Dataset Information

Micapipe: A pipeline for multimodal neuroimaging and connectome analysis.

ABSTRACT: Multimodal magnetic resonance imaging (MRI) has accelerated human neuroscience by fostering the analysis of brain microstructure, geometry, function, and connectivity across multiple scales and in living brains. The richness and complexity of multimodal neuroimaging, however, demands processing methods to integrate information across modalities and to consolidate findings across different spatial scales. Here, we present micapipe, an open processing pipeline for multimodal MRI datasets. Based on BIDS-conform input data, micapipe can generate i) structural connectomes derived from diffusion tractography, ii) functional connectomes derived from resting-state signal correlations, iii) geodesic distance matrices that quantify cortico-cortical proximity, and iv) microstructural profile covariance matrices that assess inter-regional similarity in cortical myelin proxies. The above matrices can be automatically generated across established 18 cortical parcellations (100-1000 parcels), in addition to subcortical and cerebellar parcellations, allowing researchers to replicate findings easily across different spatial scales. Results are represented on three different surface spaces (native, conte69, fsaverage5), and outputs are BIDS-conform. Processed outputs can be quality controlled at the individual and group level. micapipe was tested on several datasets and is available at https://github.com/MICA-MNI/micapipe, documented at https://micapipe.readthedocs.io/, and containerized as a BIDS App http://bids-apps.neuroimaging.io/apps/. We hope that micapipe will foster robust and integrative studies of human brain microstructure, morphology, function, cand connectivity.

SUBMITTER: Cruces RR

PROVIDER: S-EPMC10697132 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature

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Micapipe: A pipeline for multimodal neuroimaging and connectome analysis.

Cruces Raúl R RR Royer Jessica J Herholz Peer P Larivière Sara S Vos de Wael Reinder R Paquola Casey C Benkarim Oualid O Park Bo-Yong BY Degré-Pelletier Janie J Nelson Mark C MC DeKraker Jordan J Leppert Ilana R IR Tardif Christine C Poline Jean-Baptiste JB Concha Luis L Bernhardt Boris C BC

NeuroImage 20220905

Multimodal magnetic resonance imaging (MRI) has accelerated human neuroscience by fostering the analysis of brain microstructure, geometry, function, and connectivity across multiple scales and in living brains. The richness and complexity of multimodal neuroimaging, however, demands processing methods to integrate information across modalities and to consolidate findings across different spatial scales. Here, we present micapipe, an open processing pipeline for multimodal MRI datasets. Based on ...[more]

PMID: 36070839

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Project description:Recent advancements of multimodal neuroimaging such as functional MRI (fMRI) and diffusion MRI (dMRI) offers unprecedented opportunities to understand brain development. Most existing neurodevelopmental studies focus on using a single imaging modality to study microstructure or neural activations in localized brain regions. The developmental changes of brain network architecture in childhood and adolescence are not well understood. Our study made use of dMRI and resting-state fMRI imaging data sets from Philadelphia Neurodevelopmental Cohort (PNC) study to characterize developmental changes in both structural as well as functional brain connectomes. A multimodal multilevel model (MMM) is developed and implemented in PNC study to investigate brain maturation in both white matter structural connection and intrinsic functional connection. MMM addresses several major challenges in multimodal connectivity analysis. First, by using a first-level data generative model for observed measures and a second-level latent network modeling, MMM effectively infers underlying connection states from noisy imaging-based connectivity measurements. Secondly, MMM models the interplay between the structural and functional connections to capture the relationship between different brain connectomes. Thirdly, MMM incorporates covariate effects in the network modeling to investigate network heterogeneity across subpopoulations. Finally, by using a module-wise parameterization based on brain network topology, MMM is scalable to whole-brain connectomics. MMM analysis of the PNC study generates new insights in neurodevelopment during adolescence including revealing the majority of the white fiber connectivity growth are related to the cognitive networks where the most significant increase is found between the default mode and the executive control network with a 15% increase in the probability of structural connections. We also uncover functional connectome development mainly derived from global functional integration rather than direct anatomical connections. To the best of our knowledge, these findings have not been reported in the literature using multimodal connectomics. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.

Dataset Information

Micapipe: A pipeline for multimodal neuroimaging and connectome analysis.

Publications

Micapipe: A pipeline for multimodal neuroimaging and connectome analysis.

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