Phase stability in fMRI time series: Effect of noise regression, off-resonance correction and spatial filtering techniques

Gisela E. Hagberg, Marta Bianciardi, Valentina Brainovich, Antonino Mario Cassara, Bruno Maraviglia

Research output: Contribution to journalArticlepeer-review


Although the majority of fMRI studies exploit magnitude changes only, there is an increasing interest regarding the potential additive information conveyed by the phase signal. This integrated part of the complex number furnished by the MR scanners can also be used for exploring direct detection of neuronal activity and for thermography. Few studies have explicitly addressed the issue of the available signal stability in the context of phase time-series, and therefore we explored the spatial pattern of frequency specific phase fluctuations, and evaluated the effect of physiological noise components (heart beat and respiration) on the phase signal. Three categories of retrospective noise reduction techniques were explored and the temporal signal stability was evaluated in terms of a physiologic noise model, for seven fMRI measurement protocols in eight healthy subjects at 3T, for segmented CSF, gray and white matter voxels. We confirmed that for most processing methods, an efficient use of the phase information is hampered by the fact that noise from physiological and instrumental sources contributes significantly more to the phase than to the magnitude instability. Noise regression based on the phase evolution of the central k-space point, RETROICOR, or an orthonormalized combination of these were able to reduce their impact, but without bringing phase stability down to levels expected from the magnitude signal. Similar results were obtained after targeted removal of scan-to-scan variations in the bulk magnetic field by the dynamic off-resonance in k-space (DORK) method and by the temporal off-resonance alignment of single-echo time series technique (TOAST). We found that spatial high-pass filtering was necessary, and in vivo a Gaussian filter width of 20mm was sufficient to suppress physiological noise and bring the phase fluctuations to magnitude levels. Stronger filters brought the fluctuations down to levels dictated by thermal noise contributions, and for 62.5mm 3 voxels the phase stability was as low as 5mrad (0.27°). In conditions of low SNR o and high temporal sampling rate (short TR); we achieved an upper bound for the phase instabilities at 0.0017ppm, which is close to the dHb contribution to the GM/WM phase contrast.

Original languageEnglish
Pages (from-to)3748-3761
Number of pages14
Issue number4
Publication statusPublished - Feb 15 2012


  • Gradient echo EPI
  • Phase
  • Physiological noise
  • Retrospective correction
  • Time series

ASJC Scopus subject areas

  • Cognitive Neuroscience
  • Neurology


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