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spant (version 3.3.0)

MR Spectroscopy Analysis Tools

Description

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

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install.packages('spant')

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3.3.0

License

GPL-3

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Repository

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

Homepage

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

Maintainer

Martin Wilson

Last Published

March 28th, 2025

Functions in spant (3.3.0)

Return the total number of spectra in an MRS dataset.

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

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

Apply Im operator to an MRS dataset.

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

Apply Conj operator to an MRS dataset.

Return the number of data points in an MRS dataset.

Apply Mod operator to an MRS dataset.

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

Apply Arg operator to an MRS dataset.

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

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

Simulate pulse sequence acquisition.

Add noise to an mrs_data object.

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

add_noise_spec_snr

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

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

Apply a function over specified array axes.

Return a list of options for an ABfit analysis.

Apply Re operator to 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.

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

Combine a pair of basis set objects.

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

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

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

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

Baseline correction using the ALS method.

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

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

Append multiple regressor data frames into a single data frame.

Simulate an RF pulse on a single spin.

calc_peak_info_vec

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

Apply and subtract a Gaussian smoother in the spectral domain.

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

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.

Check LCModel can be run

calc_basis_corr_mat

Estimate the correlation matrix for a basis set.

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

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

basis2dyn_mrs_data

Convert a basis object to a dynamic mrs_data object.

calc_basis_crlbs

Estimate the CRLB for each element in a basis set.

Bin equally spaced spectral regions.

comb_coils_mrsi_gls

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

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

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.

Calculate the sum of squares differences between two mrs_data objects.

Calculate the spectral SNR.

comb_coils_svs_gls

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

coherence_filter

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

calc_coil_noise_sd

Calculate the noise standard deviation for each coil element.

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

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

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

calc_coil_noise_cor

Calculate the noise correlation between coil elements.

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

collapse_to_dyns

Collapse MRS data by concatenating spectra along the dynamic dimension.

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

comb_fit_tables

Combine all fitting data points into a single data frame.

Convolve two MRS data objects.

Check the TARQUIN binary can be run

Crop basis_set object based on a frequency range.

Return the default sampling frequency in Hz.

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

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.

Crop mrs_data object based on a frequency range.

Crop mrs_data object data points in the time-domain.

Return the default transmitter frequency in Hz.

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.

Combine a reference and metabolite mrs_data object.

Crop an MRSI dataset in the x-y direction

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

elliptical_mask

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

gen_baseline_reg

Generate baseline regressor.

downsample_mrs_fd

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

Extract the fit amplitudes from an object of class fit_result.

Return the default nucleus.

Transform frequency-domain data to the time-domain.

Search for MRS data files in a BIDS filesystem structure.

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

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

Find valid MRS data files recursively from a directory path.

Standard SVS 1H brain analysis pipeline.

Calculate diagnostic information for object of class fit_result.

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

fp_phase_correct

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

Generate the Fxy product operator with a specified phase.

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.

Edited SVS 1H brain analysis pipeline.

Deconvolve two MRS data objects.

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.

Return the sampling frequency in Hz of an MRS dataset.

Return the default reference value for ppm scale.

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

Generate BOLD regressors.

get_1h_braino_basis_names

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

Generate the I product operator for a single spin.

Apply a Gaussian smoother in the spectral domain.

fit_t2_te_array

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

A very simple DICOM reader.

Frequency-domain convolution based filter.

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

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

Return acquisition parameters from a MRS data object.

Apply the Fourier transform over the dynamic dimension.

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

Extract the metabolite component from an mrs_data object.

gen_impulse_reg

Generate impulse regressors.

Extract a subset of dynamic scans.

get_basis_subset

Return a subset of the input basis.

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

get_1h_spectre_basis_names

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

Generate polynomial regressors.

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

Generate the F product operator.

get_1h_brain_basis_paras

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

Generate an affine for nifti generation.

Get a mol_parameters object for a named molecule.

Extract a subset of MRS data.

Perform a fit based analysis of MRS data.

Write fit results table to a csv file.

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

fit_svs_group_results

Combine fitting results for group analysis.

