scale_amp_legacy: Apply water reference scaling to a fitting results object to...

In spant: MR Spectroscopy Analysis Tools

Apply water reference scaling to a fitting results object to yield metabolite quantities in units of "mmol per Kg wet weight".

Description

See the LCModel manual (section 10.2) on water-scaling for details on the assumptions and relevant references. Use this type of concentration scaling to compare fit results with LCModel and TARQUIN defaults. Otherwise scale_amp_molal_pvc is the preferred method. Note, the LCModel manual (section 1.3) states:

Usage

scale_amp_legacy(fit_result, ref_data, w_att = 0.7, w_conc = 35880, ...)

Arguments

fit_result	a result object generated from fitting.
ref_data	water reference MRS data object.
w_att	water attenuation factor (default = 0.7). Assumes water T2 of 80ms and a TE = 30 ms. exp(-30ms / 80ms) ~ 0.7.
w_conc	assumed water concentration (default = 35880). Default value corresponds to typical white matter. Set to 43300 for gray matter, and 55556 for phantom measurements.
...	additional arguments to get_td_amp function.

Details

"Concentrations should be labelled 'mmol per Kg wet weight'. We use the shorter (incorrect) abbreviation mM. The actual mM is the mmol per Kg wet weight multiplied by the specific gravity of the tissue, typically 1.04 in brain."

Value

a fit_result object with a rescaled results table.

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