Nothing
## ----include = FALSE----------------------------------------------------------
library(ragg)
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.width = 6,
fig.height = 5,
dev = "ragg_png"
)
## ----message = FALSE----------------------------------------------------------
library(spant)
## -----------------------------------------------------------------------------
fname <- system.file("extdata", "philips_spar_sdat_WS.SDAT", package = "spant")
## -----------------------------------------------------------------------------
mrs_data <- read_mrs(fname)
## -----------------------------------------------------------------------------
print(mrs_data)
## -----------------------------------------------------------------------------
plot(mrs_data, xlim = c(5, 0.5))
## -----------------------------------------------------------------------------
mrs_proc <- hsvd_filt(mrs_data)
mrs_proc <- align(mrs_proc, 2.01)
plot(mrs_proc, xlim = c(5, 0.5))
## ----fig.height=9-------------------------------------------------------------
basis <- sim_basis_1h_brain_press(mrs_proc)
print(basis)
stackplot(basis, xlim = c(4, 0.5), labels = basis$names, y_offset = 5)
## ----results = "hide"---------------------------------------------------------
fit_res <- fit_mrs(mrs_proc, basis)
## -----------------------------------------------------------------------------
plot(fit_res)
## -----------------------------------------------------------------------------
fit_res$res_tab
## -----------------------------------------------------------------------------
fit_res$res_tab$tNAA.sd / fit_res$res_tab$tNAA * 100
## -----------------------------------------------------------------------------
fit_res$res_tab$SNR
## -----------------------------------------------------------------------------
fit_res$res_tab$tNAA_lw
## -----------------------------------------------------------------------------
fit_res_tcr_sc <- scale_amp_ratio(fit_res, "tCr")
amps <- fit_amps(fit_res_tcr_sc)
print(t(amps))
## -----------------------------------------------------------------------------
fname_wref <- system.file("extdata", "philips_spar_sdat_W.SDAT", package = "spant")
mrs_data_wref <- read_mrs(fname_wref)
## -----------------------------------------------------------------------------
p_vols <- c(WM = 100, GM = 0, CSF = 0)
TE = 0.03
TR = 2
fit_res_molal <- scale_amp_molal_pvc(fit_res, mrs_data_wref, p_vols, TE, TR)
fit_res_molal$res_tab$tNAA
## -----------------------------------------------------------------------------
fit_res_molar <- scale_amp_molar(fit_res, mrs_data_wref)
fit_res_molar$res_tab$tNAA
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