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spant (version 3.2.0)

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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3.2.0

License

GPL-3

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Repository

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

Homepage

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

Maintainer

Martin Wilson

Last Published

February 14th, 2025

Functions in spant (3.2.0)

Apply Re operator to an MRS dataset.

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

Add noise to an mrs_data object.

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

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

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.

Simulate pulse sequence acquisition.

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

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

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

Simulate an RF pulse on a single spin.

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.

Apply a function over specified array axes.

Append multiple regressor data frames into a single data frame.

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.

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

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

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

Baseline correction using the ALS method.

basis2dyn_mrs_data

Convert a basis object to a dynamic mrs_data object.

calc_basis_corr_mat

Estimate the correlation matrix for a basis set.

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

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

Check LCModel can be run

calc_peak_info_vec

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

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

Bin equally spaced spectral regions.

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

collapse_to_dyns

Collapse MRS data by concatenating spectra along the dynamic dimension.

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

Combine a pair of basis set objects.

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

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

calc_basis_crlbs

Estimate the CRLB for each element in a basis set.

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

Check the TARQUIN binary can be run

calc_coil_noise_sd

Calculate the noise standard deviation for each coil element.

calc_coil_noise_cor

Calculate the noise correlation between coil elements.

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

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

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

Calculate the sum of squares differences between two mrs_data objects.

coherence_filter

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

comb_fit_list_result_tables

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

Calculate the spectral SNR.

comb_fit_list_fit_tables

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

Apply and subtract a Gaussian smoother in the spectral domain.

Crop an MRSI dataset in the x-y direction

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).

Convolve 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.

Combine a reference and metabolite mrs_data object.

comb_fit_tables

Combine all fitting data points into a single data frame.

crop_td_pts_end

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

decimate_mrs_fd

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

Crop basis_set object based on a frequency range.

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

decimate_mrs_td

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

elliptical_mask

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

Deconvolve two MRS data objects.

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

Extract the fit amplitudes from an object of class fit_result.

downsample_mrs_fd

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

Eddy current correction.

Calculate diagnostic information for object of class fit_result.

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

calc_design_efficiency

Calculate the efficiency of a regressor data frame.

Return the default transmitter frequency in Hz.

Perform a fit based analysis of MRS data.

Write fit results table to a csv file.

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

fit_t2_te_array

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

Perform a fft and ffshift on a vector.

Return the default nucleus.

Return the default reference value for ppm scale.

Apply the Fourier transform over the dynamic dimension.

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

Return the sampling frequency in Hz of an MRS dataset.

Transform frequency-domain data to the time-domain.

Frequency-domain convolution based filter.

Apply a Gaussian smoother in the spectral domain.

calc_ed_from_lambda

Calculate the effective dimensions of a spline smoother from lambda.

A very simple DICOM reader.

Generate the I product operator for a single spin.

Generate the Fxy product operator with a specified phase.

Return the default sampling frequency in Hz.

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.

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

Generate the F product operator.

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

Find valid MRS data files recursively from a directory path.

Search for MRS data files in a BIDS filesystem structure.

fp_phase_correct

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

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

Return the first scans of a dynamic series.

Crop mrs_data object based on a frequency range.

Expand a regressor matrix for a group analysis.

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

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

Extract the metabolite component from an mrs_data object.

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

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

Generate trapezoidal regressors.

get_1h_brain_basis_names

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

Extract a subset of dynamic scans.

Generate a MRSI voxel from an mrs_data object.

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

Return the second half of a dynamic series.

get_mrsi_voxel_xy_psf

Generate a MRSI voxel PSF from an mrs_data object.

get_basis_subset

Return a subset of the input basis.

Crop mrs_data object data points in the time-domain.

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

Get a data array from a fit result.

Grid shift MRSI data in the x/y dimension.

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.

get_uncoupled_mol

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

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

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

Return the first half of a dynamic series.

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

Get a mol_parameters object for a named molecule.

get_1h_brain_basis_paras_v3

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

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

Arrange spectral plots in a grid.

HSVD of a complex vector.

HSVD based signal filter.

Extract the reference component from an mrs_data object.

