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spant (version 3.8.0)

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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3.8.0

License

GPL-3

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Repository

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

Homepage

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

Maintainer

Martin Wilson

Last Published

December 16th, 2025

Functions in spant (3.8.0)

Return a list of options for an ABfit analysis.

abfit_opts_v1_9_0

Return a list of options for an ABfit analysis to maintain comparability with analyses performed with version 1.9.0 (and earlier) of spant.

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

Apply Re operator to an MRS dataset.

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

Simulate pulse sequence acquisition.

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

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

Combine a pair of basis set objects.

Add noise to an mrs_data object.

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.

add_noise_spec_snr

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

Simulate an RF pulse on a single spin.

Apply a function over specified array axes.

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

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

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.

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

Overwrite a subset of dynamic scans.

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.

calc_basis_corr_mat

Estimate the correlation matrix for a basis set.

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

Append multiple regressor data frames into a single data frame.

calc_basis_crlbs

Estimate the CRLB for each element in a basis set.

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

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

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

collapse_to_dyns

Collapse MRS data by concatenating spectra along the dynamic dimension.

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

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

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

basis2dyn_mrs_data

Convert a basis object to a dynamic mrs_data object.

Crop basis_set object based on a frequency range.

crop_td_pts_end

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

Crop mrs_data object data points in the time-domain.

Crop mrs_data object based on a frequency range.

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

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.

comb_coils_mrsi_gls

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

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

A very simple DICOM reader.

comb_fit_list_result_tables

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

Check LCModel can be run

downsample_mrs_fd

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

Check the TARQUIN binary can be run

Search for MRS data files in a BIDS filesystem structure.

Apply and subtract a Gaussian smoother in the spectral domain.

Apply a Gaussian smoother in the spectral domain.

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

calc_coil_noise_cor

Calculate the noise correlation between coil elements.

comb_fit_tables

Combine all fitting data points into a single data frame.

calc_coil_noise_sd

Calculate the noise standard deviation for each coil element.

calc_design_efficiency

Calculate the efficiency of a regressor data frame.

calc_ed_from_lambda

Calculate the effective dimensions of a spline smoother from lambda.

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.

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

elliptical_mask

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

Extract the fit amplitudes from an object of class fit_result.

Find valid MRS data files recursively from a directory path.

Perform a fit based analysis of MRS data.

fit_t2_te_array

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

fit_t1_tr_array

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

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

decimate_mrs_fd

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

Write fit results table to a csv file.

Return the sampling frequency in Hz of an MRS dataset.

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

Convolve two MRS data objects.

Crop an MRSI dataset in the x-y direction

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 default nucleus.

Calculate the sum of squares differences between two mrs_data objects.

Combine a reference and metabolite mrs_data object.

Calculate the spectral SNR.

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

calc_peak_info_vec

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

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

Bin equally spaced spectral regions.

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

comb_fit_list_dyns

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

Standard SVS 1H brain analysis pipeline.

Edited SVS 1H brain analysis pipeline.

Generate the F product operator.

Eddy current correction.

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

Transform frequency-domain data to the time-domain.

Apply the Fourier transform over the dynamic dimension.

Return the default reference value for ppm scale.

Generate the Fxy product operator with a specified phase.

Generate BOLD regressors.

Get a data array from a fit result.

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

Extract a subset of dynamic scans.

get_basis_subset

Return a subset of the input basis.

Return the first time-domain data point.

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

Return the second half of a dynamic series.

Return the last 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.

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.

get_mrsi_voxel_xy_psf

Generate a MRSI voxel PSF from an mrs_data object.

Generate a MRSI voxel from an mrs_data object.

Perform a fft and ffshift on a vector.

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

glm_spec_fmrs_fl

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

Generate the I product operator for a single spin.

get_guassian_pulse

Generate a gaussian pulse shape.

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.

gen_baseline_reg

Generate baseline regressor.

Get a mol_parameters object for a named molecule.

Return the first scans of a dynamic series.

Deconvolve two MRS data objects.

decimate_mrs_td

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

comb_fit_list_fit_tables

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

Generate an affine for nifti generation.

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

Return the default sampling frequency in Hz.

Return the default transmitter frequency in Hz.

get_voi_seg_psf

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

HSVD based signal filter.

HSVD of a complex vector.

Return a single voxel from a larger mrs dataset.

Perform an iffshift and ifft on a vector.

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

glm_spec_fmrs_group

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

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

Image plot method for objects of class mrs_data.

Generate trapezoidal regressors.

fp_phase_correct

Perform a zeroth order phase correction based on the phase of the first data point 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.

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

fit_t1_ti_array

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

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

Apply line-broadening to dynamic MRS data and add normally distributed noise (renoise) to reverse any associated improvement in SNR.

get_1h_brain_basis_paras_v3

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

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

get_1h_brain_basis_names

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

get_1h_brain_basis_paras_v2

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

Return the frequency scale of an MRS dataset in Hz.

glm_spec_group_linhyp

Test a group-level spectral GLM linear hypothesis.

fit_svs_group_results

Combine fitting results for group analysis.

