spant edited SVS analysis results
In spant: MR Spectroscopy Analysis Tools

library(spant)
knitr::opts_chunk$set(echo = FALSE)

{.tabset}

Edited fit plots {.tabset}

Standard

plot(params$fit_res_ed, xlim = params$plot_ppm_xlim)

Stackplot

stackplot(params$fit_res_ed, y_offset = 0.5, combine_lipmm = FALSE, labels = TRUE,
          xlim = params$plot_ppm_xlim)

# basis_names <- params$fit_res$basis$names
basis_names <- colnames(params$fit_res_ed$fits[[1]][-1:-4])
for (n in 1:length(basis_names)) {
  #if (basis_names[n] %in% colnames(params$fit_res$fits[[1]])) {
  cat("\n### ", basis_names[n], "\n", sep = "")
  plot(params$fit_res_ed, plot_sigs = basis_names[n], main = basis_names[n], 
       xlim = params$plot_ppm_xlim)
  cat("\n")
  #}
}

Edit-off fit plots {.tabset}

Standard

plot(params$fit_res, xlim = params$plot_ppm_xlim)

Stackplot

stackplot(params$fit_res, y_offset = 3, combine_lipmm = TRUE, labels = TRUE,
          xlim = params$plot_ppm_xlim)

# basis_names <- params$fit_res$basis$names
basis_names <- colnames(params$fit_res$fits[[1]][-1:-4])
for (n in 1:length(basis_names)) {
  #if (basis_names[n] %in% colnames(params$fit_res$fits[[1]])) {
  cat("\n### ", basis_names[n], "\n", sep = "")
  plot(params$fit_res, plot_sigs = basis_names[n], main = basis_names[n], 
       xlim = params$plot_ppm_xlim)
  cat("\n")
  #}
}

if (!is.null(params$summary_tab)) {
  cat("## Summary table\n")

  col.names <- c("Name", "Value")
  kable_table <- kableExtra::kbl(params$summary_tab, col.names = col.names,
                                 align = c("l", "r"))

  boot_opts <- c("striped", "hover", "condensed")
  kableExtra::kable_styling(kable_table, full_width = FALSE, position = "left",
                            bootstrap_options = boot_opts)
}

Edited results table

# ratio_str   <- params$argg$output_ratio
ratio_str   <- params$output_ratio[1]
if (params$w_ref_available) {
  col_names <- c("amps", "CI95")
  res_tab   <- sv_res_table(params$res_tab_ed_molal, format_out = TRUE)
  out_tab   <- res_tab[col_names]
  col.names <- c("Name", "Amp. (mmol/kg)", "95% CI (mmol/kg)")

  if (!is.null(params$res_tab_legacy)) {
    res_tab   <- sv_res_table(params$res_tab_ed_legacy, format_out = TRUE)
    out_tab   <- cbind(out_tab, res_tab[col_names])
    col.names <- c(col.names, "Amp. (mmol/kg)", "95% CI (mmol/kg)")
  }

  if (!is.null(ratio_str)) {
    res_tab   <- sv_res_table(params$res_tab_ed_ratio, format_out = TRUE)
    out_tab   <- cbind(out_tab, res_tab[col_names])
    col.names <- c(col.names, paste0("Amp. (/", ratio_str, ")"),
                              paste0("95% CI (/", ratio_str, ")"))
  }
  out_tab   <- cbind(out_tab, res_tab["sds_perc"])
  col.names <- c(col.names, "SD %")
} else {
  col_names <- c("amps", "CI95", "sds_perc")
  if (is.null(ratio_str)) {
    res_tab   <- sv_res_table(params$res_tab_ed_unscaled, format_out = TRUE)
    out_tab   <- res_tab[col_names]
    col.names <- c("Name", "Amp. (a.u.)", "95% CI (a.u.)", "SD %")
  } else {
    res_tab   <- sv_res_table(params$res_tab_ed_ratio, format_out = TRUE)
    out_tab   <- res_tab[col_names]
    col.names <- c("Name", paste0("Amp. (/", ratio_str, ")"),
                   paste0("95% CI (/", ratio_str, ")"), "SD %")
  }
}

boot_opts <- c("striped", "hover", "condensed")

kable_table <- kableExtra::kbl(out_tab, col.names = col.names,
                               align = rep("r", 10))