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

Generate an affine for nifti generation.

Generate a SVS acquisition volume from an mrs_data object.

Extract a subset of MRS data.

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

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.

Integrate a spectral region.

Standard SVS 1H brain analysis pipeline.

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

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

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.

Generate polynomial regressors.

fit_t1_ti_array

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

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

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

gen_impulse_reg

Generate impulse regressors.

fit_t1_tr_array

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

get_1h_brain_basis_paras_v1

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

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

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

Print fit coordinates from a single index.

mask_xy_ellipse

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

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

Generate BOLD regressors.

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

gen_baseline_reg

Generate baseline regressor.

Apply the max operator to an interpolated MRS dataset.

mask_xy_corners

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

get_1h_brain_basis_paras

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

gridplot.mrs_data

Arrange spectral plots in a grid.

Calculate the mean spectrum from an mrs_data object.

Return a single voxel from a larger mrs dataset.

Return the spin number for a given nucleus.

Return a single slice from a larger MRSI dataset.

get_voi_seg_psf

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

Display an interactive orthographic projection plot of a nifti object.

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

Display an orthographic projection plot of a nifti object.

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.

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

Return acquisition parameters from a MRS data object.

Return the first time-domain data point.

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

Get the quantum coherence matrix for a spin system.

Print a summary of mrs_data parameters.

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

Correct linear frequency drift.

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

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

glm_spec_group_linhyp

Test a group-level spectral GLM linear hypothesis.

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

glm_spec_fmrs_group

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

Generate a MRSI VOI from an mrs_data object.

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

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

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

Read an LCModel formatted coord file containing fit information.

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

Return the frequency scale of an MRS dataset in Hz.

Apply the max operator to an MRS dataset.

Perform an iffshift and ifft on a vector.

Calculate the median dynamic data.

Return the last scans of a dynamic series.

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.

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

Return the mean of a list of mrs_data objects.

Apply phasing parameters to MRS data.

Resample a basis-set to match a mrs_data acquisition.

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).

Resample an image to match a target image space.

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.

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

glm_spec_fmrs_fl

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

Image plot 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).

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

mean_vec_blocks

Calculate the mean of adjacent blocks in a vector.

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

preproc_svs_dataset

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

Convert mrs_data object to a vector.

Perform l2 regularisation artefact suppression.

scale_amp_water_ratio

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

Plot regressors as an image.

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

scale_amp_ratio_value

Scale fitted amplitudes to a ratio of signal amplitude.

read_pulse_ascii

Read an ASCII formatted pulse file.

phase_ref_1h_brain

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

HSVD of an mrs_data object.

read_pulse_bruker

Read a Bruker formatted pulse file

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

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_molal

Apply water reference scaling to a fitting results object to yield metabolite quantities in millimolar (mM) units (mol / kg of tissue water).

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.

seq_slaser_ideal

sLASER sequence with ideal pulses.

seq_spin_echo_ideal

Spin echo sequence with ideal pulses.

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.

Apply frequency shifts to basis set signals.

print.fit_result

Print a summary of an object of class fit_result.

Reader for csv fit results generated by TARQUIN.

Apply a frequency shift to MRS data.

spant_sim_fmrs_dataset

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

Objects exported from other packages

read_tqn_result

Reader for csv results generated by TARQUIN.

Mask an MRSI dataset in the x-y direction

Repeat an array over a given dimension.

Simulate a basis file using TARQUIN.

Calculate the mean dynamic data.

Calculate the pairwise means across a dynamic data set.

Set the number of transients for an mrs_data object.

read_siemens_txt_hdr

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

interleave_dyns

Interleave the first and second half of a dynamic series.

make_basis_from_raw

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

Calculate the mean spectrum from an mrs_data object.

Mask an MRS dataset in the dynamic dimension.

seq_press_ideal

PRESS sequence with ideal pulses.

seq_pulse_acquire

Simple pulse and acquire sequence with ideal pulses.

mean_dyn_blocks

Calculate the mean of adjacent dynamic scans.

spant_simulation_benchmark

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

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).

Signal space projection method for lipid suppression.

