MR Spectroscopy Analysis Tools

Documentation for package ‘spant’ version 2.22.0

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A B C D E F G H I K L M N O P Q R S T V W Z

spant: spectroscopy analysis tools.

-- A --

abfit_opts	Return a list of options for an ABfit analysis.
abfit_opts_v1_9_0	Return a list of options for an ABfit analysis to maintain comparability with analyses performed with version 1.9.0 (and earlier) of spant.
acquire	Simulate pulse sequence acquisition.
add_noise	Add noise to an mrs_data object.
add_noise_spec_snr	Add noise to an mrs_data object to match a given SNR.
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 filter.
append_basis	Combine a pair of basis set objects.
append_coils	Append MRS data across the coil dimension, assumes they matched across the other dimensions.
append_dyns	Append MRS data across the dynamic dimension, assumes they matched across the other dimensions.
append_regs	Append multiple regressor data frames into a single data frame.
apply_axes	Apply a function over specified array axes.
apply_mrs	Apply a function across given dimensions of a MRS data object.
apply_pulse	Simulate an RF pulse on a single spin.
Arg.mrs_data	Apply Arg operator to an MRS dataset.
array2mrs_data	Convert a 7 dimensional array in into a mrs_data object. The array dimensions should be ordered as : dummy, X, Y, Z, dynamic, coil, FID.
auto_phase	Perform zeroth-order phase correction based on the minimisation of the squared difference between the real and magnitude components of the spectrum.

-- B --

back_extrap_ar	Back extrapolate time-domain data points using an autoregressive model.
basis2dyn_mrs_data	Convert a basis object to a dynamic mrs_data object.
basis2mrs_data	Convert a basis object to an mrs_data object - where basis signals are spread across the dynamic dimension.
bbase	Generate a spline basis, slightly adapted from : "Splines, knots, and penalties", Eilers 2010.
bc_als	Baseline correction using the ALS method.
bc_constant	Remove a constant baseline offset based on a reference spectral region.
bc_gauss	Apply and subtract a Gaussian smoother in the spectral domain.
bc_poly	Fit and subtract a polynomial to each spectrum in a dataset.
bc_spline	Fit and subtract a smoothing spline to each spectrum in a dataset.
beta2lw	Covert a beta value in the time-domain to an equivalent linewidth in Hz: x * exp(-i * t * t * beta).
bin_spec	Bin equally spaced spectral regions.

-- 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_design_efficiency	Calculate the efficiency of a regressor data frame.
calc_ed_from_lambda	Calculate the effective dimensions of a spline smoother from lambda.
calc_peak_info_vec	Calculate the FWHM of a peak from a vector of intensity values.
calc_sd_poly	Perform a polynomial fit, subtract and return the standard deviation of the residuals.
calc_spec_diff	Calculate the sum of squares differences between two mrs_data objects.
calc_spec_snr	Calculate the spectral SNR.
check_lcm	Check LCModel can be run
check_tqn	Check the TARQUIN binary can be run
circ_mask	Create a logical circular mask spanning the full extent of an n x n matrix.
coherence_filter	Zero all coherence orders other than the one supplied as an argument.
collapse_to_dyns	Collapse MRS data by concatenating spectra along the dynamic dimension.
collapse_to_dyns.fit_result	Collapse MRS data by concatenating spectra along the dynamic dimension.
collapse_to_dyns.mrs_data	Collapse MRS data by concatenating spectra along the dynamic dimension.
comb_coils	Combine coil data based on the first data point of a reference signal.
comb_coils_mrsi_gls	Combine MRSI coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).
comb_coils_svs_gls	Combine SVS coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).
comb_fit_list_fit_tables	Combine all fitting data points from a list of fits into a single data frame.
comb_fit_list_result_tables	Combine the fit result tables from a list of fit results.
comb_fit_tables	Combine all fitting data points into a single data frame.
comb_metab_ref	Combine a reference and metabolite mrs_data object.
Conj.mrs_data	Apply Conj operator to an MRS dataset.
conv_mrs	Convolve two MRS data objects.
crop_basis	Crop 'basis_set' object based on a frequency range.
crop_spec	Crop 'mrs_data' object based on a frequency range.
crop_td_pts	Crop 'mrs_data' object data points in the time-domain.
crop_td_pts_end	Crop 'mrs_data' object data points at the end of the FID.
crop_td_pts_pot	Crop 'mrs_data' object data points in the time-domain rounding down to the next smallest power of two (pot). Data that already has a pot length will not be changed.
crop_xy	Crop an MRSI dataset in the x-y direction
crossprod_3d	Compute the vector cross product between vectors x and y. Adapted from http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function

