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spant (version 3.4.0)

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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3.4.0

License

GPL-3

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Repository

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

Homepage

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

Maintainer

Martin Wilson

Last Published

June 11th, 2025

Functions in spant (3.4.0)

Return the total number of spectra in an MRS dataset.

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

Apply Mod operator to an MRS dataset.

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

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

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

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.

Simulate pulse sequence acquisition.

Return a list of options for an ABfit analysis.

add_noise_spec_snr

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

Add noise to an mrs_data object.

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

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

Combine a pair of basis set objects.

Apply a function over specified array axes.

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.

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

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

Append multiple regressor data frames into a single data frame.

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

Apply Re operator to an MRS dataset.

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

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

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

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

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

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

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

Apply and subtract a Gaussian smoother in the spectral domain.

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

collapse_to_dyns

Collapse MRS data by concatenating spectra along the dynamic dimension.

calc_ed_from_lambda

Calculate the effective dimensions of a spline smoother from lambda.

calc_design_efficiency

Calculate the efficiency of a regressor data frame.

Check the TARQUIN binary can be run

Check LCModel can be run

calc_peak_info_vec

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

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

basis2dyn_mrs_data

Convert a basis object to a dynamic mrs_data object.

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

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

Calculate the sum of squares differences between two mrs_data objects.

Bin equally spaced spectral regions.

Calculate the spectral SNR.

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.

coherence_filter

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

Baseline correction using the ALS method.

Convolve two MRS data objects.

Combine a reference and metabolite mrs_data object.

Crop mrs_data object data points in the time-domain.

Crop basis_set object based on a frequency range.

Crop an MRSI dataset in the x-y direction

calc_coil_noise_cor

Calculate the noise correlation between coil elements.

comb_fit_list_fit_tables

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

Deconvolve two MRS data objects.

comb_fit_list_result_tables

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

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.

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

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

Return the default sampling frequency in Hz.

crop_td_pts_end

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

calc_coil_noise_sd

Calculate the noise standard deviation for each coil element.

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.

A very simple DICOM reader.

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

Return the default reference value for ppm scale.

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

calc_basis_corr_mat

Estimate the correlation matrix for a basis set.

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

calc_basis_crlbs

Estimate the CRLB for each element in a basis set.

Transform frequency-domain data to the time-domain.

comb_coils_svs_gls

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

comb_coils_mrsi_gls

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

fp_phase_correct

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

Perform a fit based analysis of MRS data.

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

Write fit results table to a csv file.

gen_baseline_reg

Generate baseline regressor.

Eddy current correction.

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.

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

Generate BOLD regressors.

Standard SVS 1H brain analysis pipeline.

Perform a fft and ffshift on a vector.

Edited SVS 1H brain analysis pipeline.

fit_t1_ti_array

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

Frequency-domain convolution based filter.

Apply a Gaussian smoother in the spectral domain.

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

fit_t1_tr_array

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

Search for MRS data files in a BIDS filesystem structure.

gen_impulse_reg

Generate impulse regressors.

Return the first half of a dynamic series.

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

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

Generate trapezoidal regressors.

get_1h_brain_basis_names

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

Find valid MRS data files recursively from a directory path.

Generate polynomial regressors.

get_1h_brain_basis_paras_v3

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

Expand a regressor matrix for a group analysis.

get_guassian_pulse

Generate a gaussian pulse shape.

get_1h_brain_basis_paras_v2

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

Return the first scans of a dynamic series.

Return a single slice from a larger MRSI dataset.

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

Return the spin number for a given nucleus.

Extract the metabolite component from an mrs_data object.

Return the last scans of a dynamic series.

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

Generate a MRSI VOI from an mrs_data object.

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

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

fit_svs_group_results

Combine fitting results for group analysis.

glm_spec_fmrs_group

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

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

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

Integrate a spectral region.

interleave_dyns

Interleave the first and second half of a dynamic series.

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

Arrange spectral plots in a grid.

Grid shift MRSI data in the x/y dimension.

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

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.

elliptical_mask

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

Generate the I product operator for a single spin.

Generate the Fxy product operator with a specified phase.

Apply the Fourier transform over the dynamic dimension.

Return the sampling frequency in Hz of an MRS dataset.

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

glm_spec_group_linhyp

Test a group-level spectral GLM linear hypothesis.

