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spant (version 3.6.0)

MR Spectroscopy Analysis Tools

Description

Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data. The package includes methods for spectral fitting: Wilson (2021) , Wilson (2025) and spectral alignment: Wilson (2018) .

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install.packages('spant')

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3.6.0

License

GPL-3

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Repository

https://github.com/martin3141/spant/

Homepage

https://spantdoc.wilsonlab.co.uk/

Maintainer

Martin Wilson

Last Published

September 22nd, 2025

Functions in spant (3.6.0)

Apply Arg operator to an MRS dataset.

Apply Conj operator to an MRS dataset.

Complex rounding function taken from complexplus package to reduce the number of spant dependencies.

Apply Mod operator to an MRS dataset.

Apply Im operator to an MRS dataset.

Return the total number of spectra in an MRS dataset.

Return the total number of acquired transients for an MRS dataset.

Return the total number of coil elements in an MRS dataset.

Return the total number of dynamic scans in an MRS dataset.

Return the number of data points in an MRS dataset.

Add noise to an mrs_data object.

Return a list of options for an ABfit analysis.

Return the total number of y locations in an MRS dataset.

Return the total number of z locations in an MRS dataset.

Return the total number of x locations in an MRS dataset.

add_noise_spec_snr

Add noise to an mrs_data object to match a given SNR.

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.

Apodise MRSI data in the x-y direction with a k-space filter.

Apply a function across given dimensions of a MRS data object.

Append MRS data across the coil dimension, assumes they matched across the other dimensions.

Simulate pulse sequence acquisition.

Align spectra to a reference frequency using a convolution based method.

Return a list of options for an ABfit analysis with regularision.

Apply Re operator to an MRS dataset.

Combine a pair of basis set objects.

Simulate an RF pulse on a single spin.

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.

Apply a function over specified array axes.

Append multiple regressor data frames into a single data frame.

basis2dyn_mrs_data

Convert a basis object to a dynamic mrs_data object.

Append MRS data across the dynamic dimension, assumes they matched across the other dimensions.

Back extrapolate time-domain data points using an autoregressive model.

Perform zeroth-order phase correction based on expected baseline regions.

Generate a spline basis, slightly adapted from : "Splines, knots, and penalties", Eilers 2010.

Perform zeroth-order phase correction based on the minimisation of the squared difference between the real and magnitude components of the spectrum.

Baseline correction using the ALS method.

Fit and subtract a polynomial to each spectrum in a dataset.

Remove a constant baseline offset based on a reference spectral region.

Convert a basis object to an mrs_data object - where basis signals are spread across the dynamic dimension.

Apply and subtract a Gaussian smoother in the spectral domain.

Bin equally spaced spectral regions.

calc_coil_noise_sd

Calculate the noise standard deviation for each coil element.

calc_ed_from_lambda

Calculate the effective dimensions of a spline smoother from lambda.

calc_basis_crlbs

Estimate the CRLB for each element in a basis set.

Covert a beta value in the time-domain to an equivalent linewidth in Hz: x * exp(-i * t * t * beta).

Fit and subtract a smoothing spline to each spectrum in a dataset.

coherence_filter

Zero all coherence orders other than the one supplied as an argument.

calc_coil_noise_cor

Calculate the noise correlation between coil elements.

calc_design_efficiency

Calculate the efficiency of a regressor data frame.

Calculate the spectral SNR.

Check LCModel can be run

calc_peak_info_vec

Calculate the FWHM of a peak from a vector of intensity values.

collapse_to_dyns

Collapse MRS data by concatenating spectra along the dynamic dimension.

comb_fit_tables

Combine all fitting data points into a single data frame.

Crop mrs_data object based on a frequency range.

Create a logical circular mask spanning the full extent of an n x n matrix.

calc_basis_corr_mat

Estimate the correlation matrix for a basis set.

Check the TARQUIN binary can be run

Combine a reference and metabolite mrs_data object.

comb_fit_list_fit_tables

Combine all fitting data points from a list of fits into a single data frame.

Calculate the sum of squares differences between two mrs_data objects.

Combine coil data based on the first data point of a reference signal.

Crop basis_set object based on a frequency range.

Crop mrs_data object data points in the time-domain.

comb_coils_mrsi_gls

Combine MRSI coil data using the GLS method presented by An et al JMRI 37:1445-1450 (2013).

Perform a polynomial fit, subtract and return the standard deviation of the residuals.

Convolve two MRS data objects.