-- D --

decimate_mrs_fd	Decimate an MRS signal to half the original sampling frequency by filtering in the frequency domain before down sampling.
decimate_mrs_td	Decimate an MRS signal by filtering in the time domain before downsampling.
deconv_mrs	Deconvolve two MRS data objects.
def_acq_paras	Return (and optionally modify using the input arguments) 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_nuc	Return the default nucleus.
def_ref	Return the default reference value for ppm scale.
dicom_reader	A very simple DICOM reader.
diff_mrs	Apply the diff operator to an MRS dataset in the FID/spectral dimension.
downsample_mrs_fd	Downsample an MRS signal by a factor of 2 using an FFT "brick-wall" filter.
downsample_mrs_td	Downsample an MRS signal by a factor of 2 by removing every other data point in the time-domain. Note, signals outside the new sampling frequency will be aliased.
dyn_acq_times	Return a time scale vector of acquisition times for a dynamic MRS scan. The first temporal scan is assigned a value of 0.

-- E --

ecc	Eddy current correction.
elliptical_mask	Create an elliptical mask stored as a matrix of logical values.
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.
fd_conv_filt	Frequency-domain convolution based filter.
fd_gauss_smo	Apply a Gaussian smoother in the spectral domain.
find_bids_mrs	Search for MRS data files in a BIDS filesystem structure.
find_mrs_files	Find valid MRS data files recursively from a directory path.
fit_amps	Extract the fit amplitudes from an object of class 'fit_result'.
fit_diags	Calculate diagnostic information for object of class 'fit_result'.
fit_mrs	Perform a fit based analysis of MRS data.
fit_res2csv	Write fit results table to a csv file.
fit_t1_ti_array	Fit a T1 recovery curve, from multiple TIs, to a set of amplitudes.
fit_t1_tr_array	Fit a T1 recovery curve, from multiple TRs, to a set of amplitudes.
fit_t2_te_array	Fit a T2 relaxation curve, from multiple TEs, to a set of amplitudes.
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.
fp_scale	Scale the first time-domain data point in an mrs_data object.
fs	Return the sampling frequency in Hz of an MRS dataset.
ft_dyns	Apply the Fourier transform over the dynamic dimension.
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 --