if (params$w_ref_available & !is.null(params$res_tab_ed_legacy)) {
  extra_cols  <- ifelse(is.null(ratio_str), 1, 3)
  header_str  <- c(" " = 1, "standard concentration scaling" = 2,
                   "legacy concentration scaling" = 2, " " = extra_cols)

  kable_table <- kableExtra::add_header_above(kable_table, header_str)
}

kableExtra::kable_styling(kable_table, full_width = FALSE, position = "left",
                          bootstrap_options = boot_opts)

if (params$w_ref_available) {
cat("See the [spant User Guide](https://spantdoc.wilsonlab.co.uk/water_scaling) for details on water scaling.\n")
#  cat("^1^ Concentrations listed in molal units: moles of solute / mass of solvent. See the following papers for details :\n\nGasparovic C, Chen H, Mullins PG. Errors in 1H-MRS estimates of brain metabolite concentrations caused by failing to take into account tissue-specific signal relaxation. NMR Biomed. 2018 Jun;31(6):e3914. https://doi.org/10.1002/nbm.3914\n\nGasparovic C, Song T, Devier D, Bockholt HJ, Caprihan A, Mullins PG, Posse S, Jung RE, Morrison LA. Use of tissue water as a concentration reference for proton spectroscopic imaging. Magn Reson Med. 2006 Jun;55(6):1219-26. https://doi.org/10.1002/mrm.20901\n\n")  
#  cat("^2^ Concentrations listed in pseduo-molar units: moles of solute / (mass of solvent + mass of tissue). These values are included for legacy puposes, for example to directly compare results from the default scaling method used by LCModel and TARQUIN. See sections 1.3 and 10.2 of the [LCModel manual](http://s-provencher.com/pub/LCModel/manual/manual.pdf) for details.")
}

Edit-off results table

# ratio_str   <- params$argg$output_ratio
ratio_str   <- params$output_ratio[1]
if (params$w_ref_available) {
  col_names <- c("amps", "CI95")
  res_tab   <- sv_res_table(params$res_tab_molal, format_out = TRUE)
  out_tab   <- res_tab[col_names]
  col.names <- c("Name", "Amp. (mmol/kg)", "95% CI (mmol/kg)")

  if (!is.null(params$res_tab_legacy)) {
    res_tab   <- sv_res_table(params$res_tab_legacy, format_out = TRUE)
    out_tab   <- cbind(out_tab, res_tab[col_names])
    col.names <- c(col.names, "Amp. (mmol/kg)", "95% CI (mmol/kg)")
  }

  if (!is.null(ratio_str)) {
    res_tab   <- sv_res_table(params$res_tab_ratio, format_out = TRUE)
    out_tab   <- cbind(out_tab, res_tab[col_names])
    col.names <- c(col.names, paste0("Amp. (/", ratio_str, ")"),
                              paste0("95% CI (/", ratio_str, ")"))
  }
  out_tab   <- cbind(out_tab, res_tab["sds_perc"])
  col.names <- c(col.names, "SD %")
} else {
  col_names <- c("amps", "CI95", "sds_perc")
  if (is.null(ratio_str)) {
    res_tab   <- sv_res_table(params$res_tab_unscaled, format_out = TRUE)
    out_tab   <- res_tab[col_names]
    col.names <- c("Name", "Amp. (a.u.)", "95% CI (a.u.)", "SD %")
  } else {
    res_tab   <- sv_res_table(params$res_tab_ratio, format_out = TRUE)
    out_tab   <- res_tab[col_names]
    col.names <- c("Name", paste0("Amp. (/", ratio_str, ")"),
                   paste0("95% CI (/", ratio_str, ")"), "SD %")
  }
}

boot_opts <- c("striped", "hover", "condensed")

kable_table <- kableExtra::kbl(out_tab, col.names = col.names,
                               align = rep("r", 10))

if (params$w_ref_available & !is.null(params$res_tab_legacy)) {
  extra_cols  <- ifelse(is.null(ratio_str), 1, 3)
  header_str  <- c(" " = 1, "standard concentration scaling" = 2,
                   "legacy concentration scaling" = 2, " " = extra_cols)