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_dyns

Combine a list of fit results into a single fit result object across the dynamic dimension.

comb_fit_list_result_tables

Combine the fit result tables from a list of fit results.

Return (and optionally modify using the input arguments) a list of the default acquisition parameters.

Return the default sampling frequency in Hz.

Return the default number of data points in the spectral dimension.

decimate_mrs_td

Decimate an MRS signal by filtering in the time domain before downsampling.

decimate_mrs_fd

Decimate an MRS signal to half the original sampling frequency by filtering in the frequency domain before down sampling.

Compute the vector cross product between vectors x and y. Adapted from http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function

Deconvolve two MRS data objects.

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.

Apply the diff operator to an MRS dataset in the FID/spectral dimension.

A very simple DICOM reader.

crop_td_pts_end

Crop mrs_data object data points at the end of the FID.

Eddy current correction.

Return the default reference value for ppm scale.

Crop an MRSI dataset in the x-y direction

Return a time scale vector of acquisition times for a dynamic MRS scan. The first temporal scan is assigned a value of 0.

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.

downsample_mrs_fd

Downsample an MRS signal by a factor of 2 using an FFT "brick-wall" filter.

Return the default nucleus.

Return the default transmitter frequency in Hz.

elliptical_mask

Create an elliptical mask stored as a matrix of logical values.

Find valid MRS data files recursively from a directory path.

Apply a Gaussian smoother in the spectral domain.

Search for MRS data files in a BIDS filesystem structure.

Fit a single asymmetric pseudo-Voigt resonance in the frequency domain.

Extract the fit amplitudes from an object of class fit_result.

fp_phase_correct

Perform a zeroth order phase correction based on the phase of the first data point in the time-domain.

fit_t1_tr_array

Fit a T1 recovery curve, from multiple TRs, to a set of amplitudes.

fit_t1_ti_array

Fit a T1 recovery curve, from multiple TIs, to a set of amplitudes.

GUI interface for the standard SVS 1H brain analysis pipeline, this is a work in progress, and not ready for serious use.

Estimate the standard deviation of the noise from a segment of an mrs_data object.

Standard SVS 1H brain analysis pipeline.

Frequency-domain convolution based filter.

fit_t2_te_array

Fit a T2 relaxation curve, from multiple TEs, to a set of amplitudes.

Perform a fit based analysis of MRS data.

Write fit results table to a csv file.

Calculate diagnostic information for object of class fit_result.

fit_svs_group_results

Combine fitting results for group analysis.

Transform frequency-domain data to the time-domain.

Edited SVS 1H brain analysis pipeline.

Perform a fft and fftshift on a matrix with each column replaced by its shifted fft.

Create a two dimensional Gaussian window function stored as a matrix.

Return the phase of the first data point in the time-domain.

Apply the Fourier transform over the dynamic dimension.

Perform a fft and ffshift on a vector.

Generate the Fxy product operator with a specified phase.

Scale the first time-domain data point in an mrs_data object.

Generate the I product operator for a single spin.

gen_baseline_reg

Generate baseline regressor.

Return the sampling frequency in Hz of an MRS dataset.

Generate the F product operator.

Generate regressors by convolving a specified response function with a stimulus.

get_1h_brain_basis_names

Return a character vector of common 1H molecules found in healthy human brain.

get_1h_brain_basis_paras_v1

Return a list of mol_parameter objects suitable for 1H brain MRS analyses.

Generate BOLD regressors.

gen_numeric_reg

Generate a regressor from a numeric vector.

Generate polynomial regressors.

Extract a subset of dynamic scans.

get_basis_subset

Return a subset of the input basis.

Generate trapezoidal regressors.

get_1h_brain_basis_paras_v3

Return a list of mol_parameter objects suitable for 1H brain MRS analyses.

Return the first half of a dynamic series.

Expand a regressor matrix for a group analysis.

get_1h_brain_basis_paras_v2

Return a list of mol_parameter objects suitable for 1H brain MRS analyses.

Return even numbered dynamic scans starting from 1 (2,4,6...).

get_1h_brain_basis_paras

Return a list of mol_parameter objects suitable for 1H brain MRS analyses.

gen_impulse_reg

Generate impulse regressors.

get_1h_braino_basis_names

Return a character vector of molecules included in the GE BRAINO phantom.

get_1h_spectre_basis_names

Return a character vector of molecules included in the Gold Star Phantoms SPECTRE phantom.

Return the first scans of a dynamic series.

