decomposed into a subset of large-scale functional networks, but the specific spatial topographies of these networks and the names used to describe them can vary across studies. Such discordance has hampered interpretation and convergence of research findings across the field. To address this problem, we have developed the Network Correspondence Toolbox (NCT) to permit researchers to examine and report spatial correspondence between their novel neuroimaging results and sixteen widely used functional brain atlases, consistent with recommended reporting standards developed by the Organization for Human Brain Mapping. The atlases included in the toolbox show some topographical convergence for specific networks, such as those labeled as "default" or "visual". Network naming varies across atlases, particularly for networks spanning frontoparietal association cortices. For this reason, quantitative comparison with multiple atlases is recommended to benchmark novel neuroimaging findings. We provide several exemplar demonstrations using the Human Connectome Project task fMRI results and UK Biobank independent component analysis maps to illustrate how researchers can use the NCT to report their own findings through quantitative evaluation against multiple published atlases. The NCT provides a convenient means for computing Dice coefficients with spin test permutations to determine the magnitude and statistical significance of correspondence among user-defined maps and existing atlas labels. The NCT also includes functionality to incorporate additional atlases in the future. The adoption of the NCT will make it easier for network neuroscience researchers to report their findings in a standardized manner, thus aiding reproducibility and facilitating comparisons between studies to produce interdisciplinary insights.

neuroscience↗

bioRxiv2023

A hierarchical Bayesian brain parcellation framework for fusion of functional imaging datasets

One important barrier in the development of complex models of human brain organization is the lack of a large and comprehensive task-based neuro-imaging dataset. Therefore, current atlases of functional brain organization are mainly based on single and homogeneous resting-state datasets. Here, we propose a hierarchical Bayesian framework that can learn a probabilistically defined brain parcellation across numerous task-based and resting-state datasets, exploiting their combined strengths. The framework is partitioned into a spatial arrangement model that defines the probability of a specific individual brain parcellation, and a set of dataset-specific emission models that defines the probability of the observed data given the individual brain organization. We show that the framework optimally combines information from different datasets to achieve a new population-based atlas of the human cerebellum. Furthermore, we demonstrate that, using only 10 min of individual data, the framework is able to generate individual brain parcellations that outperform group atlases.

neuroscience↗