Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
tools:lcmodel [2023/11/09 14:13] – sdm63tools:lcmodel [2026/05/22 15:12] (current) – will
Line 1: Line 1:
 ====== LC Model ====== ====== LC Model ======
 +{{ :tools:lcmodel_manual.pdf |}}
 +
 LCModel was utilized to quantify the spectral data (in the range of 1.8–4.0 ppm) (Provencher, 2001), which consist of default macromolecule components and 14 basis metabolite functions (N-acetylaspartate (NAA), N-acetylaspartylglutamate (NAAG), aspartate, lactate, creatine (Cre), γ-aminobutyric acid (GABA), glucose, glutamate (Glu), glutamine, glutathione, glycerophosphorylcholine (GPC), phosphorylcholine (PCh), myoinositol, and taurine). LCModel outputs contain Cramer-Rao Lower Bounds (CRLB), which provide an expression of the uncertainty of the estimate for each metabolite. The CRLB provides an estimate of the lowest achievable variance for an estimator and is used as an indicator of how well the measurement of a given metabolite fits the ideal spectrum for that metabolite, providing an assessment of data quality. Additionally, outputs were used to visually inspect spectra and model fit, which we used as a first-pass exclusion criteria for data, along with the CRLB. LCModel was utilized to quantify the spectral data (in the range of 1.8–4.0 ppm) (Provencher, 2001), which consist of default macromolecule components and 14 basis metabolite functions (N-acetylaspartate (NAA), N-acetylaspartylglutamate (NAAG), aspartate, lactate, creatine (Cre), γ-aminobutyric acid (GABA), glucose, glutamate (Glu), glutamine, glutathione, glycerophosphorylcholine (GPC), phosphorylcholine (PCh), myoinositol, and taurine). LCModel outputs contain Cramer-Rao Lower Bounds (CRLB), which provide an expression of the uncertainty of the estimate for each metabolite. The CRLB provides an estimate of the lowest achievable variance for an estimator and is used as an indicator of how well the measurement of a given metabolite fits the ideal spectrum for that metabolite, providing an assessment of data quality. Additionally, outputs were used to visually inspect spectra and model fit, which we used as a first-pass exclusion criteria for data, along with the CRLB.
 \\ \\
Line 15: Line 17:
   * https://github.com/schorschinho/LCModel   * https://github.com/schorschinho/LCModel
   * ''/Volumes/Hera/Raw/MRprojects/7TBrainMech/CSIProcessing''   * ''/Volumes/Hera/Raw/MRprojects/7TBrainMech/CSIProcessing''
 +
 +===== Lac =====
 +Shifting the lower bound of modeling range in ''csi.control''' to ''PPMEND=0.5'' will include Lac. [[:grants:7t]]'s ''TE'' is not optimal for this range. most Lac.SD (CRLB) are out of range. Also worth noting, rerunning with the modified range changes the estimates of other metabolite concentrations.
 +{{.:pasted:20260522-151026.png}}
 +{{.:pasted:20260522-151212.png}}