Get the point spread function (PSF) for a 2D phase encoded MRSI scan.

Return acquisition parameters from a MRS data object.

get_guassian_pulse

Generate a gaussian pulse shape.

Generate an affine for nifti generation.

Get a data array from a fit result.

Get a mol_parameters object for a named molecule.

Generate a double gamma model of the HRF as used in SPM.

Get the indices of data points lying between two values (end > x > start).

Print the command to run the LCModel command-line program.

Extract the metabolite component from an mrs_data object.

Generate a MRSI voxel from an mrs_data object.

Return a character array of names that may be used with the get_mol_paras function.

Return the first time-domain data point.

get_mrsi_voxel_xy_psf

Generate a MRSI voxel PSF from an mrs_data object.

Return odd numbered dynamic scans starting from 1 (1,3,5...).

Return the second half of a dynamic series.

Extract the reference component from an mrs_data object.

Generate a MRSI VOI from an mrs_data object.

Return a single slice from a larger MRSI dataset.

Return the spin number for a given nucleus.

Calculate the partial volume estimates for each voxel in a 2D MRSI dataset.

Return the white matter, gray matter and CSF composition of a volume.

Calculate the centre of gravity for an image containing 0 and 1's.

Return a single voxel from a larger mrs dataset.

get_voi_seg_psf

Return the white matter, gray matter and CSF composition of a volume.

glm_spec_fmrs_group

Perform group-level spectral GLM analysis of an fMRS dataset.

Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0.

Return the last scans of a dynamic series.

HSVD of an mrs_data object.

gridplot.mrs_data

Arrange spectral plots in a grid.

Grid shift MRSI data in the x/y dimension.

Extract a subset of MRS data.

get_uncoupled_mol

Generate a mol_parameters object for a simple spin system with one resonance.

Print the command to run the TARQUIN command-line program.

Generate a SVS acquisition volume from an mrs_data object.

Arrange spectral plots in a grid.

glm_spec_fmrs_fl

Perform first-level spectral GLM analysis of an fMRS dataset.

Perform a GLM analysis of dynamic MRS data in the spectral domain.

HSVD of a complex vector.

Integrate a spectral region.

Return the frequency scale of an MRS dataset in Hz.

Install the spant command-line interface scripts to a system path.

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

Perform an ifft and ifftshift on a matrix with each column replaced by its shifted ifft.

Invert odd numbered dynamic scans starting from 1 (1,3,5...).

HSVD based signal filter.

glm_spec_group_linhyp

Test a group-level spectral GLM linear hypothesis.

Invert even numbered dynamic scans starting from 1 (2,4,6...).

Perform an iffshift and ifft on a vector.

Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).

Mask an MRS dataset in the dynamic dimension.

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

Perform l2 regularisation artefact suppression.

interleave_dyns

Interleave the first and second half of a dynamic series.

Check if an object is defined, which is the same as being not NULL.

Correct linear frequency drift.

Image plot method for objects of class mrs_data.

Apply line-broadening (apodisation) to MRS data or basis object.

Covert a linewidth in Hz to an equivalent alpha value in the time-domain ie: x * exp(-t * alpha).

Check if the chemical shift dimension of an MRS data object is in the frequency domain.

Matrix exponential function taken from complexplus package to reduce the number of spant dependencies.

Mask fit result spectra depending on a vector of bool values.

Convert a matrix (with spectral points in the column dimension and dynamics in the row dimensions) into a mrs_data object.

match_lineshape

Apply Voigt line-broadening to match a reference spectrum.

make_basis_from_raw

Make a basis-set object from a directory containing LCModel formatted RAW files.

Mask a 2D MRSI dataset in the x-y dimension.

Calculate the pairwise means across a dynamic data set.

Apply the max operator to an MRS dataset.

Apply the max operator to an interpolated MRS dataset.

Return the mean of a list of mrs_data objects.

Calculate the mean dynamic data.

mean_dyns_scheme

Average sets of dynamics according to a scheme vector.

mean_dyn_blocks

Calculate the mean of adjacent dynamic scans.

Calculate the median dynamic data.

Calculate the mean spectrum from an mrs_data object.

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.

Perform an ifftshift on a matrix, with each column replaced by its shifted result.

Print fit coordinates from a single index.

Calculate the mean spectrum from an mrs_data object.

Convert mrs_data object to a vector.

Mask an MRSI dataset in the x-y direction

Create a BIDS file structure from a vector of data paths or list of mri/mrs data objects.