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

mask_xy_ellipse

Mask the voxels outside an elliptical region spanning the MRSI dataset in the x-y plane.

mask_xy_corners

Mask the four corners of an MRSI dataset in the x-y plane.

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

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

get_basis_subset

Return a subset of the input basis.

Return acquisition parameters from a MRS data object.

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

Extract the reference component from an mrs_data object.

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

Generate a SVS acquisition volume from an mrs_data object.

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

get_uncoupled_mol

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

Extract a subset of dynamic scans.

Generate an affine for nifti generation.

Extract a subset of MRS data.

Get a mol_parameters object for a named molecule.

Apply the max operator to an MRS dataset.

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

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

Calculate the median dynamic data.

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

Return the second half of a dynamic series.

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

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

Return the default transmitter frequency in Hz.

Plot the spectral standard deviation.

plot_voi_overlay

Plot a volume as an image overlay.

Robust Alignment to a Target Spectrum (RATS).

Return the default nucleus.

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

Mask an MRS dataset in the dynamic dimension.

Perform l2 regularisation artefact suppression.

Display an orthographic projection plot of a nifti object.

Image plot method for objects of class mrs_data.

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

make_basis_from_raw

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

Apply a weighting to the FID to enhance spectral resolution.

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

read_tqn_result

Reader for csv results generated by TARQUIN.

Read MRS data from the filesystem.

Read an LCModel formatted coord file containing fit information.

Display an interactive orthographic projection plot of a nifti object.

downsample_mrs_fd

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

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

plot.fit_result

Plot the fitting results of an object of class fit_result.

Plotting method for objects of class mrs_data.

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_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_water_ratio

Scale metabolite amplitudes as a ratio to the unsuppressed water amplitude.

get_voi_seg_psf

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

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.

glm_spec_fmrs_fl

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

HSVD of a complex vector.

HSVD based signal filter.

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

Return a single voxel from a larger mrs dataset.

gridplot.mrs_data

Arrange spectral plots in a grid.

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

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

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

Return the mean of a list of mrs_data objects.

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

mean_vec_blocks

Calculate the mean of adjacent blocks in a vector.

Plot regressors as an image.

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

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.

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

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_steam_ideal

STEAM sequence with ideal pulses.

scale_basis_amp

Scale a basis object by a scalar.

Preprocess and perform quality assessment of a single SVS data set.

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

read_pulse_bruker

Read a Bruker formatted pulse file

rectangular_mask

Create a rectangular mask stored as a matrix of logical values.

Extract the fit amplitudes from an object of class fit_result.

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.

seq_steam_ideal_cof

STEAM sequence with ideal pulses and coherence order filtering to simulate gradient crushers.

sim_basis_mm_lip_lcm

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

Objects exported from other packages

Remove a subset of dynamic scans.

Correct linear frequency drift.

Calculate the pairwise means across a dynamic data set.

scale_amp_molar2molal_pvc

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

scale_amp_legacy

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

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.

Calculate the standard deviation spectrum from an mrs_data object.

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

Calculate the mean dynamic data.

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

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

recon_twix_2d_mrsi

Reconstruct 2D MRSI data from a twix file loaded with read_mrs.

Simulate a mol_parameter object.

set_def_acq_paras

Set the default acquisition parameters.

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

Set the repetition time of an MRS dataset.

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

seq_press_ideal

PRESS sequence with ideal pulses.

seq_pulse_acquire

Simple pulse and acquire sequence with ideal pulses.

scale_amp_ratio

Scale fitted amplitudes to a ratio of signal amplitude.

spant_simulation_benchmark

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

scale_amp_ratio_value

Scale fitted amplitudes to a ratio of signal amplitude.

Simulate an mrs_data object containing simulated Gaussian noise.

Return the sum of a list of mrs_data objects.

Decompose an mrs_data object into white and gray matter spectra.

Sum two mrs_data objects.

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).

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

Plot a slice from a 7 dimensional array.

Print fit coordinates from a single index.

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

Calculate diagnostic information for object of class fit_result.

fit_t2_te_array

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

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

Set the number of transients for an mrs_data object.

Sort the basis-set elements alphabetically.

Perform a mathematical operation on a spectral region.

spant: spectroscopy analysis tools.

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_seg

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

Simulate a basis file using TARQUIN.

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

Zero-fill MRS data in the time domain.

Return the repetition time of an MRS dataset.

