Biology subjects

Ganji, S.

Publications and source records attributed to Ganji, S..

3 recordsLinked to original sources

bioRxiv2026

Real-time AI integration for MR to detect artifacts and guide pulse sequence adaptations

This work presents a first-of-its-kind artificial intelligence (AI-)integrated MR pulse sequence that detects out-of-voxel (OOV) artifacts in real-time (within-TR) and responds prospectively by updating the crusher gradient scheme. Per Excitation Real-time Execution & Guided Responses with Integrated Neural-network Evaluation (PEREGRINE), allows for deployment of deep learning models and pulse sequence updates. In this study, PEREGRINE operated a time-domain (TD) and frequency-domain (FD) convolutional autoencoder that detect OOV artifacts. Scans without (AI-off) and with (AI-on) updates were collected from the medial prefrontal cortex of healthy volunteers using a MEGA-edited MRS experiment. The degree of OOV contamination (OOV Score) was quantified per transient based upon the prevalence of OOV signals in the TD and FD data. OOV Scores above a user-defined threshold triggered an update of the crusher gradient scheme, iterating through 48 permutations (6 axis transpositions x 8 polarity flips). Within each 2-second TR, PEREGRINE successfully provided single-transient OOV Scores and updated gradients accordingly. No difference was observed between the OOV Scores from the full ("Full" condition) AI-on and AI-off sessions due to the AI-on scan cycling over better and worse gradient permutations relative to the AI-off scan. However, the AI-on scan had significantly lower OOV Scores than the AI-off scan when selecting the transients where PEREGRINE persisted ("Dwell" condition) on a given gradient permutation. Ultimately, Fit Quality Number (FQN) from linear combination modeling improved significantly for the AI-on compared to the AI-off scan. PEREGRINE enabled an adaptive and AI-integrated sequence allowing for real-time evaluation and response to OOV artifacts, identifying gradient modifications that produced less OOV contamination. Graphical AbstractO_ST_ABSGraphical Abstract SummaryC_ST_ABSPEREGRINE, Per Excitation Real-time Execution & Guided Responses with Integrated Neural-network Evaluation, allows for pulse sequence updates using on-scanner deployed neural networks. To demonstrate the utility, PEREGRINE was used to operate two neural networks (time/frequency domain), trained to detect out-of-voxel artifacts, during a MEGA-edited MRS experiment in the prefrontal cortex. When artifacts were detected, PEREGRINE updated the crusher gradients within the same TR. Real-time, adaptive, and AI-driven MR will provide a long-awaited solution for combatting artifacts and poor data quality. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=167 SRC="FIGDIR/small/722724v2_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@cc01e0org.highwire.dtl.DTLVardef@18f4083org.highwire.dtl.DTLVardef@1d48c8corg.highwire.dtl.DTLVardef@1574ba7_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract Figure C_FIG

neuroscience↗

bioRxiv2024

Mitochondrial Oxidative Phosphorylation Capacity in Skeletal Muscle Measured by Ultrafast Z-Spectroscopy (UFZ) MRI at 3T

BackgroundTo investigate the feasibility of rapid CEST MRI acquisition for evaluating oxidative phosphorylation (OXPHOS) in human skeletal muscle at 3 Tesla, utilizing ultrafast Z-spectroscopy (UFZ) MRI combined with the Polynomial and Lorentzian line-shape Fitting (PLOF) technique. MethodsUFZ MRI on muscle was evaluated with turbo spin echo (TSE) and segmented 3D EPI readouts. Five healthy subjects performed in-magnet plantar flexion exercise (PFE) and subsequent changes of amide, phosphocreatine (PCr) and partial PCr mixed creatine (Cr+) CEST dynamic signals post-exercise were enabled by PLOF fitting. PCr/Cr CEST signal was further refined through pH correction by using the ratios between PCr/Cr and amide signals, named PCAR/CAR, respectively. ResultsUFZ MRI with TSE readout significantly reduces acquisition time, achieving a temporal resolution of <50 seconds for collecting high-resolution Z-spectra. Following PFE, the recovery/decay times ({tau}) for both PCr and Cr in the gastrocnemius muscle of the calf were notably longer when determined using PCr/Cr CEST compared to those after pH correction with amideCEST, namely [Formula] s and{tau} PCr = 98.1 {+/-} 20.4 s versus{tau} CAR =36.4 {+/-} 18.6 s and{tau} PCAR = 43.0 {+/-} 13.0 s, respectively. Literature values of{tau} PCr obtained via 31P MRS closely resemble those obtained from pH-corrected PCr/Cr CEST signals. ConclusionThe outcomes suggest potential of UFZ MRI as a robust tool for non-invasive assessment of mitochondrial function in skeletal muscles. pH correction is critical for the reliable OXPHOS measurement by CEST.

biophysics↗

bioRxiv2023

Downfield Proton MRSI with whole-brain coverage at 3T

PurposeTo develop a 3D downfield magnetic resonance spectroscopic imaging (DF-MRSI) protocol with whole brain coverage and post-processing pipeline for creation of metabolite maps. MethodsA 3D, circularly phase-encoded version of the previously developed 2D DF-MRSI sequence with [Formula] spectral-spatial excitation and frequency selective refocusing was implemented and tested in 5 healthy volunteers at 3T. Downfield metabolite maps with a nominal spatial resolution of 0.7 cm3 were recorded in 8 slices at 3T in a scan time of 22m 40s. An MRSI post-processing pipeline was developed to create DF metabolite maps. Metabolite concentrations and uncertainty estimates were compared between region differences for nine downfield peaks. ResultsLCModel analysis showed CRLB average values of 3-4% for protein amide resonances in the three selected regions (anterior cingulate (ACC), dorsolateral prefrontal cortex (DLPFC), and centrum semiovale (CSO)); CRLBs were somewhat higher for individual peaks but for the most part were less than 20%. While DF concentration maps were visually quite homogeneous throughout the brain, general linear regression analysis corrected for multiple comparisons found significant differences between CSO and DLPFC for peaks at 7.09 ppm (p= 0.014), 7.90 ppm (p=0.009), 8.18 ppm (p=0.009), combined amides (p=0.009), and between ACC and DLPFC for the 7.30 ppm peak (p=0.020). CRLB values were not significantly different between brain regions for any of the DF peaks. Conclusion3D DF-MRSI of the human brain at 3T with wide spatial coverage for the mapping of exchangeable amide and other resonances is feasible at a nominal spatial resolution of 0.7 cm3.

bioengineering↗