fMRI goes individual

Spatiotemporal multiscale ICA could invariantly extract task (motor) modes from wavelet subbands of fMRI data

BACKGROUND AND OBJECTIVE

. Given a timeseries of task-evoked functional MRI (fMRI) images (4D spatiotemporal data), we can extract the task mode by statistical independent component analysis (ICA). If the 4D data are spatiotemporally decomposed into subbands (multiresolutions in both time and space), is ICA still capable of extracting the task modes at multiscales? We answer this question using the well-established fingertapping motor-task experiments at 3T and 7T. The positive answer informs that a brain task is spatiotemporal separable at ICA decomposition and shift invariant at multiscales during activation over a finite region.

METHODS

. We collected a set of task fMRI datasets from sixteen subjects performing fingertapping at 3T and one single dataset from a different subject at 7T. For each 4D fMRI dataset, we first performed temporal wavelet transform (1D WT) at 3 levels using different wavelets (e.g. 'db1','db2', and 'sym4'), then extracted the task modes from the WT subbands via ICA (as called multi-timescale ICA). Meanwhile, we also performed task mode extraction by applying ICA to 3D spatial WT subbands (as called multi-spacescale ICA). Upon the multiscale ICA results, we identified the primary motor task modes in the motor cortex, in comparison to the raw fMRI data analysis (at level 0).

RESULTS

. In the 7T experiment, the multiscale ICA across 3 timescale levels and 2 spacescale levels could extract the primary task modes at a tasktcorr of 0.90 and 0.86, respectively, compared to 0.87 for the ICA task extraction from raw data. In the 3T experiment, the multiscale could extract the primary task mode with 0.92 and 0.91, while the ICA task extraction from raw data was 0.91.

CONCLUSION

. ICA could extract the primary motor task modes from wavelet-decomposed multi-timescale and multi-spacescale subbands, construing the broad spatial activation (extent >>voxel size) of the brain motor task performed in a long duration (>>TR). Our experimental results show the brain functional activity signal is spatiotemporal separable as well as shift invariant at multiscales in both time and space.

Computed inverse MRI (CIMRI) for intrinsic brain magnetic susceptibility mapping

In magnetic resonance imaging (MRI), tissue magnetization in the main field B₀ is a necessary preparation for magnetic resonance signal formation that imposes an inherent dipole effect on MRI signals, which predisposes an artifact on tissue MRI. In the MRI principle, T2*-weighted MRI can be described by a cascade of data transformations: from the source of tissue magnetic susceptibility (denoted by χ) to the output of complex-valued T2* image (in a magnitude and phase pair). Under the linear approximation of the T2* phase MRI, we can computationally reconstruct the source χ by quantitative susceptibility mapping (QSM), which is an inverse solution that is modeled by computed inverse MRI (CIMRI). For a brain function study using MRI (fMRI), we can reconstruct a timeseries of brain χ images to represent the intrinsic brain function activity called functional QSM (fQSM). This intrinsic depiction is defined as the removal of the artifactual dipole effect and other MRI-introduced distortions from phase data through inverse mapping. With one high-resolution QSM experiment and one group (20 subjects) low-resolution fQSM experiment, we show that the dipole effect manifests as ripples around vessels and a spatial split at a local activation blob and that the dipole effect could be removed by CIMRI. In the context of inverse imaging or undoing MRI transformations (including dipole convolution), we computationally achieve brain intrinsic structural depiction by QSM and intrinsic functional depiction by fQSM.

