title: Optimal compressed sensing reconstructions of fMRI using 2D deterministic and stochastic sampling geometries.
abstract: BACKGROUND
  Compressive sensing can provide a promising framework for accelerating fMRI image acquisition by allowing reconstructions from a limited number of frequency-domain samples. Unfortunately, the majority of compressive sensing studies are based on stochastic sampling geometries that cannot guarantee fast acquisitions that are needed for fMRI. The purpose of this study is to provide a comprehensive optimization framework that can be used to determine the optimal 2D stochastic or deterministic sampling geometry, as well as to provide optimal reconstruction parameter values for guaranteeing image quality in the reconstructed images.
  
  
  METHODS
  We investigate the use of frequency-space (k-space) sampling based on: (i) 2D deterministic geometries of dyadic phase encoding (DPE) and spiral low pass (SLP) geometries, and (ii) 2D stochastic geometries based on random phase encoding (RPE) and random samples on a PDF (RSP). Overall, we consider over 36 frequency-sampling geometries at different sampling rates. For each geometry, we compute optimal reconstructions of single BOLD fMRI ON & OFF images, as well as BOLD fMRI activity maps based on the difference between the ON and OFF images. We also provide an optimization framework for determining the optimal parameters and sampling geometry prior to scanning.
  
  
  RESULTS
  For each geometry, we show that reconstruction parameter optimization converged after just a few iterations. Parameter optimization led to significant image quality improvements. For activity detection, retaining only 20.3% of the samples using SLP gave a mean PSNR value of 57.58 dB. We also validated this result with the use of the Structural Similarity Index Matrix (SSIM) image quality metric. SSIM gave an excellent mean value of 0.9747 (max = 1). This indicates that excellent reconstruction results can be achieved. Median parameter values also gave excellent reconstruction results for the ON/OFF images using the SLP sampling geometry (mean SSIM > =0.93). Here, median parameter values were obtained using mean-SSIM optimization. This approach was also validated using leave-one-out.
  
  
  CONCLUSIONS
  We have found that compressive sensing parameter optimization can dramatically improve fMRI image reconstruction quality. Furthermore, 2D MRI scanning based on the SLP geometries consistently gave the best image reconstruction results. The implication of this result is that less complex sampling geometries will suffice over random sampling. We have also found that we can obtain stable parameter regions that can be used to achieve specific levels of image reconstruction quality when combined with specific k-space sampling geometries. Furthermore, median parameter values can be used to obtain excellent reconstruction results.
authors.affiliation: Department of Electrical and Computer Engineering, University of New Mexico, Albuquerque, NM 87131, USA.
authors.forename: Oliver
authors.initials: O
authors.lastname: Jeromin
authors.forename: Marios S
authors.initials: MS
authors.lastname: Pattichis
authors.forename: Vince D
authors.initials: VD
authors.lastname: Calhoun
mesh_terms: D000465:Algorithms; D001921:Brain / Q000502:physiology*; D001931:Brain Mapping / Q000379:methods*; D044962:Data Compression / Q000379:methods*; D003627:Data Interpretation, Statistical; D005071:Evoked Potentials / Q000502:physiology*; D006801:Humans; D007089:Image Enhancement / Q000379:methods*; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D008279:Magnetic Resonance Imaging / Q000379:methods*; D018401:Sample Size; D013269:Stochastic Processes