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

scale_amp_ratio

Scale fitted amplitudes to a ratio of signal amplitude.

plot.fit_result

Plot the fitting results of an object of class fit_result.

plot_slice_fit_inter

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

Plotting method for objects of class mrs_data.

sub_median_dyns

Subtract the median dynamic spectrum from a dynamic series.

stackplot.mrs_data

Stackplot plotting method for objects of class mrs_data.

stackplot.fit_result

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

reson_table2mrs_data

Generate mrs_data from a table of single Lorentzian resonances.

Plot a slice from a 7 dimensional array.

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

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

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

Calculate the sum across receiver coil elements.

Simulate a mol_parameter object.

set_precomp_mode

Set the precompute mode.

set_precomp_verbose

Set the verbosity of the precompute function.

Return a list of options for VARPRO based fitting.

scale_amp_molar2molal_pvc

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

Robust Alignment to a Target Spectrum (RATS).

Apply a weighting to the FID to enhance spectral resolution.

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

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

Calculate the sum of data dynamics.

Transform time-domain data to the frequency-domain.

Decompose an mrs_data object into white and gray matter spectra.

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.

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

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

Perform a mathematical operation on a spectral region.

set_def_acq_paras

Set the default acquisition parameters.

Convert a vector into a mrs_data object.

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

Return the sum of a list of mrs_data objects.

zero_td_pts_end

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

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

Zero-fill MRS data in the time domain.

write_mrs_nifti

Write MRS data object to file in NIFTI format.

write_pulse_ascii

Write an ASCII formatted pulse file.

Time-domain convolution based filter.

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

plot_voi_overlay

Plot a volume as an image overlay.

mrs_data2spec_mat

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

varpro_basic_opts

Return a list of options for a basic VARPRO analysis.

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

Simulate an mrs_data object containing simulated Gaussian noise.

sim_th_excit_profile

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

Produce a plot with multiple traces.

recon_twix_2d_mrsi

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

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

Export a one-page pdf of a single fit result

Plot the spectral standard deviation.

Perform a t-test on spectral data points.

svs_1h_brain_batch_analysis

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

rectangular_mask

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

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

CPMG style sequence with ideal pulses.

Simulate a basis set object.

Set the repetition time of an MRS dataset.

Calculate the standard deviation spectrum from an mrs_data object.

sim_basis_mm_lip_lcm

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

Read MRS data from the filesystem.

plot_slice_map_inter

Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.

Read a basis file in LCModel .basis format.

sim_basis_1h_brain

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

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.

svs_1h_brain_analysis

Standard SVS 1H brain analysis pipeline.

seq_mega_press_ideal

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

Sum two mrs_data objects.

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

Calculate the standard deviation spectrum from an mrs_data object.

seq_press_2d_shaped

PRESS sequence with shaped refocusing pulses.

Replicate a scan in the dynamic dimension.

Simulate an mrs_data object containing complex zero valued samples.

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

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

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.

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

Read MRS data using the TARQUIN software package.

Replicate a scan over a given dimension.

spant: spectroscopy analysis tools.

seq_steam_ideal_cof

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

seq_steam_ideal

STEAM sequence with ideal pulses.

Remove a subset of dynamic scans.

Subtract the first dynamic spectrum from a dynamic series.

write_basis_tqn

Generate a basis file using TARQUIN.

Create a spin system object for pulse sequence simulation.

Scale mrs_data to a spectral region.

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

Sort the basis-set elements alphabetically.

svs_1h_brain_analysis_dev

Standard SVS 1H brain analysis pipeline.

zero_higher_orders

Zero all coherences including and above a given order.

Smooth data across the dynamic dimension with a Gaussian kernel.

Time-domain spectral registration.

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.

Return the echo time of an MRS dataset.

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.

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

Return the repetition time of an MRS dataset.

Subtract the mean dynamic spectrum from a dynamic series.

Write MRS data object to file.

varpro_3_para_opts

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

Apply Mod operator to an MRS dataset.

Apply Im operator to an MRS dataset.

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

Apply Conj operator to 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 acquired transients for an MRS dataset.

Return the total number of spectra 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.