Generate a SVS acquisition volume from an mrs_data object.

glm_spec_fmrs_group

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

get_guassian_pulse

Generate a gaussian pulse shape.

Generate a MRSI voxel from an mrs_data object.

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

Perform a fft and ffshift on a vector.

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

get_1h_brain_basis_paras_v1

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

Return the first scans of a dynamic series.

glm_spec_group_linhyp

Test a group-level spectral GLM linear hypothesis.

get_1h_brain_basis_paras_v2

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

Perform an iffshift and ifft on a vector.

Return the frequency scale of an MRS dataset in Hz.

get_mrsi_voxel_xy_psf

Generate a MRSI voxel PSF from an mrs_data object.

Get a data array from a fit result.

Return the second half of a dynamic series.

get_1h_brain_basis_paras_v3

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

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

Return the first time-domain data point.

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

Grid shift MRSI data in the x/y dimension.

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

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.

Expand a regressor matrix for a group analysis.

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

Generate a MRSI VOI from an mrs_data object.

Arrange spectral plots in a grid.

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

Generate trapezoidal regressors.

get_1h_brain_basis_names

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

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

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

Return the first half of a dynamic series.

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

Return a single slice from a larger MRSI dataset.

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.

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

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

Extract the reference component from an mrs_data object.

Perform l2 regularisation artefact suppression.

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

get_voi_seg_psf

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

Return the spin number for a given nucleus.

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

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

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.

make_basis_from_raw

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

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

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

gridplot.mrs_data

Arrange spectral plots in a grid.

HSVD of an mrs_data object.

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

Mask an MRS dataset in the dynamic dimension.

HSVD based signal filter.

mean_dyn_blocks

Calculate the mean of adjacent dynamic scans.

Calculate the mean spectrum from an mrs_data object.

HSVD of a complex vector.

Calculate the median dynamic data.

get_uncoupled_mol

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

Apply the max operator to an MRS dataset.

Convert mrs_data object to a vector.

Return a single voxel from a larger mrs dataset.

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

Return the mean of a list of mrs_data objects.

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

Apply the max operator to an interpolated MRS dataset.

Calculate the mean spectrum from an mrs_data object.

plot_slice_fit_inter

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

Print fit coordinates from a single index.

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

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

Image plot method for objects of class mrs_data.

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

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

Integrate a spectral region.

interleave_dyns

Interleave the first and second half of a dynamic series.

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

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

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

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

Plot the spectral standard deviation.

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

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

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

Calculate the pairwise means across a dynamic data set.

Calculate the mean dynamic data.

Mask an MRSI dataset in the x-y direction

mean_vec_blocks

Calculate the mean of adjacent blocks in a vector.

Correct linear frequency drift.

Apply phasing parameters to MRS data.

Display an interactive orthographic projection plot of a nifti object.

Display an orthographic projection plot of a nifti object.

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

Plot regressors as an image.

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

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

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

phase_ref_1h_brain

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

mrs_data2spec_mat

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

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

read_siemens_txt_hdr

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

Plot a slice from a 7 dimensional array.

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

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

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.

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 an LCModel formatted coord file containing fit information.

Print a summary of mrs_data parameters.

Get the quantum coherence matrix for a spin system.

Objects exported from other packages

read_pulse_ascii

Read an ASCII formatted pulse file.

plot_voi_overlay

Plot a volume as an image overlay.

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.

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

Repeat an array over a given dimension.

Remove a subset of dynamic scans.

reson_table2mrs_data

Generate mrs_data from a table of single Lorentzian resonances.

scale_amp_ratio_value

Scale fitted amplitudes to a ratio of signal amplitude.

scale_amp_legacy

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

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

Export a one-page pdf of a single fit result

Plotting method for objects of class mrs_data.

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).

preproc_svs_dataset

Preprocess and perform quality assessment of one or more SVS data sets.

plot.fit_result

Plot the fitting results of an object of class fit_result.

print.fit_result

Print a summary of an object of class fit_result.

Robust Alignment to a Target Spectrum (RATS).