Split MRS data containing multiple spectra into a list of single spectra datasets.

Apply the Modulus operator to the time-domain MRS signal.

mean_vec_blocks

Calculate the mean of adjacent blocks in a vector.

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).

plot.fit_result

Plot the fitting results of an object of class fit_result.

Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.

Perform a fftshift on a matrix, with each column replaced by its shifted result.

Papoulis-Gerchberg (PG) algorithm method for k-space extrapolation.

Search for the highest peak in a spectral region and return the frequency, height and FWHM.

mrs_data2spec_mat

Convert mrs_data object to a matrix, with spectral points in the column dimension and dynamics in the row dimension.

plot_voi_overlay_seg

Plot a volume as an overlay on a segmented brain volume.

Return the ppm scale of an MRS dataset or fit result.

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.

Create a BIDS file structure from a vector of MRS data paths or list of mrs_data objects.

Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.

Plot a 2D slice from an MRSI fit result object.

Display an interactive orthographic projection plot of a nifti object.

Plot the spectral standard deviation.

Plotting method for objects of class mrs_data.

Display an orthographic projection plot of a nifti object.

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 a slice from a 7 dimensional array.

Export a one-page pdf of a single fit result

plot_slice_fit_inter

Plot a 2D slice from an MRSI fit result object.

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.

Save function results to file and load on subsequent calls to avoid repeat computation.

Robust Alignment to a Target Spectrum (RATS).

Apply a weighting to the FID to enhance spectral resolution.

Get the quantum coherence matrix for a spin system.

Print a summary of mrs_data parameters.

Plot regressors as an image.

Convenience function to plot a baseline estimate with the original data.

read_basis_niidir

Read a basis folder containing one NIfTI MRS file for each basis element.

read_pulse_ascii

Read an ASCII formatted pulse file.

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 an LCModel formatted coord file containing fit information.

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_dkd_moco_log

Read the log from Dinesh's MoCo sLASER sequence.

read_siemens_txt_hdr

Read the text format header found in Siemens IMA and TWIX data files.

Objects exported from other packages

Read a .pta formatted pulse file compatible with Siemens PulseTool.

Reader for csv fit results generated by TARQUIN.

read_pulse_bruker

Read a Bruker formatted pulse file

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.

Read MRS data from the filesystem.

read_tqn_result

Reader for csv results generated by TARQUIN.

Reconstruct complex time-domain data from the real part of frequency-domain data.

Reconstruct complex time-domain data from the real part of frequency-domain data.

Repeat an array over a given dimension.

Replicate a scan over a given dimension.

Replicate a scan in the dynamic dimension.

Read MRS data using the TARQUIN software package.

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). This function is depreciated, please use scale_amp_legacy instead.

Remove a subset of dynamic scans.

Resample a VOI to match a target image space using nearest-neighbour interpolation.

Resample an image to match a target image space.

scale_amp_legacy

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

Reslice a nifti object to match the orientation of mrs data.

Resample a basis-set to match a mrs_data acquisition.

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).

reson_table2mrs_data

Generate mrs_data from a table of single Lorentzian resonances.

scale_amp_molar2molal_pvc

Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.

scale_amp_ratio_value

Scale fitted amplitudes to a ratio of signal amplitude.

scale_amp_ratio

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 an mrs_data object by a scalar or vector or amplitudes.

scale_basis_from_singlet

Scale a basis-set to be consistent with spant assumptions for water scaling.

Calculate the standard deviation spectrum from an mrs_data object.

Calculate the standard deviation spectrum from an mrs_data object.

Scale mrs_data to a spectral region.

scale_basis_amp

Scale a basis object by a scalar.

seq_mega_press_ideal

MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.

seq_slaser_ideal

sLASER sequence with ideal pulses.

seq_press_ideal

PRESS sequence with ideal pulses.

seq_pulse_acquire

Simple pulse and acquire sequence with ideal pulses.

CPMG style sequence with ideal pulses.

Return a time scale vector to match the FID of an MRS data object.

Segment T1 weighted MRI data using FSL FAST and write to file. Runs deface and bet as preprocessing steps by default.

seq_press_2d_shaped

PRESS sequence with shaped refocusing 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.

Set the command to run the LCModel command-line program.

Set the number of transients for an mrs_data object.

set_mask_xy_mat

Set the masked voxels in a 2D MRSI dataset to given spectrum.

set_precomp_mode

Set the precompute mode.

set_def_acq_paras

Set the default acquisition parameters.

