Professional Education

  • Bachelor of Science, Stanford University, EE-BS (2008)
  • Bachelor of Science, Stanford University, BIOL-BSH (2008)
  • Doctor of Philosophy, Massachusetts Institute of Technology (2014)

Stanford Advisors


All Publications

  • Fast quantitative susceptibility mapping using 3D EPI and total generalized variation NEUROIMAGE Langkammer, C., Bredies, K., Poser, B. A., Barth, M., Reishofer, G., Fan, A. P., Bilgic, B., Fazekas, F., Mainero, C., Ropele, S. 2015; 111: 622-630


    Quantitative susceptibility mapping (QSM) allows new insights into tissue composition and organization by assessing its magnetic property. Previous QSM studies have already demonstrated that magnetic susceptibility is highly sensitive to myelin density and fiber orientation as well as to para- and diamagnetic trace elements. Image resolution in QSM with current approaches is limited by the long acquisition time of 3D scans and the need for high signal to noise ratio (SNR) to solve the dipole inversion problem. We here propose a new total-generalized-variation (TGV) based method for QSM reconstruction, which incorporates individual steps of phase unwrapping, background field removal and dipole inversion in a single iteration, thus yielding a robust solution to the reconstruction problem. This approach has beneficial characteristics for low SNR data, allowing for phase data to be rapidly acquired with a 3D echo planar imaging (EPI) sequence. The proposed method was evaluated with a numerical phantom and in vivo at 3 and 7 T. Compared to total variation (TV), TGV-QSM enforced higher order smoothness which yielded solutions closer to the ground truth and prevented stair-casing artifacts. The acquisition time for images with 1mm isotropic resolution and whole brain coverage was 10s on a clinical 3 Tesla scanner. In conclusion, 3D EPI acquisition combined with single-step TGV reconstruction yields reliable QSM images of the entire brain with 1mm isotropic resolution in seconds. The short acquisition time combined with the robust reconstruction may enable new QSM applications in less compliant populations, clinical susceptibility tensor imaging, and functional resting state examinations.

    View details for DOI 10.1016/j.neuroimage.2015.02.041

    View details for Web of Science ID 000352224100054

    View details for PubMedID 25731991

  • Regional quantification of cerebral venous oxygenation from MRI susceptibility during hypercapnia NEUROIMAGE Fan, A. P., Evans, K. C., Stout, J. N., Rosen, B. R., Adalsteinsson, E. 2015; 104: 146-155


    There is an unmet medical need for noninvasive imaging of regional brain oxygenation to manage stroke, tumor, and neurodegenerative diseases. Oxygenation imaging from magnetic susceptibility in MRI is a promising new technique to measure local venous oxygen extraction fraction (OEF) along the cerebral venous vasculature. However, this approach has not been tested in vivo at different levels of oxygenation. The primary goal of this study was to test whether susceptibility imaging of oxygenation can detect OEF changes induced by hypercapnia, via CO2 inhalation, within selected a priori brain regions. Ten healthy subjects were scanned at 3T with a 32-channel head coil. The end-tidal CO2 (ETCO2) was monitored continuously and inspired gases were adjusted to achieve steady-state conditions of eucapnia (413mmHg) and hypercapnia (504mmHg). Gradient echo phase images and pseudo-continuous arterial spin labeling (pcASL) images were acquired to measure regional OEF and CBF respectively during eucapnia and hypercapnia. By assuming constant cerebral oxygen consumption throughout both gas states, regional CBF values were computed to predict the local change in OEF in each brain region. Hypercapnia induced a relative decrease in OEF of -42.3% in the straight sinus, -39.9% in the internal cerebral veins, and approximately -50% in pial vessels draining each of the occipital, parietal, and frontal cortical areas. Across volunteers, regional changes in OEF correlated with changes in ETCO2. The reductions in regional OEF (via phase images) were significantly correlated (P<0.05) with predicted reductions in OEF derived from CBF data (via pcASL images). These findings suggest that susceptibility imaging is a promising technique for OEF measurements, and may serve as a clinical biomarker for brain conditions with aberrant regional oxygenation.