gausswin_2d	Create a two dimensional Gaussian window function stored as a matrix.
gen_baseline_reg	Generate baseline regressor.
gen_bold_reg	Generate BOLD regressors.
gen_conv_reg	Generate regressors by convolving a specified response function with a stimulus.
gen_F	Generate the F product operator.
gen_F_xy	Generate the Fxy product operator with a specified phase.
gen_group_reg	Expand a regressor matrix for a group analysis.
gen_I	Generate the I product operator for a single spin.
gen_impulse_reg	Generate impulse regressors.
gen_poly_reg	Generate polynomial regressors.
gen_trap_reg	Generate trapezoidal regressors.
get_1h_braino_basis_names	Return a character vector of molecules included in the GE BRAINO phantom.
get_1h_brain_basis_names	Return a character vector of common 1H molecules found in healthy human brain.
get_1h_brain_basis_paras	Return a list of 'mol_parameter' objects suitable for 1H brain MRS analyses.
get_1h_brain_basis_paras_v1	Return a list of 'mol_parameter' objects suitable for 1H brain MRS analyses.
get_1h_brain_basis_paras_v2	Return a list of 'mol_parameter' objects suitable for 1H brain MRS analyses.
get_1h_brain_basis_paras_v3	Return a list of 'mol_parameter' objects suitable for 1H brain MRS analyses.
get_1h_spectre_basis_names	Return a character vector of molecules included in the Gold Star Phantoms SPECTRE phantom.
get_2d_psf	Get the point spread function (PSF) for a 2D phase encoded MRSI scan.
get_acq_paras	Return acquisition parameters from a MRS data object.
get_basis_subset	Return a subset of the input basis.
get_dyns	Extract a subset of dynamic scans.
get_even_dyns	Return even numbered dynamic scans starting from 1 (2,4,6...).
get_fh_dyns	Return the first half of a dynamic series.
get_fit_map	Get a data array from a fit result.
get_fp	Return the first time-domain data point.
get_guassian_pulse	Generate a gaussian pulse shape.
get_head_dyns	Return the first scans of a dynamic series.
get_lcm_cmd	Print the command to run the LCModel command-line program.
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_mrsi2d_seg	Calculate the partial volume estimates for each voxel in a 2D MRSI dataset.
get_mrsi_voi	Generate a MRSI VOI from an 'mrs_data' object.
get_mrsi_voxel	Generate a MRSI voxel from an 'mrs_data' object.
get_mrsi_voxel_xy_psf	Generate a MRSI voxel PSF from an 'mrs_data' object.
get_mrs_affine	Generate an affine for nifti generation.
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_sh_dyns	Return the second half of a dynamic series.
get_slice	Return a single slice from a larger MRSI dataset.
get_spin_num	Return the spin number for a given nucleus.
get_subset	Extract a subset of MRS data.
get_svs_voi	Generate a SVS acquisition volume from an 'mrs_data' object.
get_tail_dyns	Return the last scans of a dynamic series.
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_tqn_cmd	Print the command to run the TARQUIN command-line program.
get_uncoupled_mol	Generate a 'mol_parameters' object for a simple spin system with one resonance.
get_voi_cog	Calculate the centre of gravity for an image containing 0 and 1's.
get_voi_seg	Return the white matter, gray matter and CSF composition of a volume.
get_voi_seg_psf	Return the white matter, gray matter and CSF composition of a volume.
get_voxel	Return a single voxel from a larger mrs dataset.
glm_spec	Perform a GLM analysis of dynamic MRS data in the spectral domain.
glm_spec_fmrs_fl	Perform first-level spectral GLM analysis of an fMRS dataset.
glm_spec_fmrs_group	Perform group-level spectral GLM analysis of an fMRS dataset.
glm_spec_group_linhyp	Test a group-level spectral GLM linear hypothesis.
gridplot	Arrange spectral plots in a grid.
gridplot.mrs_data	Arrange spectral plots in a grid.
grid_shift_xy	Grid shift MRSI data in the x/y dimension.

-- H --

hsvd	HSVD of an mrs_data object.
hsvd_filt	HSVD based signal filter.
hsvd_vec	HSVD of a complex vector.
hz	Return the frequency scale of an MRS dataset in Hz.

-- I --

ift_shift	Perform an iffshift and ifft on a vector.
ift_shift_mat	Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft.
Im.mrs_data	Apply Im operator to an MRS dataset.
image.mrs_data	Image plot method for objects of class mrs_data.
img2kspace_xy	Transform 2D MRSI data to k-space in the x-y direction.
Imzap	Complex rounding function taken from complexplus package to reduce the number of spant dependencies.
interleave_dyns	Interleave the first and second half of a dynamic series.
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...).
is.def	Check if an object is defined, which is the same as being not NULL.
is_fd	Check if the chemical shift dimension of an MRS data object is in the frequency domain.