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

Apply a weighting to the FID to enhance spectral resolution.

scale_amp_water_ratio

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

Read a basis file in LCModel .basis format.

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_ratio

Scale fitted amplitudes to a ratio of signal amplitude.

scale_amp_molar2molal_pvc

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

set_precomp_mode

Set the precompute mode.

set_mask_xy_mat

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

sim_basis_mm_lip_lcm

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

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

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.

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

seq_pulse_acquire

Simple pulse and acquire sequence with ideal pulses.

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

seq_slaser_ideal

sLASER sequence with ideal pulses.

Apply a frequency shift to MRS data.

sim_th_excit_profile

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

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).

Set the repetition time of an MRS dataset.

Replicate a scan in the dynamic dimension.

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.

Simulate a basis file using TARQUIN.

Replicate a scan over a given dimension.

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

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.

scale_basis_from_singlet

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

scale_basis_amp

Scale a basis object by a scalar.

Reader for csv fit results generated by TARQUIN.

read_pulse_bruker

Read a Bruker formatted pulse file

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

Calculate the standard deviation spectrum from an mrs_data object.

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

set_def_acq_paras

Set the default acquisition parameters.

spant_sim_fmrs_dataset

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

Set the number of transients for an mrs_data object.

read_tqn_result

Reader for csv results generated by TARQUIN.

Scale mrs_data to a spectral region.

Simulate an mrs_data object containing complex zero valued samples.

stackplot.fit_result

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

spant_simulation_benchmark

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

Smooth data across the dynamic dimension with a Gaussian kernel.

CPMG style sequence with ideal pulses.

seq_mega_press_ideal

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

Return the repetition time of an MRS dataset.

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.

Calculate the standard deviation spectrum from an mrs_data object.

seq_spin_echo_ideal

Spin echo sequence with ideal pulses.

seq_steam_ideal

STEAM sequence with ideal pulses.

Read MRS data from the filesystem.

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

set_precomp_verbose

Set the verbosity of the precompute function.

Read MRS data using the TARQUIN software package.

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

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

Return the sum of a list of mrs_data objects.

stackplot.mrs_data

Stackplot plotting method for objects of class mrs_data.

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

Sort the basis-set elements alphabetically.

seq_steam_ideal_cof

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

Resample a basis-set to match a mrs_data acquisition.

Zero-fill MRS data in the time domain.

zero_td_pts_end

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

Decompose an mrs_data object into white and gray matter spectra.

Subtract the first dynamic spectrum from a dynamic series.

Perform a mathematical operation on a spectral region.

Subtract the mean dynamic spectrum from a dynamic series.

Time-domain spectral registration.

spant_abfit_benchmark

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

spant: spectroscopy analysis tools.

Create a spin system object for pulse sequence simulation.

Return the echo time of an MRS dataset.

Transform time-domain data to the frequency-domain.

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.

Write MRS data object to file.

svs_1h_brain_analysis

Standard SVS 1H brain analysis pipeline.

svs_1h_brain_analysis_dev

Standard SVS 1H brain analysis pipeline.

write_basis_tqn

Generate a basis file using TARQUIN.

Time-domain convolution based filter.

Resample an image to match a target image space.

seq_press_2d_shaped

PRESS sequence with shaped refocusing pulses.

seq_press_ideal

PRESS sequence with ideal pulses.

Apply frequency shifts to basis set signals.

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.

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).

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 simulated Gaussian noise.

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

Calculate the sum of data dynamics.

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

varpro_basic_opts

Return a list of options for a basic VARPRO analysis.

Return a list of options for VARPRO based fitting.

Sum two mrs_data objects.

Signal space projection method for lipid suppression.

Simulate a mol_parameter object.

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

write_pulse_ascii

Write an ASCII formatted pulse file.

write_mrs_nifti

Write MRS data object to file in NIFTI format.

sub_median_dyns

Subtract the median dynamic spectrum from a dynamic series.

Produce a plot with multiple traces.

Perform a t-test on spectral data points.

svs_1h_brain_batch_analysis

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

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.

Calculate the sum across receiver coil elements.