    View details for DOI 10.1016/j.neuroimage.2014.09.068

    View details for Web of Science ID 000345393800015

    View details for PubMedID 25300201

  • Quantitative oxygen extraction fraction from 7-Tesla MRI phase: reproducibility and application in multiple sclerosis JOURNAL OF CEREBRAL BLOOD FLOW AND METABOLISM Fan, A. P., Govindarajan, S. T., Kinkel, R. P., Madigan, N. K., Nielsen, A. S., Benner, T., Tinelli, E., Rosen, B. R., Adalsteinsson, E., Mainero, C. 2015; 35 (1): 131-139


    Quantitative oxygen extraction fraction (OEF) in cortical veins was studied in patients with multiple sclerosis (MS) and healthy subjects via magnetic resonance imaging (MRI) phase images at 7 Tesla (7 T). Flow-compensated, three-dimensional gradient-echo scans were acquired for absolute OEF quantification in 23 patients with MS and 14 age-matched controls. In patients, we collected T2*-weighted images for characterization of white matter, deep gray matter, and cortical lesions, and also assessed cognitive function. Variability of OEF across readers and scan sessions was evaluated in a subset of volunteers. OEF was averaged from 2 to 3 pial veins in the sensorimotor, parietal, and prefrontal cortical regions for each subject (total of ~10 vessels). We observed good reproducibility of mean OEF, with intraobserver coefficient of variation (COV)=2.1%, interobserver COV=5.2%, and scan-rescan COV=5.9%. Patients exhibited a 3.4% reduction in cortical OEF relative to controls (P=0.0025), which was not different across brain regions. Although oxygenation did not relate with measures of structural tissue damage, mean OEF correlated with a global measure of information processing speed. These findings suggest that cortical OEF from 7-T MRI phase is a reproducible metabolic biomarker that may be sensitive to different pathologic processes than structural MRI in patients with MS.

    View details for DOI 10.1038/jcbfm.2014.187

    View details for Web of Science ID 000347392200016

    View details for PubMedID 25352043

  • Fast Quantitative Susceptibility Mapping with L1-Regularization and Automatic Parameter Selection MAGNETIC RESONANCE IN MEDICINE Bilgic, B., Fan, A. P., Polimeni, J. R., Cauley, S. F., Bianciardi, M., Adalsteinsson, E., Wald, L. L., Setsompop, K. 2014; 72 (5): 1444-1459


    To enable fast reconstruction of quantitative susceptibility maps with total variation penalty and automatic regularization parameter selection.?(1) -Regularized susceptibility mapping is accelerated by variable splitting, which allows closed-form evaluation of each iteration of the algorithm by soft thresholding and fast Fourier transforms. This fast algorithm also renders automatic regularization parameter estimation practical. A weighting mask derived from the magnitude signal can be incorporated to allow edge-aware regularization.Compared with the nonlinear conjugate gradient (CG) solver, the proposed method is 20 times faster. A complete pipeline including Laplacian phase unwrapping, background phase removal with SHARP filtering, and ?(1) -regularized dipole inversion at 0.6 mm isotropic resolution is completed in 1.2 min using MATLAB on a standard workstation compared with 22 min using the CG solver. This fast reconstruction allows estimation of regularization parameters with the L-curve method in 13 min, which would have taken 4 h with the CG algorithm. The proposed method also permits magnitude-weighted regularization, which prevents smoothing across edges identified on the magnitude signal. This more complicated optimization problem is solved 5 times faster than the nonlinear CG approach. Utility of the proposed method is also demonstrated in functional blood oxygen level-dependent susceptibility mapping, where processing of the massive time series dataset would otherwise be prohibitive with the CG solver.Online reconstruction of regularized susceptibility maps may become feasible with the proposed dipole inversion.

    View details for DOI 10.1002/mrm.25029

    View details for Web of Science ID 000343873900026

    View details for PubMedID 24259479

  • Quantitative Oxygenation Venography from MRI Phase MAGNETIC RESONANCE IN MEDICINE Fan, A. P., Bilgic, B., Gagnon, L., Witzel, T., Bhat, H., Rosen, B. R., Adalsteinsson, E. 2014; 72 (1): 149-159