-- K --

kspace2img_xy

Transform 2D MRSI data from k-space to image space in the x-y direction.

-- L --

l2_reg	Perform l2 regularisation artefact suppression.
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.list	Apply line-broadening (apodisation) to MRS data or basis object.
lb.mrs_data	Apply line-broadening (apodisation) to MRS data or basis object.
lofdc	Correct linear frequency drift.
lw2alpha	Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).
lw2beta	Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).

-- M --

make_basis_from_raw	Make a basis-set object from a directory containing LCModel formatted RAW files.
mask_dyns	Mask an MRS dataset in the dynamic dimension.
mask_fit_res	Mask fit result spectra depending on a vector of bool values.
mask_xy	Mask an MRSI dataset in the x-y direction
mask_xy_corners	Mask the four corners of an MRSI dataset in the x-y plane.
mask_xy_ellipse	Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.
mask_xy_mat	Mask a 2D MRSI dataset in the x-y dimension.
mat2mrs_data	Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.
matexp	Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.
max_mrs	Apply the max operator to an MRS dataset.
max_mrs_interp	Apply the max operator to an interpolated MRS dataset.
mean.list	Calculate the mean spectrum from an mrs_data object.
mean.mrs_data	Calculate the mean spectrum from an 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.
mean_mrs_list	Return the mean of a list of mrs_data objects.
mean_vec_blocks	Calculate the mean of adjacent blocks in a vector.
median_dyns	Calculate the median dynamic data.
Mod.mrs_data	Apply Mod operator to an MRS dataset.
mod_td	Apply the Modulus operator to the time-domain MRS signal.
mrs_data2basis	Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
mrs_data2bids	Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.
mrs_data2mat	Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
mrs_data2spec_mat	Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.
mrs_data2vec	Convert mrs_data object to a vector.
mvfftshift	Perform a fftshift on a matrix, with each column replaced by its shifted result.
mvifftshift	Perform an ifftshift on a matrix, with each column replaced by its shifted result.

-- N --

n2coord	Print fit coordinates from a single index.
Ncoils	Return the total number of coil elements in an MRS dataset.
Ndyns	Return the total number of dynamic scans in an MRS dataset.
nifti_flip_lr	Flip the x data dimension order of a nifti image. This corresponds to flipping MRI data in the left-right direction, assuming the data in save in neurological format (can check with fslorient program).
Npts	Return the number of data points in an MRS dataset.
Nspec	Return the total number of spectra in an MRS dataset.
Ntrans	Return the total number of acquired transients for an MRS dataset.
Nx	Return the total number of x locations in an MRS dataset.
Ny	Return the total number of y locations in an MRS dataset.
Nz	Return the total number of z locations in an MRS dataset.

-- O --

one_page_pdf	Export a one-page pdf of a single fit result
ortho3	Display an orthographic projection plot of a nifti object.
ortho3_inter	Display an interactive orthographic projection plot of a nifti object.

-- P --

peak_info	Search for the highest peak in a spectral region and return the frequency, height and FWHM.
pg_extrap_xy	Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation.
phase	Apply phasing parameters to MRS data.
phase_ref_1h_brain	Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.
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_bc	Convenience function to plot a baseline estimate with the original data.
plot_reg	Plot regressors as an image.
plot_slice_fit	Plot a 2D slice from an MRSI fit result object.
plot_slice_fit_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_spec_sd	Plot the spectral standard deviation.
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 or fit result.
ppm.fit_result	Return the ppm scale of an MRS dataset or fit result.
ppm.mrs_data	Return the ppm scale of an MRS dataset or fit result.
precomp	Save function results to file and load on subsequent calls to avoid repeat computation.
preproc_svs	Preprocess and perform quality assessment of a single SVS data set.
preproc_svs_dataset	Preprocess and perform quality assessment of one or more SVS data sets.
print.fit_result	Print a summary of an object of class 'fit_result'.
print.mrs_data	Print a summary of mrs_data parameters.

