MR Spectroscopy Analysis Tools

Documentation for package ‘spant’ version 0.6.0

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spant: spectroscopy analysis tools.

-- A --

align	Align spectra to a reference frequency using a convolution based method.
apodise_xy	Apodise MRSI data in the x-y direction with a k-space hamming filter.
append_dyns	Append MRS data across the dynamic dimension, assumes they matched across the other dimensions.
apply_pvc	Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.

-- B --

basis2mrs_data	Convert a basis object to an mrs_data object - where basis signals are spread across the dynamic dimension.
beta2lw	Covert a beta value in the time-domain to an equivalent linewidth in Hz: x * exp(-i * t * t * beta)

-- C --

calc_coil_noise_cor	Calculate the noise correlation between coil elements.
calc_coil_noise_sd	Calculate the noise standard deviation for each coil element.
calc_peak_info	Search for the highest peak in a spectral region and return the frequency, height and FWHM.
calc_sd_poly	Perform a polynomial fit, subtract and return the standard deviation of the residuals.
calc_spec_snr	Calculate the spectral SNR.
check_lcm	Check LCModel can be run
check_tqn	Check the TARQUIN binary can be run
combine_metab_ref	Combine a reference and metabolite mrs_data object.
comb_coils	Combine coil data based on the first data point of a reference signal.
conj	Conjugate MRS data.
crop_spec	Crop 'mrs_data' object based on a frequency range.

-- D --

def_acq_paras	Return a list of the default acquisition parameters.
def_fs	Return the default sampling frequency in Hz.
def_ft	Return the default transmitter frequency in Hz.
def_N	Return the default number of data points in the spectral dimension.
def_ref	Return the default reference value for ppm scale.
dyns	Return the number of dynamic scans in an MRS dataset.

-- E --

ecc	Eddy current correction.
est_noise_sd	Estimate the standard deviation of the noise from a segment of an mrs_data object.

-- F --

fd2td	Transform frequency-domain data to the time-domain.
fit_diags	Calculate diagnostic information for object of class 'fit_result'
fit_mrs	Perform a fit based analysis of MRS data.
fit_tab2csv	Write fit results table to a csv file.
fp_phase	Return the phase of the first data point in the time-domain.
fp_phase_correct	Perform a zeroth order phase correction based on the phase of the first data point in the time-domain.
fs	Return the sampling frequency in Hz of an MRS dataset.
ft_shift	Perform a fft and ffshift on a vector.
ft_shift_mat	Perform a fft and fftshift on a matrix with each column replaced by its shifted fft.

-- G --

get_1h_brain_basis_paras	Return a list of 'mol_parameter' objects suitable for 1H brain MRS analyses.
get_acq_paras	Return acquisition parameters from a MRS data object.
get_dyns	Extract a subset of dynamic scans.
get_even_dyns	Return even numbered dynamic scans starting from 1 (2,4,6...).
get_fit_map	Get a data array from a fit result
get_fp	Return the first time-domain data point.
get_metab	Extract the metabolite component from an mrs_data object.
get_mol_names	Return a character array of names that may be used with the 'get_mol_paras' function.
get_mol_paras	Get a 'mol_parameters' object for a named molecule.
get_odd_dyns	Return odd numbered dynamic scans starting from 1 (1,3,5...).
get_ref	Extract the reference component from an mrs_data object.
get_seg_ind	Get the indices of data points lying between two values (end > x > start).
get_slice	Return a single slice from a larger MRSI dataset.
get_svs_voi	Generate a SVS acquisition volume from an 'mrs_data' object.
get_td_amp	Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0.
get_uncoupled_mol	Generate a 'mol_parameters' object for a simple spin system with one resonance.
get_voi_seg	Return the white matter, gray matter and CSF composition of a volume.
get_voxel	Return a single voxel from a larger mrs dataset.

-- H --

hsvd_filt

HSVD based signal filter.

-- I --

ift_shift	Perform an iffshift and ifft on a vector.
image.mrs_data	Image plot method for objects of class mrs_data.
int_spec	Integrate a spectral region.
inv_even_dyns	Invert even numbered dynamic scans starting from 1 (2,4,6...).
inv_odd_dyns	Invert odd numbered dynamic scans starting from 1 (1,3,5...).

-- L --

lb	Apply line-broadening (apodisation) to MRS data or basis object.
lb.basis_set	Apply line-broadening (apodisation) to MRS data or basis object.
lb.mrs_data	Apply line-broadening (apodisation) to MRS data or basis object.
lw2beta	Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-i * t * t * beta)

-- M --

mat2mrs_data	Convert a matrix (with spectral points in the row dimension and dynamics in the column dimensions) into a mrs_data object.
mean_dyns	Calculate the mean dynamic data.
mean_dyn_blocks	Calculate the mean of adjacent dynamic scans.
mean_dyn_pairs	Calculate the pairwise means across a dynamic data set.
mrs_data2basis	Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
mrs_data2mat	Convert mrs_data object to a matrix, with spectral points in the row dimension and dynamics in the column dimension.
mvfftshift	Perform a fftshift on a matrix, with each column replaced by its shifted result.

