title: Assessment of data acquisition parameters, and analysis techniques for noise reduction in spinal cord fMRI data.
abstract: OBJECTIVE
  The purpose of this work is to characterize the noise in spinal cord functional MRI, assess current methods aimed at reducing noise, and optimize imaging parameters.
  
  
  METHODS
  Functional MRI data were acquired at multiple echo times and the contrast-to-noise ratio (CNR) was calculated. Independently, the repetition time was systematically varied with and without parallel imaging, to maximize BOLD sensitivity and minimize type I errors. Noise in the images was characterized by examining the frequency spectrum, and investigating whether autocorrelations exist. The efficacy of several physiological noise reduction methods in both null (no stimuli) and task (thermal pain paradigm) data was also assessed. Finally, our previous normalization methods were extended.
  
  
  RESULTS
  The echo time with the highest functional CNR at 3 Tesla is at roughly 75msec. Parallel imaging reduced the variance and the presence of autocorrelations, however the BOLD response in task data was more robust in data acquired without parallel imaging. Model-free based approaches further increased the detection of active voxels in the task data. Finally, inter-subject registration was improved.
  
  
  CONCLUSIONS
  Results from this study provide a rigorous characterization of the properties of the noise and assessment of data acquisition and analysis methods for spinal cord and brainstem fMRI.
authors.affiliation: Centre for Neuroscience Studies, Queen's University, Kingston, Ontario, Canada.
authors.forename: R L
authors.initials: RL
authors.lastname: Bosma
authors.affiliation: Centre for Neuroscience Studies, Queen's University, Kingston, Ontario, Canada. Electronic address: stromanp@queensu.ca.
authors.forename: P W
authors.initials: PW
authors.lastname: Stroman
mesh_terms: D000465:Algorithms; D016477:Artifacts; D005260:Female; D006801:Humans; D007089:Image Enhancement / Q000379:methods*; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D008279:Magnetic Resonance Imaging / Q000379:methods*; D008297:Male; D009434:Neural Pathways / Q000502:physiology; D058748:Pain Perception / Q000502:physiology*; D017288:Pain Threshold / Q000502:physiology*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D059629:Signal-To-Noise Ratio; D013116:Spinal Cord / Q000502:physiology*; D055815:Young Adult
keywords: Brainstem; Contrast-to-noise; False positives; Normalization; Spinal cord; fMRI