-- Q --

qn_states

Get the quantum coherence matrix for a spin system.

-- R --

rats	Robust Alignment to a Target Spectrum (RATS).
Re.mrs_data	Apply Re operator to an MRS dataset.
read_basis	Read a basis file in LCModel .basis format.
read_ima_coil_dir	Read a directory containing Siemens MRS IMA files and combine along the coil dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required between two directories.
read_ima_dyn_dir	Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.
read_lcm_coord	Read an LCModel formatted coord file containing fit information.
read_mrs	Read MRS data from a file.
read_mrs_tqn	Read MRS data using the TARQUIN software package.
read_pulse_ascii	Read an ASCII formatted pulse file.
read_pulse_bruker	Read a Bruker formatted pulse file
read_pulse_pta	Read a .pta formatted pulse file compatible with Siemens PulseTool.
read_siemens_txt_hdr	Read the text format header found in Siemens IMA and TWIX data files.
read_tqn_fit	Reader for csv fit results generated by TARQUIN.
read_tqn_result	Reader for csv results generated by TARQUIN.
recon_imag	Reconstruct complex time-domain data from the real part of frequency-domain data.
recon_imag_vec	Reconstruct complex time-domain data from the real part of frequency-domain data.
recon_twix_2d_mrsi	Reconstruct 2D MRSI data from a twix file loaded with read_mrs.
rectangular_mask	Create a rectangular mask stored as a matrix of logical values.
rep_array_dim	Repeat an array over a given dimension.
rep_dyn	Replicate a scan in the dynamic dimension.
rep_mrs	Replicate a scan over a given dimension.
resample_basis	Resample a basis-set to match a mrs_data acquisition.
resample_img	Resample an image to match a target image space.
resample_voi	Resample a VOI to match a target image space using nearest-neighbour interpolation.
reslice_to_mrs	Reslice a nifti object to match the orientation of mrs data.
reson_table2mrs_data	Generate mrs_data from a table of single Lorentzian resonances.
re_weighting	Apply a weighting to the FID to enhance spectral resolution.
rm_dyns	Remove a subset of dynamic scans.