  kable_table <- kableExtra::add_header_above(kable_table, header_str)
}

kableExtra::kable_styling(kable_table, full_width = FALSE, position = "left",
                          bootstrap_options = boot_opts)

if (params$w_ref_available) {
cat("See the [spant User Guide](https://spantdoc.wilsonlab.co.uk/water_scaling) for details on water scaling.\n")
#  cat("^1^ Concentrations listed in molal units: moles of solute / mass of solvent. See the following papers for details :\n\nGasparovic C, Chen H, Mullins PG. Errors in 1H-MRS estimates of brain metabolite concentrations caused by failing to take into account tissue-specific signal relaxation. NMR Biomed. 2018 Jun;31(6):e3914. https://doi.org/10.1002/nbm.3914\n\nGasparovic C, Song T, Devier D, Bockholt HJ, Caprihan A, Mullins PG, Posse S, Jung RE, Morrison LA. Use of tissue water as a concentration reference for proton spectroscopic imaging. Magn Reson Med. 2006 Jun;55(6):1219-26. https://doi.org/10.1002/mrm.20901\n\n")  
#  cat("^2^ Concentrations listed in pseduo-molar units: moles of solute / (mass of solvent + mass of tissue). These values are included for legacy puposes, for example to directly compare results from the default scaling method used by LCModel and TARQUIN. See sections 1.3 and 10.2 of the [LCModel manual](http://s-provencher.com/pub/LCModel/manual/manual.pdf) for details.")
}

if (!is.null(dyn_data_uncorr_ed_off)) {
  cat("## Dynamic plots {.tabset}\n")
  if (!is.null(dyn_data_corr_ed_off)) {
    cat("### Edit-off with dyn. correction\n")
    if (is.null(params$plot_ppm_xlim)) {
      image(dyn_data_corr_ed_off, xlim = c(4, 0.5), vline = 2.01,
            vline_col = "black")
    } else {
      image(dyn_data_corr_ed_off, xlim = params$plot_ppm_xlim, vline = 2.01,
            vline_col = "black")
    }
  }
  if (!is.null(dyn_data_corr_ed_on)) {
    cat("\n\n### Edit-on with dyn. correction\n")
    if (is.null(params$plot_ppm_xlim)) {
      image(dyn_data_corr_ed_on, xlim = c(4, 0.5), vline = 3.03,
            vline_col = "black")
    } else {
      image(dyn_data_corr_ed_on, xlim = params$plot_ppm_xlim, vline = 3.03,
            vline_col = "black")
    }
  }
  cat("\n\n### Edit-off without dyn. correction\n")
  if (is.null(params$plot_ppm_xlim)) {
    image(dyn_data_uncorr_ed_off, xlim = c(4, 0.5), vline = 2.01,
          vline_col = "black")
  } else {
    image(dyn_data_uncorr_ed_off, xlim = params$plot_ppm_xlim, vline = 2.01,
          vline_col = "black")
  }
  cat("\n\n### Edit-on without dyn. correction\n")
  if (is.null(params$plot_ppm_xlim)) {
    image(dyn_data_uncorr_ed_on, xlim = c(4, 0.5), vline = 3.03,
          vline_col = "black")
  } else {
    image(dyn_data_uncorr_ed_on, xlim = params$plot_ppm_xlim, vline = 3.03,
          vline_col = "black")
  }
}

if (!is.null(params$mri) | !is.null(params$mri_seg)) {
  cat("## MRI {.tabset}\n")
}

if (!is.null(params$mri)) {
  cat("### Voxel position\n")
  voi <- get_svs_voi(params$fit_res$data, params$mri)
  plot_voi_overlay(params$mri, voi)
}

if (!is.null(params$mri_seg)) {
  cat("### Voxel segmetation\n")
  voi <- get_svs_voi(params$fit_res$data, params$mri_seg)
  seg_vols <- plot_voi_overlay_seg(params$mri_seg, voi)
}