Optimising neonatal fMRI data analysis: Design and validation of an extended dHCP preprocessing pipeline to characterise noxious-evoked brain activity in infants

The infant brain is unlike the adult brain, with considerable differences in morphological, neurodynamic, and haemodynamic features. As the majority of current MRI analysis tools were designed for use in adults, a primary objective of the Developing Human Connectome Project (dHCP) is to develop optimised methodological pipelines for the analysis of neonatal structural, resting state, and diffusion MRI data. Here, in an independent neonatal dataset we have extended and optimised the dHCP fMRI preprocessing pipeline for the analysis of stimulus-response fMRI data. We describe and validate this extended dHCP fMRI preprocessing pipeline to analyse changes in brain activity evoked following an acute noxious stimulus applied to the infant's foot. We compare the results obtained from this extended dHCP pipeline to results obtained from a typical FSL FEAT-based analysis pipeline, evaluating the pipelines' outputs using a wide range of tests. We demonstrate that a substantial increase in spatial specificity and sensitivity to signal can be attained with a bespoke neonatal preprocessing pipeline through optimised motion and distortion correction, ICA-based denoising, and haemodynamic modelling. The improved sensitivity and specificity, made possible with this extended dHCP pipeline, will be paramount in making further progress in our understanding of the development of sensory processing in the infant brain.

Effect of Spatial Smoothing on Task fMRI ICA and Functional Connectivity

Spatial smoothing is a widely used preprocessing step in functional magnetic resonance imaging (fMRI) data analysis. In this work, we report on the spatial smoothing effect on task-evoked fMRI brain functional mapping and functional connectivity. Initially, we decomposed the task fMRI data into a collection of components or networks by independent component analysis (ICA). The designed task paradigm helps identify task-modulated ICA components (highly correlated with the task stimuli). For the ICA-extracted primary task component, we then measured the task activation volume at the task response foci. We used the task timecourse (designed) as a reference to order the ICA components according to the task correlations of the ICA timecourses. With the re-ordered ICA components, we calculated the inter-component function connectivity (FC) matrix (correlations among the ICA timecourses). By repeating the spatial smoothing of fMRI data with a Gaussian smoothing kernel with a full width at half maximum (FWHM) of {1, 3, 6, 9, 12, 15, 20, 25, 30, 35} mm, we measured the spatial smoothing effects. Our results show spatial smoothing reveals the following effects: (1) It decreases the task extraction performance of single-subject ICA more than that of multi-subject ICA; (2) It increases the task volume of multi-subject ICA more than that of single-subject ICA; (3) It strengthens the functional connectivity of single-subject ICA more than that of multi-subject ICA; and (4) It impacts the positive-negative imbalance of single-subject ICA more than that of multi-subject ICA. Our experimental results suggest a 2~3 voxel FWHM spatial smoothing for single-subject ICA in achieving an optimal balance of functional connectivity, and a wide range (2~5 voxels) of FWHM for multi-subject ICA.

Brain functional BOLD perturbation modelling for forward fMRI and inverse mapping

Purpose

To computationally separate dynamic brain functional BOLD responses from static background in a brain functional activity for forward fMRI signal analysis and inverse mapping.

Methods

A brain functional activity is represented in terms of magnetic source by a perturbation model: χ = χ₀ +δχ, with δχ for BOLD magnetic perturbations and χ₀ for background. A brain fMRI experiment produces a timeseries of complex-valued images (T2* images), whereby we extract the BOLD phase signals (denoted by δP) by a complex division. By solving an inverse problem, we reconstruct the BOLD δχ dataset from the δP dataset, and the brain χ distribution from a (unwrapped) T2* phase image. Given a 4D dataset of task BOLD fMRI, we implement brain functional mapping by temporal correlation analysis.

Results

Through a high-field (7T) and high-resolution (0.5mm in plane) task fMRI experiment, we demonstrated in detail the BOLD perturbation model for fMRI phase signal separation (P + δP) and reconstructing intrinsic brain magnetic source (χ and δχ). We also provided to a low-field (3T) and low-resolution (2mm) task fMRI experiment in support of single-subject fMRI study. Our experiments show that the δχ-depicted functional map reveals bidirectional BOLD χ perturbations during the task performance.

Conclusions

The BOLD perturbation model allows us to separate fMRI phase signal (by complex division) and to perform inverse mapping for pure BOLD δχ reconstruction for intrinsic functional χ mapping. The full brain χ reconstruction (from unwrapped fMRI phase) provides a new brain tissue image that allows to scrutinize the brain tissue idiosyncrasy for the pure BOLD δχ response through an automatic function/structure co-localization.