-- S --

scale_amp_molal	Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
scale_amp_molal_pvc	Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).
scale_amp_molar	Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / Litre of tissue).
scale_amp_molar2molal_pvc	Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
scale_amp_ratio	Scale fitted amplitudes to a ratio of signal amplitude.
scale_amp_ratio_value	Scale fitted amplitudes to a ratio of signal amplitude.
scale_amp_water_ratio	Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude.
scale_basis_amp	Scale a basis object by a scalar.
scale_basis_from_singlet	Scale a basis-set to be consistent with spant assumptions for water scaling.
scale_mrs_amp	Scale an mrs_data object by a scalar or vector or amplitudes.
scale_spec	Scale mrs_data to a spectral region.
sd	Calculate the standard deviation spectrum from an mrs_data object.
sd.mrs_data	Calculate the standard deviation spectrum from an mrs_data object.
seconds	Return a time scale vector to match the FID of an MRS data object.
seq_cpmg_ideal	CPMG style sequence with ideal pulses.
seq_mega_press_ideal	MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
seq_press_2d_shaped	PRESS sequence with shaped refocusing pulses.
seq_press_ideal	PRESS sequence with ideal pulses.
seq_pulse_acquire	Simple pulse and acquire sequence with ideal pulses.
seq_slaser_ideal	sLASER sequence with ideal pulses.
seq_spin_echo_ideal	Spin echo sequence with ideal pulses.
seq_steam_ideal	STEAM sequence with ideal pulses.
seq_steam_ideal_cof	STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.
seq_steam_ideal_young	STEAM sequence with ideal pulses using the z-rotation gradient simulation method described by Young et al JMR 140, 146-152 (1999).
set_def_acq_paras	Set the default acquisition parameters.
set_lcm_cmd	Set the command to run the LCModel command-line program.
set_lw	Apply line-broadening to an mrs_data object to achieve a specified linewidth.
set_mask_xy_mat	Set the masked voxels in a 2D MRSI dataset to given spectrum.
set_Ntrans	Set the number of transients for an mrs_data object.
set_precomp_mode	Set the precompute mode.
set_precomp_verbose	Set the verbosity of the precompute function.
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.
set_tr	Set the repetition time of an MRS dataset.
shift	Apply a frequency shift to MRS data.
shift_basis	Apply frequency shifts to basis set signals.
sim_basis	Simulate a basis set object.
sim_basis_1h_brain	Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.
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_mm_lip_lcm	Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.
sim_basis_tqn	Simulate a basis file using TARQUIN.
sim_brain_1h	Simulate MRS data with a similar appearance to normal brain (by default).
sim_mol	Simulate a 'mol_parameter' object.
sim_noise	Simulate an mrs_data object containing simulated Gaussian noise.
sim_resonances	Simulate a MRS data object containing a set of simulated resonances.
sim_th_excit_profile	Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.
sim_zero	Simulate an mrs_data object containing complex zero valued samples.
smooth_dyns	Smooth data across the dynamic dimension with a Gaussian kernel.
sort_basis	Sort the basis-set elements alphabetically.
spant	spant: spectroscopy analysis tools.
spant_abfit_benchmark	Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.
spant_mpress_drift	Example MEGA-PRESS data with significant B0 drift.
spant_simulation_benchmark	Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.
spant_sim_fmrs_dataset	Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.
spec_decomp	Decompose an mrs_data object into white and gray matter spectra.
spec_op	Perform a mathematical operation on a spectral region.
spin_sys	Create a spin system object for pulse sequence simulation.
spm_pve2categorical	Convert SPM style segmentation files to a single categorical image where the numerical values map as: 0) Other, 1) CSF, 2) GM and 3) WM.
ssp	Signal space projection method for lipid suppression.
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.
sub_first_dyn	Subtract the first dynamic spectrum from a dynamic series.
sub_mean_dyns	Subtract the mean dynamic spectrum from a dynamic series.
sub_median_dyns	Subtract the median dynamic spectrum from a dynamic series.
sum_coils	Calculate the sum across receiver coil elements.
sum_dyns	Calculate the sum of data dynamics.
sum_mrs	Sum two mrs_data objects.
sum_mrs_list	Return the sum of a list of mrs_data objects.
svs_1h_brain_analysis	Standard SVS 1H brain analysis pipeline.
svs_1h_brain_analysis_dev	Standard SVS 1H brain analysis pipeline.
svs_1h_brain_batch_analysis	Batch interface to the standard SVS 1H brain analysis pipeline.

-- T --

td2fd	Transform time-domain data to the frequency-domain.
tdsr	Time-domain spectral registration.
td_conv_filt	Time-domain convolution based filter.
te	Return the echo time of an MRS dataset.
tr	Return the repetition time of an MRS dataset.
t_test_spec	Perform a t-test on spectral data points.

-- V --

varpro_3_para_opts	Return a list of options for VARPRO based fitting with 3 free parameters.
varpro_basic_opts	Return a list of options for a basic VARPRO analysis.
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	Write MRS data object to file.
write_mrs_nifti	Write MRS data object to file in NIFTI format.
write_pulse_ascii	Write an ASCII formatted pulse file.

-- Z --

zero_fade_spec	Fade a spectrum to zero by frequency domain multiplication with a tanh function. Note this operation distorts data points at the end of the FID.
zero_higher_orders	Zero all coherences including and above a given order.
zero_td_pts_end	Set 'mrs_data' object data points at the end of the FID to zero.
zf	Zero-fill MRS data in the time domain.
zf.basis_set	Zero-fill MRS data in the time domain.
zf.list	Zero-fill MRS data in the time domain.
zf.mrs_data	Zero-fill MRS data in the time domain.
zf_xy	Zero-fill MRSI data in the k-space x-y direction.