Journal: NeuroImage

Article Title: Searching Reproducible Brain Features using NeuroMark: Templates for Different Age Populations and Imaging Modalities

doi: 10.1016/j.neuroimage.2024.120617

Figure Lengend Snippet: List of NeuroMark Templates.

Article Snippet: We adopted the resting-state fMRI dataset from the human connectome project development (HCP-D, https://www.humanconnectome.org/study/hcp-lifespan-development ) to build the NeuroMark template for developmental studies (NeuroMark_fMRI_Develomental_3.0).

Techniques: Functional Assay, Diffusion-based Assay

Journal: Frontiers in Neuroscience

Article Title: Signal Fluctuation Sensitivity: An Improved Metric for Optimizing Detection of Resting-State fMRI Networks

doi: 10.3389/fnins.2016.00180

Figure Lengend Snippet: The dynamic phantom produces tightly controlled changes in functional MRI signal, establishing a ground truth for quantifying dynamic fidelity of scanner outputs to signal inputs. (A,B) The dynamic phantom uses concentric cylinders filled with agarose gels. The inner cylinder is coupled to an MRI-compatible pneumatic motor and fiber optic feedback system. (C) The inner cylinder is longitudinally compartmentalized into four chambers. One of two calibrated agarose gels with different concentrations is contained in each; the gels are in direct contact. The outer cylinder contains a single agarose gel. Because magnetic susceptibility changes as a function of agarose concentration, precisely timed rotation of the inner cylinder between images creates a “gradient” effect, in which different proportions of each agarose compartment pass through—and are averaged over—a region of interest. Motion across the “gradient” thus is capable of producing smooth dynamic changes in fMRI signal (bottom panel of C ). (D) The top two panels demonstrate “active” voxels within the inner cylinder of the phantom along the gel-gel interfaces; these voxels exhibit strong input-output fidelity. The bottom two panels show that the inactive outer cylinder and inactive inner cylinder voxels are indistinguishable. For validation of phantom performance, a simple event-related design is pictured in D. During the phantom scanning for SFS experiments, the phantom utilized a more complex input mimicking human resting-state fluctuations ( Figure 4A ).

Article Snippet: Resting-state fMRI protocols are easily standardized, require minimal patient compliance, and permit exploratory analyses; as such, they would appear to be well positioned for both clinical neurodiagnostics as well as large-scale international bio-repositories established for epidemiological research.

Techniques: Functional Assay, Agarose Gel Electrophoresis, Concentration Assay, Biomarker Discovery

Journal: Frontiers in Neuroscience

Article Title: Signal Fluctuation Sensitivity: An Improved Metric for Optimizing Detection of Resting-State fMRI Networks

doi: 10.3389/fnins.2016.00180

Figure Lengend Snippet: Dynamic phantom results show dynamic fidelity positively correlates with signal fluctuation sensitivity (SFS) and negatively correlates with classical temporal signal to noise ratio (tSNR). (A) To accurately mimic human resting-state fluctuations in the dynamic phantom, we utilized a complex pink-noise waveform as shown by the dotted line. The 10-min input function originated from our previous neuroimaging data and was subsequently programmed into the phantom. The dynamic phantom inputs are derived from position tracking during rotation. A representative output fMRI signal is superimposed ( fMRI Output axis), as acquired under Acquisition B: 3T magnet, 64 Channel head-coil, at TR = 1080 ms (see Table ). This waveform input was used for all nine phantom fMRI scans. (B) Input-output fidelity was positively correlated with SFS (median r = 0.67, see Table ) and negatively correlated with tSNR (median r = –0.63, see Table ). Groups presented here match the scanning parameters presented in the subsequent human data: acquisition A is a 3 Tesla magnet with a 32-channel headcoil ( TR = 2000 ms), acquisition B is a 3 Tesla magnet with a 64-channel headcoil ( TR = 1080 ms), and acquisition C is a 7 Tesla magnet with a 32-channel head coil ( TR = 802 ms). Table provides detailed acquisition parameters for each scan, while Table provides detailed results from all nine dynamic phantom scans.

Article Snippet: Resting-state fMRI protocols are easily standardized, require minimal patient compliance, and permit exploratory analyses; as such, they would appear to be well positioned for both clinical neurodiagnostics as well as large-scale international bio-repositories established for epidemiological research.

Techniques: Derivative Assay

Journal: Frontiers in Neuroscience

Article Title: Signal Fluctuation Sensitivity: An Improved Metric for Optimizing Detection of Resting-State fMRI Networks

doi: 10.3389/fnins.2016.00180

Figure Lengend Snippet: Local and long-range functional connectivity across the default mode network positively correlates with SFS and negatively correlates with tSNR. (A) We calculated SFS regional homogeneity (ReHo, a commonly used measure of neural synchrony in fMRI) for each individual subject across the medial prefrontal cortex ( mPFC ), posterior cingulate cortex ( PCC ), and right and left lateral parietal lobes ( RLP and LLP ). (B,C) Within-subject detection sensitivity for ReHo positively correlates with SFS and negatively correlates with tSNR (scatter plots shown for a single representative subject; group r for N = 36). (D) We see that the same pattern occurs for long-range connectivity between default mode network regions medial prefrontal cortex (mPFC) and posterior cingulate cortex (PCC) between subjects. As spatial smoothing artificially increases ReHo by producing correlations between contiguous voxels, shown data are unsmoothed.

Article Snippet: Resting-state fMRI protocols are easily standardized, require minimal patient compliance, and permit exploratory analyses; as such, they would appear to be well positioned for both clinical neurodiagnostics as well as large-scale international bio-repositories established for epidemiological research.

Techniques: Functional Assay