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).

Generate an asymmetric pseudo-Voigt resonance in the frequency domain.

sim_basis_1h_brain

Simulate a basis-set suitable for 1H brain MRS analysis acquired with a PRESS sequence. Note, ideal pulses are assumed.

Set the command to run the TARQUIN command-line program.

Set the number of time-domain data points, truncating or zero-filling as appropriate.

sim_basis_mm_lip_lcm

Simulate a macromolecular and lipid basis-set suitable for 1H brain MRS analysis.

Set the repetition time of an MRS dataset.

Set the ppm reference value (eg ppm value at 0Hz).

Simulate a basis set object.

Apply line-broadening to an mrs_data object to achieve a specified linewidth.

Apply frequency shifts to basis set signals.

set_precomp_verbose

Set the verbosity of the precompute function.

Apply a frequency shift to MRS data.

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.

Simulate an mrs_data object containing complex zero valued samples.

Simulate a mol_parameter object.

sim_th_excit_profile

Simulate an ideal pulse excitation profile by smoothing a top-hat function with a Gaussian.

spant: spectroscopy analysis tools.

Sort the basis-set elements alphabetically.

Smooth data across the dynamic dimension with a Gaussian kernel.

Simulate a MRS data object containing a set of simulated resonances.

spant_simulation_benchmark

Simulate a typical metabolite basis set for benchmarking. Timing metrics will be printed on completion.

Simulate an mrs_data object containing simulated Gaussian noise.

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.

Simulate a basis file using TARQUIN.

Simulate MRS data with a similar appearance to normal brain (by default).

Create a spin system object for pulse sequence simulation.

spant_abfit_benchmark

Simulate and fit some spectra with ABfit for benchmarking purposes. Basic timing and performance metrics will be printed.

Perform a mathematical operation on a spectral region.

Decompose an mrs_data object into white and gray matter spectra.

spant_sim_fmrs_dataset

Simulate an example fMRS dataset for a block design fMRS experiment and export a BIDS structure.

Signal space projection method for lipid suppression.

stackplot.fit_result

Plot the fitting results of an object of class fit_result with individual basis set components shown.

Produce a plot with multiple traces.

Subtract the first dynamic spectrum from a dynamic series.

Sum two mrs_data objects.

sub_median_dyns

Subtract the median dynamic spectrum from a dynamic series.

sub_odd_from_even_dyns

Subtract the odd dynamic scans from the even dynamic scans.

Calculate the sum of data dynamics.

Subtract the mean dynamic spectrum from a dynamic series.

subtract_rest_task

Subtract mean rest spectrum from mean task spectrum after applying optimal linebroadening to the mean task spectrum. Usually used to correct for the BOLD lineshape narrowing effect in 1H fMRS data.

Calculate the sum across receiver coil elements.

Perform a t-test on spectral data points.

svs_1h_brain_batch_analysis

Batch interface to the standard SVS 1H brain analysis pipeline.

Return the echo time of an MRS dataset.

svs_1h_brain_analysis_dev

Standard SVS 1H brain analysis pipeline.

stackplot.mrs_data

Stackplot plotting method for objects of class mrs_data.

Time-domain spectral registration.

svs_1h_brain_analysis

Standard SVS 1H brain analysis pipeline.

sub_even_from_odd_dyns

Subtract the even dynamic scans from the odd dynamic scans.

Transform time-domain data to the frequency-domain.

Time-domain convolution based filter.

Write MRS data object to file.

varpro_basic_opts

Return a list of options for a basic VARPRO analysis.

Return a list of options for VARPRO based fitting.

Write a basis object to an LCModel .basis formatted file.

varpro_3_para_opts

Return a list of options for VARPRO based fitting with 3 free parameters.

Convert a vector into a mrs_data object.

Return the repetition time of an MRS dataset.

write_basis_tqn

Generate a basis file using TARQUIN.

Return the sum of a list of mrs_data objects.

write_basis_niidir

Write a basis object to folder containing one NIfTI MRS file for each basis element.

write_mrs_nifti

Write MRS data object to file in NIFTI format.

Output a table of fit amplitudes and error estimates for a single-voxel fit.

zero_higher_orders

Zero all coherences including and above a given order.

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-fill MRSI data in the k-space x-y direction.

Zero-fill MRS data in the time domain.

write_pulse_ascii

Write an ASCII formatted pulse file.

zero_td_pts_end

Set mrs_data object data points at the end of the FID to zero.