Spectral plots {.tabset}

Edited cropped

if (!is.null(params$fit_res_ed$res_tab$phase)) {
  phase_offset <- params$fit_res_ed$res_tab$phase
} else {
  phase_offset <- 0
}

if (!is.null(params$fit_res_ed$res_tab$phi1)) {
  phi1_offset <- params$fit_res_ed$res_tab$phi1
} else {
  phi1_offset <- 0
}

if (!is.null(params$fit_res_ed$res_tab$shift)) {
  shift_offset <- params$fit_res_ed$res_tab$shift
} else {
  shift_offset <- 0
}

proc_spec_ed <- params$fit_res_ed$data
proc_spec_ed <- phase(proc_spec_ed, phase_offset, phi1_offset)
proc_spec_ed <- shift(proc_spec_ed, shift_offset, units = "ppm")
proc_spec_ed <- zf(proc_spec_ed)

if (is.null(params$plot_ppm_xlim)) {
  plot(proc_spec_ed, xlim = c(4, 0.2))
} else {
  plot(proc_spec_ed, xlim = params$plot_ppm_xlim)
}

Edit-off cropped

if (!is.null(params$fit_res$res_tab$phase)) {
  phase_offset <- params$fit_res$res_tab$phase
} else {
  phase_offset <- 0
}

if (!is.null(params$fit_res$res_tab$phi1)) {
  phi1_offset <- params$fit_res$res_tab$phi1
} else {
  phi1_offset <- 0
}

if (!is.null(params$fit_res$res_tab$shift)) {
  shift_offset <- params$fit_res$res_tab$shift
} else {
  shift_offset <- 0
}

proc_spec <- params$fit_res$data
proc_spec <- phase(proc_spec, phase_offset, phi1_offset)
proc_spec <- shift(proc_spec, shift_offset, units = "ppm")
proc_spec <- zf(proc_spec)

if (is.null(params$plot_ppm_xlim)) {
  plot(proc_spec, xlim = c(4, 0.2))
} else {
  plot(proc_spec, xlim = params$plot_ppm_xlim)
}

Edited full

plot(proc_spec_ed)

Edit-off full

plot(proc_spec)

if (params$w_ref_available) {
  cat("### Water reference resonance\n")
  # w_ref_proc <- shift(w_ref, shift_offset, units = "ppm")
  w_ref_proc <- auto_phase(w_ref, xlim = c(5.3, 4))
  w_ref_proc <- zf(w_ref_proc)
  plot(w_ref_proc, xlim = c(5.3, 4))
}

Edit-off diagnostics

name  <- NULL
value <- NULL

if (!is.null(params$fit_res$res_tab$SNR)) {
  name  <- c(name, "Spectral signal to noise ratio")
  value <- c(value, round_dp(params$fit_res$res_tab$SNR, 2))
}

if (!is.null(params$fit_res$res_tab$SRR)) {
  name  <- c(name, "Spectral signal to residual ratio")
  value <- c(value, round_dp(params$fit_res$res_tab$SRR, 2))
}

if (!is.null(params$fit_res$res_tab$FWHM)) {
  name  <- c(name, "Spectral linewidth (ppm)")
  value <- c(value, round_dp(params$fit_res$res_tab$FWHM, 4))
}

if (!is.null(params$fit_res$res_tab$tNAA_lw)) {
  name  <- c(name, "tNAA linewidth (ppm)")
  value <- c(value, round_dp(params$fit_res$res_tab$tNAA_lw, 4))
}

if (!is.null(params$fit_res$res_tab$NAA_lw)) {
  name  <- c(name, "NAA linewidth (ppm)")
  value <- c(value, round_dp(params$fit_res$res_tab$NAA_lw, 4))
}

if (!is.null(params$fit_res$res_tab$tCho_lw)) {
  name  <- c(name, "tCho linewidth (ppm)")
  value <- c(value, round_dp(params$fit_res$res_tab$tCho_lw, 4))
}

if (!is.null(params$fit_res$res_tab$Cho_lw)) {
  name  <- c(name, "Cho linewidth (ppm)")
  value <- c(value, round_dp(params$fit_res$res_tab$Cho_lw, 4))
}

if (!is.null(params$fit_res$res_tab$tCr_lw)) {
  name  <- c(name, "tCr linewidth (ppm)")
  value <- c(value, round_dp(params$fit_res$res_tab$tCr_lw, 4))
}

if (!is.null(params$fit_res$res_tab$Cr_lw)) {
  name  <- c(name, "Cr linewidth (ppm)")
  value <- c(value, round_dp(params$fit_res$res_tab$Cr_lw, 4))
}