    To demonstrate acquisition and processing methods for quantitative oxygenation venograms that map in vivo oxygen saturation (SvO2 ) along cerebral venous vasculature.Regularized quantitative susceptibility mapping (QSM) is used to reconstruct susceptibility values and estimate SvO2 in veins. QSM with ?1 and ?2 regularization are compared in numerical simulations of vessel structures with known magnetic susceptibility. Dual-echo, flow-compensated phase images are collected in three healthy volunteers to create QSM images. Bright veins in the susceptibility maps are vectorized and used to form a three-dimensional vascular mesh, or venogram, along which to display SvO2 values from QSM.Quantitative oxygenation venograms that map SvO2 along brain vessels of arbitrary orientation and geometry are shown in vivo. SvO2 values in major cerebral veins lie within the normal physiological range reported by (15) O positron emission tomography. SvO2 from QSM is consistent with previous MR susceptometry methods for vessel segments oriented parallel to the main magnetic field. In vessel simulations, ?1 regularization results in less than 10% SvO2 absolute error across all vessel tilt orientations and provides more accurate SvO2 estimation than ?2 regularization.The proposed analysis of susceptibility images enables reliable mapping of quantitative SvO2 along venograms and may facilitate clinical use of venous oxygenation imaging.

    View details for DOI 10.1002/mrm.24918

    View details for Web of Science ID 000337624400017

    View details for PubMedID 24006229

  • Phase-based regional oxygen metabolism (PROM) using MRI MAGNETIC RESONANCE IN MEDICINE Fan, A. P., Benner, T., Bolar, D. S., Rosen, B. R., Adalsteinsson, E. 2012; 67 (3): 669-678


    Venous oxygen saturation (Y(v) ) in cerebral veins and the cerebral metabolic rate of oxygen (CMRO(2)) are important indicators for brain function and disease. Although MRI has been used for global measurements of these parameters, currently there is no recognized technique to quantify regional Y(v) and CMRO(2) using noninvasive imaging. This article proposes a technique to quantify CMRO(2) from independent MRI estimates of Y(v) and cerebral blood flow. The approach uses standard gradient-echo and arterial spin labeling acquisitions to make these measurements. Using MR susceptometry on gradient-echo phase images, Y(v) was quantified for candidate vein segments in gray matter that approximate a long cylinder parallel to the main magnetic field. Local cerebral blood flow for the identified vessel was determined from a corresponding region in the arterial spin labeling perfusion map. Fick's principle of arteriovenous difference was then used to quantify CMRO(2) locally around each vessel. Application of this method in young, healthy subjects provided gray matter averages of 59.6% 2.3% for Y(v), 51.7 6.4 mL/100 g/min for cerebral blood flow, and 158 18 ?mol/100 g/min for CMRO(2) (mean SD, n = 12), which is consistent with values previously reported by positron emission tomography and MRI.

    View details for DOI 10.1002/mrm.23050

    View details for Web of Science ID 000300683900011

    View details for PubMedID 21713981

  • MicroRNA Processing Pathway Regulates Olfactory Neuron Morphogenesis CURRENT BIOLOGY Berdnik, D., Fan, A. P., Potter, C. J., Luo, L. 2008; 18 (22): 1754-1759


    The microRNA (miRNA) processing pathway produces miRNAs as posttranscriptional regulators of gene expression. The nuclear RNase III Drosha catalyzes the first processing step together with the dsRNA binding protein DGCR8/Pasha generating pre-miRNAs [1, 2]. The next cleavage employs the cytoplasmic RNase III Dicer producing miRNA duplexes [3, 4]. Finally, Argonautes are recruited with miRNAs into an RNA-induced silencing complex for mRNA recognition (Figure 1A). Here, we identify two members of the miRNA pathway, Pasha and Dicer-1, in a forward genetic screen for mutations that disrupt wiring specificity of Drosophila olfactory projection neurons (PNs). The olfactory system is built as discrete map of highly stereotyped neuronal connections [5, 6]. Each PN targets dendrites to a specific glomerulus in the antennal lobe and projects axons stereotypically into higher brain centers [7-9]. In selected PN classes, pasha and Dicer-1 mutants cause specific PN dendrite mistargeting in the antennal lobe and altered axonal terminations in higher brain centers. Furthermore, Pasha and Dicer-1 act cell autonomously in postmitotic neurons to regulate dendrite and axon targeting during development. However, Argonaute-1 and Argonaute-2 are dispensable for PN morphogenesis. Our findings suggest a role for the miRNA processing pathway in establishing wiring specificity in the nervous system.

    View details for DOI 10.1016/j.cub.2008.09.045

    View details for Web of Science ID 000261244800025

    View details for PubMedID 19013069

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