-- N --

N	Return the number of data points in an MRS dataset.
n2coord	Print fit coordinates from a single index.
Nspec	Return the total number of spectra in an MRS dataset.

-- P --

phase	Apply phasing parameters to MRS data.
plot.fit_result	Plot the fitting results of an object of class 'fit_result'.
plot.mrs_data	Plotting method for objects of class mrs_data.
plot_fit_slice	Plot a 2D slice from an MRSI fit result object
plot_fit_slice_inter	Plot a 2D slice from an MRSI fit result object
plot_slice_map	Plot a slice from a 7 dimensional array
plot_slice_map_inter	Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum
plot_voi_overlay	Plot a volume as an image overlay.
plot_voi_overlay_seg	Plot a volume as an overlay on a segmented brain volume.
ppm	Return the ppm scale of an MRS dataset.
press_ideal	PRESS sequence with ideal pulses.
print.fit_result	Print a summary of an object of class 'fit_result'.
print.mrs_data	Print a summary of mrs_data parameters.
pulse_acquire	Simple pulse and acquire sequence with ideal pulses.
pulse_acquire_31p	Simple pulse and acquire sequence with ideal pulses.

-- R --

read_basis	Read a basis file in LCModel .basis format.
read_lcm_coord	Read an LCModel formatted coord file containing fit information.
read_mrs	Read MRS data from a file.
read_mrs_dpt	Read MRS data stored in dangerplot (dpt) v3 format.
read_mrs_tqn	Read MRS data using the TARQUIN software package.
read_tqn_fit	Reader for csv fit results generated by TARQUIN.
read_tqn_result	Reader for csv results generated by TARQUIN.
rep_dyn	Replicate a scan in the dynamic dimension.
resample_voi	Resample a VOI to match a target image space.
rm_dyns	Remove a subset of dynamic scans.

-- S --

scale_amp_molal_pvc	Apply partial volume correction to a fitting result object.
scale_amp_molar	Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol/litre).
scale_amp_ratio	Scale fitted amplitudes to a ratio of signal amplitude.
scale_amp_water_ratio	Scale metabolite amplitudes as a ratio to the unsupressed water amplitude.
seconds	Return a time scale vector to match the FID of an MRS data object.
set_def_acq_paras	Set the default acquisition parameters.
set_lcm_cmd	Set the command to run the LCModel command-line program.
set_ref	Set the ppm reference value (eg ppm value at 0Hz).
set_td_pts	Set the number of time-domain data points, truncating or zero-filling as appropriate.
set_tqn_cmd	Set the command to run the TARQUIN command-line program.
shift	Apply a frequency shift to MRS data
sim_basis	Simulate a basis set object.
sim_basis_1h_brain_press	Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
sim_basis_tqn	Simulate a basis file using TARQUIN.
sim_mol	Simulate a 'mol_parameter' object.
sim_noise	Simulate a time-domain mrs_data object containing simulated Gaussian noise.
sim_resonances	Simulate a MRS data object containing a set of simulated resonances.
spant	spant: spectroscopy analysis tools.
spant_mpress_drift	Example MEGA-PRESS data with significant B0 drift.
spin_echo_ideal	Spin echo sequence with ideal pulses.
spin_echo_ideal_31p	Spin echo sequence with ideal pulses.
stackplot	Produce a plot with multiple traces.
stackplot.fit_result	Plot the fitting results of an object of class 'fit_result' with individual basis set components shown.
stackplot.mrs_data	Stackplot plotting method for objects of class mrs_data.
sum_coils	Calculate the sum across receiver coil elements.
sum_dyns	Calculate the sum of data dynamics.

-- T --

td2fd	Transform time-domain data to the frequency-domain.
td_conv_filt	Time-domain convolution based filter.

-- V --

varpro_3_para_opts	Return a list of options for VARPRO based fitting with 3 free parameters: • zero'th order phase correction • global damping • global frequency shift.
varpro_opts	Return a list of options for VARPRO based fitting.
vec2mrs_data	Convert a vector into a mrs_data object.

-- W --

write_basis	Write a basis object to an LCModel .basis formatted file.
write_basis_tqn	Generate a basis file using TARQUIN.
write_mrs_dpt_v2	Write MRS data object to file in dangerplot (dpt) v2 format.

-- Z --

zf	Zero-fill MRS data in the time domain.
zf_xy	Zero-fill MRSI data in the k-space x-y direction.