if (!is.null(params$fit_res$res_tab$phase)) {
  name  <- c(name, "Zero-order phase (degrees)")
  value <- c(value, round_dp(params$fit_res$res_tab$phase, 1))
}

if (!is.null(params$fit_res$res_tab$phi1)) {
  name  <- c(name, "First-order phase (ms)")
  value <- c(value, round_dp(params$fit_res$res_tab$phi1, 3))
}

if (!is.null(params$fit_res$res_tab$shift)) {
  name  <- c(name, "Frequency offset (ppm)")
  value <- c(value, round_dp(params$fit_res$res_tab$shift, 4))
}

if (params$w_ref_available) {
  name  <- c(name,  "Water amplitude", "Water suppression efficiency (%)")
  value <- c(value, format(params$res_tab_molal$w_amp),
             round_dp(params$res_tab_molal$ws_eff, 3))
}

if (params$fit_res$method == "ABFIT") {
  name  <- c(name, "Fit quality number (FQN)",
             "Baseline effective d.f. per ppm",
             "Lineshape asymmetry")
  value <- c(value, round_dp(params$fit_res$res_tab$FQN, 2),
             round_dp(params$fit_res$res_tab$bl_ed_pppm, 2),
             round_dp(params$fit_res$res_tab$asym, 2))
}

diag_tab <- data.frame(name, value)
kableExtra::kable_styling(kableExtra::kbl(diag_tab, align = c("l", "r"),
                                          col.names = c("Name", "Value")),
                          full_width = FALSE, position = "left",
                          bootstrap_options = boot_opts)

if (!is.null(params$p_vols)) {
  cat("### Partial volume measures\n")
  perc_vols  <- c(params$p_vols[["WM"]], params$p_vols[["GM"]],
                  params$p_vols[["CSF"]], params$p_vols[["Other"]])
  p_vols_tab <- data.frame(type = c("WM", "GM", "CSF", "Other"),
                           perc = perc_vols)
  kableExtra::kable_styling(kableExtra::kbl(p_vols_tab, align = c("l", "r"),
                                            col.names = c("Type", "% volume")),
                            full_width = FALSE, position = "left",
                            bootstrap_options = boot_opts)
}

Provenance

packageVersion("spant")
Sys.time()
print(params$fit_res$data, full = TRUE)
print(params$w_ref, full = TRUE)
print(argg)

{-}

Please cite the following if you found ABfit and spant useful in your research:

Wilson M. Adaptive baseline fitting for 1H MR spectroscopy analysis. Magn Reson Med. 2021 Jan;85(1):13-29. https://doi.org/10.1002/mrm.28385

Wilson, M. spant: An R package for magnetic resonance spectroscopy analysis. Journal of Open Source Software. 2021 6(67), 3646. https://doi.org/10.21105/joss.03646

Wilson M. Robust retrospective frequency and phase correction for single-voxel MR spectroscopy. Magn Reson Med. 2019 May;81(5):2878-2886. https://doi.org/10.1002/mrm.27605

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spant documentation built on April 4, 2025, 1:40 a.m.

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spant
MR Spectroscopy Analysis Tools

spant edited SVS analysis results
In spant: MR Spectroscopy Analysis Tools

{.tabset}

Edited fit plots {.tabset}

Standard

Stackplot

Edit-off fit plots {.tabset}

Standard

Stackplot

Edited results table

Edit-off results table

Spectral plots {.tabset}

Edited cropped

Edit-off cropped

Edited full

Edit-off full

Edit-off diagnostics

Provenance

{-}

Try the spant package in your browser

R Package Documentation

Browse R Packages

We want your feedback!

spant MR Spectroscopy Analysis Tools

spant edited SVS analysis results In spant: MR Spectroscopy Analysis Tools

{.tabset}

Edited fit plots {.tabset}

Standard

Stackplot

Edit-off fit plots {.tabset}

Standard

Stackplot

Edited results table

Edit-off results table

Spectral plots {.tabset}

Edited cropped

Edit-off cropped

Edited full

Edit-off full

Edit-off diagnostics

Provenance

{-}

Try the spant package in your browser

R Package Documentation

Browse R Packages

We want your feedback!

spant
MR Spectroscopy Analysis Tools

spant edited SVS analysis results
In spant: MR Spectroscopy Analysis Tools