Write MRS data object to file.

write_mrs_nifti

Write MRS data object to file in NIFTI format.

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

Return the echo time of an MRS dataset.

Calculate the sum of data dynamics.

Calculate the sum across receiver coil elements.

Create a spin system object for pulse sequence simulation.

Generate the F product operator.

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.

Return the first time-domain data point.

Get a data array from a fit result.

Generate a MRSI voxel from an mrs_data object.

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

write_basis_tqn

Generate a basis file using TARQUIN.

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

Transform time-domain data to the frequency-domain.

Perform a t-test on spectral data points.

get_mrsi_voxel_xy_psf

Generate a MRSI voxel PSF from an mrs_data object.

spant_abfit_benchmark

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

Read a basis file in LCModel .basis format.

read_dkd_moco_log

Read the log from Dinesh's MoCo sLASER sequence.

Return the frequency scale of an MRS dataset in Hz.

stackplot.mrs_data

Stackplot plotting method for objects of class mrs_data.

zero_higher_orders

Zero all coherences including and above a given order.

svs_1h_brain_batch_analysis

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

spant_sim_fmrs_dataset

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

zero_td_pts_end

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

Subtract the first dynamic spectrum from a dynamic series.

svs_1h_brain_analysis_dev

Standard SVS 1H brain analysis pipeline.

Perform an iffshift and ifft on a vector.

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

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

reson_table2mrs_data

Generate mrs_data from a table of single Lorentzian resonances.

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

Calculate the mean spectrum from an mrs_data object.

Apply the max operator to an interpolated MRS dataset.

Convert mrs_data object to a vector.

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

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

HSVD of an mrs_data object.

Calculate the standard deviation spectrum from an mrs_data object.

Scale mrs_data to a spectral region.

Apply phasing parameters to MRS data.

set_precomp_verbose

Set the verbosity of the precompute function.

set_precomp_mode

Set the precompute mode.

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

Calculate the mean spectrum from an mrs_data object.

mrs_data2spec_mat

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

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

Mask an MRSI dataset in the x-y direction

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

mean_dyn_blocks

Calculate the mean of adjacent dynamic scans.

Repeat an array over a given dimension.

Print a summary of mrs_data parameters.

phase_ref_1h_brain

Corrected zero order phase and chemical shift offset in 1H MRS data from the brain.

Get the quantum coherence matrix for a spin system.

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).

Replicate a scan in the dynamic dimension.

Resample an image to match a target image space.

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

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

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

svs_1h_brain_analysis

Standard SVS 1H brain analysis pipeline.

Export a one-page pdf of a single fit result

varpro_3_para_opts

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

read_pulse_ascii

Read an ASCII formatted pulse file.

Read MRS data using the TARQUIN software package.

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

Resample a basis-set to match a mrs_data acquisition.

seq_spin_echo_ideal

Spin echo sequence with ideal pulses.

Reader for csv fit results generated by TARQUIN.

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.

plot_slice_fit_inter

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

seq_slaser_ideal

sLASER sequence with ideal pulses.

read_siemens_txt_hdr

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

Replicate a scan over a given dimension.

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.

varpro_basic_opts

Return a list of options for a basic VARPRO analysis.

write_pulse_ascii

Write an ASCII formatted pulse file.

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

Simulate an mrs_data object containing complex zero valued samples.

sim_basis_1h_brain

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

Simulate a basis set object.

scale_basis_from_singlet

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

Smooth data across the dynamic dimension with a Gaussian kernel.

Produce a plot with multiple traces.

Scale an mrs_data object by a scalar or vector or amplitudes.

Apply a frequency shift to MRS data.

Apply frequency shifts to basis set signals.

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

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

set_mask_xy_mat

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

CPMG style sequence with ideal pulses.

Signal space projection method for lipid suppression.

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

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.

Subtract the mean dynamic spectrum from a dynamic series.

sim_th_excit_profile

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

sub_median_dyns

Subtract the median dynamic spectrum from a dynamic series.

Time-domain convolution based filter.

Time-domain spectral registration.

stackplot.fit_result

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

Convert a vector into a mrs_data object.

Return a list of options for VARPRO based fitting.

Apply Im operator to an MRS dataset.

Apply Conj operator to an MRS dataset.

Return the number of data points in an MRS dataset.

Apply Arg operator to an MRS dataset.

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

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