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Bernier M, Chamberland M, Houde JC, et al. Using fMRI non-local means denoising to uncover activation in sub-cortical structures at 1.5 T for guided HARDI tractography. Front Hum Neurosci. 2014;8:715doi: 10.3389/fnhum.2014.00715.
Bernier, M., Chamberland, M., Houde, J. C., Descoteaux, M., & Whittingstall, K. (2014). Using fMRI non-local means denoising to uncover activation in sub-cortical structures at 1.5 T for guided HARDI tractography. Frontiers in human neuroscience, 8715. https://doi.org/10.3389/fnhum.2014.00715
Bernier, Michaël, et al. "Using fMRI non-local means denoising to uncover activation in sub-cortical structures at 1.5 T for guided HARDI tractography." Frontiers in human neuroscience vol. 8 (2014): 715. doi: https://doi.org/10.3389/fnhum.2014.00715
Bernier M, Chamberland M, Houde JC, Descoteaux M, Whittingstall K. Using fMRI non-local means denoising to uncover activation in sub-cortical structures at 1.5 T for guided HARDI tractography. Front Hum Neurosci. 2014 Sep 11;8:715. doi: 10.3389/fnhum.2014.00715. eCollection 2014. PMID: 25309391; PMCID: PMC4160992.
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Front Hum Neurosci. 2014 Sep 11;8:715. doi: 10.3389/fnhum.2014.00715. eCollection 2014.

Using fMRI non-local means denoising to uncover activation in sub-cortical structures at 1.5 T for guided HARDI tractography.

Frontiers in human neuroscience

Michaël Bernier, Maxime Chamberland, Jean-Christophe Houde, Maxime Descoteaux, Kevin Whittingstall

Affiliations

  1. Department of Nuclear Medecine and Radiobiology, Faculty of Medicine and Health Science, University of Sherbrooke Sherbrooke, QC, Canada ; Department of Diagnostic Radiology, Faculty of Medicine and Health Science, University of Sherbrooke Sherbrooke, QC, Canada.
  2. Department of Nuclear Medecine and Radiobiology, Faculty of Medicine and Health Science, University of Sherbrooke Sherbrooke, QC, Canada.
  3. Computer Science Department, Faculty of Science, University of Sherbrooke Sherbrooke, QC, Canada.

PMID: 25309391 PMCID: PMC4160992 DOI: 10.3389/fnhum.2014.00715

Abstract

In recent years, there has been ever-increasing interest in combining functional magnetic resonance imaging (fMRI) and diffusion magnetic resonance imaging (dMRI) for better understanding the link between cortical activity and connectivity, respectively. However, it is challenging to detect and validate fMRI activity in key sub-cortical areas such as the thalamus, given that they are prone to susceptibility artifacts due to the partial volume effects (PVE) of surrounding tissues (GM/WM interface). This is especially true on relatively low-field clinical MR systems (e.g., 1.5 T). We propose to overcome this limitation by using a spatial denoising technique used in structural MRI and more recently in diffusion MRI called non-local means (NLM) denoising, which uses a patch-based approach to suppress the noise locally. To test this, we measured fMRI in 20 healthy subjects performing three block-based tasks : eyes-open closed (EOC) and left/right finger tapping (FTL, FTR). Overall, we found that NLM yielded more thalamic activity compared to traditional denoising methods. In order to validate our pipeline, we also investigated known structural connectivity going through the thalamus using HARDI tractography: the optic radiations, related to the EOC task, and the cortico-spinal tract (CST) for FTL and FTR. To do so, we reconstructed the tracts using functionally based thalamic and cortical ROIs to initiates seeds of tractography in a two-level coarse-to-fine fashion. We applied this method at the single subject level, which allowed us to see the structural connections underlying fMRI thalamic activity. In summary, we propose a new fMRI processing pipeline which uses a recent spatial denoising technique (NLM) to successfully detect sub-cortical activity which was validated using an advanced dMRI seeding strategy in single subjects at 1.5 T.

Keywords: HARDI; dMRI; denoising; fMRI; non-local means; seeding strategy; tractography

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