# FASB: an integrated processing pipeline for Functional Analysis of simultaneous Spinal cord-Brain fMRI

## TL;DR

A new pipeline called FASB improves spinal cord and brain fMRI processing, enabling better analysis of sensory and motor pathways in humans.

## Contribution

FASB introduces an optimized acquisition protocol and processing pipeline for spinal cord-brain fMRI, with novel methods for handling low tSNR spinal voxels.

## Key findings

- FASB outperforms existing methods in motion correction, registration accuracy, and detection power in group-level analysis.
- FASB identifies task-based activations in sensorimotor networks across the central nervous system during a handgrip task.
- Significant functional connectivity is observed between brain regions and cervical spinal cord dorsal and ventral horns during the task.

## Abstract

Simultaneous functional magnetic resonance imaging (fMRI) of the spinal cord and brain represents a powerful method for examining both ascending sensory and descending motor pathways in humans
in vivo
. However, its image acquisition protocols, and processing pipeline are less well established. This limitation is mainly due to technical difficulties related to spinal cord fMRI, and problems with the logistics stemming from a large field of view covering both brain and cervical cord. Here, we propose an acquisition protocol optimized for both anatomical and functional images, as well as an optimized integrated image processing pipeline, which consists of a novel approach for automatic modeling and mitigating the negative impact of spinal voxels with low temporal signal to noise ratio (tSNR). We validate our integrated pipeline, named FASB, using simultaneous fMRI data acquired during the performance of a motor task, as well as during resting-state conditions. We demonstrate that FASB outperforms the current spinal fMRI processing methods in three domains, including motion correction, registration to the spinal cord template, and improved detection power of the group-level analysis by removing the effects of participant-specific low tSNR voxels, typically observed at the disk level. Using FASB, we identify significant task-based activations in the expected sensorimotor network associated with a unilateral handgrip force production task across the entire central nervous system, including the contralateral sensorimotor cortex, thalamus, striatum, cerebellum, brainstem, as well as ipsilateral ventral horn at C5-C8 cervical levels. Additionally, our results show significant task-based functional connectivity between the key sensory and motor brain areas and the dorsal and ventral horns of the cervical cord. Overall, our proposed acquisition protocol and processing pipeline provide a robust method for characterizing the activation and functional connectivity of distinct cortical, subcortical, brainstem and spinal cord regions in humans.