Calculate diagnostic information for object of class fit_result.

fit_svs_edited_group_results

Combine edited fitting results for group analysis.

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

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

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

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

mask_xy_ellipse

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

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

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

mean_dyn_blocks

Calculate the mean of adjacent dynamic scans.

Calculate the pairwise means across a dynamic data set.

Mask an MRS dataset in the dynamic dimension.

Frequency-domain convolution based filter.

Match files based on a vector of input paths and a glob pattern. The glob pattern is appended to each path and should match one file only.

Expand a regressor matrix for a group analysis.

gen_impulse_reg

Generate impulse regressors.

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

Apply the max operator to an MRS dataset.

Apply the max operator to an interpolated MRS dataset.

Calculate the median dynamic data.

Extract a subset of MRS data.

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

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

Print fit coordinates from a single index.

Return the spin number for a given nucleus.

Display an orthographic projection plot of a nifti object.

Display an interactive orthographic projection plot of a nifti object.

Correct linear frequency drift.

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

get_uncoupled_mol

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

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

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

Calculate the mean 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 spectrum from an mrs_data object.

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

Export a one-page pdf of a single fit result

Extract the metabolite component from an mrs_data object.

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

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

Calculate the mean dynamic data.

Apply phasing parameters to MRS data.

plot_voi_overlay_seg

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

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 regressors as an image.

Grid shift MRSI data in the x/y dimension.

Arrange spectral plots in a grid.

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

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

Plot the spectral standard deviation.

gen_numeric_reg

Generate a regressor from a numeric vector.

Apply a weighting to the FID to enhance spectral resolution.

plot_slice_map_inter

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

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

plot_voi_overlay

Plot a volume as an image overlay.

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

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

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

get_1h_spectre_basis_names

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

Generate polynomial regressors.

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

recon_twix_2d_mrsi

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

Get the quantum coherence matrix for a spin system.

Read MRS data using the TARQUIN software package.

Robust Alignment to a Target Spectrum (RATS).

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

read_pulse_bruker

Read a Bruker formatted pulse file

Read a basis file in LCModel .basis format.

get_1h_braino_basis_names

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

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

Return a single slice from a larger MRSI dataset.

Extract the reference component from an mrs_data object.

mean_dyns_scheme

Average sets of dynamics according to a scheme vector.

Perform l2 regularisation artefact suppression.

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 ppm scale of an MRS dataset or fit result.

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.

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

Replicate a scan over a given dimension.

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

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

Resample an image to match a target image space.

Return the mean of a list of mrs_data objects.

scale_basis_amp

Scale a basis object by a scalar.

scale_amp_water_ratio

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

reson_table2mrs_data

Generate mrs_data from a table of single Lorentzian resonances.

Calculate the standard deviation spectrum from an mrs_data object.

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

mean_vec_blocks

Calculate the mean of adjacent blocks in a vector.

match_lineshape

Apply Voigt line-broadening to match a reference spectrum.

mrs_data2spec_mat

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

Read an LCModel formatted coord file containing fit information.

scale_basis_from_singlet

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

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

Convert mrs_data object to a vector.

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

scale_amp_ratio

Scale fitted amplitudes to a ratio of signal amplitude.

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

Plotting method for objects of class mrs_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.

set_def_acq_paras

Set the default acquisition parameters.

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).

read_siemens_txt_hdr

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

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).

seq_press_2d_shaped

PRESS sequence with shaped refocusing pulses.

Reader for csv fit results generated by TARQUIN.

sim_basis_mm_lip_lcm

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

Perform a mathematical operation on a spectral region.

Decompose an mrs_data object into white and gray matter spectra.

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

read_dkd_moco_log

Read the log from Dinesh's MoCo sLASER sequence.

Subtract the mean dynamic spectrum from a dynamic series.

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

seq_mega_press_ideal

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

set_mask_xy_mat

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

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

spant_abfit_benchmark

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

Simulate an mrs_data object containing simulated Gaussian noise.

Set the number of transients for an mrs_data object.

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).

plot_slice_fit_inter

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

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

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

sub_median_dyns

Subtract the median dynamic spectrum from a dynamic series.

svs_1h_brain_analysis_dev

Standard SVS 1H brain analysis pipeline.

HSVD of an mrs_data object.

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

Generate a MRSI VOI from an mrs_data object.

Generate a SVS acquisition volume from an mrs_data object.

Return the first half of a dynamic series.

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

svs_1h_brain_batch_analysis

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

Simulate a basis file using TARQUIN.

Trim a vector of filesystem paths.

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

set_precomp_verbose

Set the verbosity of the precompute function.

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

svs_1h_brain_analysis

Standard SVS 1H brain analysis pipeline.

varpro_3_para_opts

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

set_precomp_mode

Set the precompute mode.

preproc_svs_dataset

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

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

Return the repetition time of an MRS dataset.

Return the echo time of an MRS dataset.

write_basis_niidir

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

Plot a slice from a 7 dimensional array.

write_basis_tqn

Generate a basis file using TARQUIN.

Read MRS data from the filesystem.

Sum two mrs_data objects.

spant: spectroscopy analysis tools.

Create a spin system object for pulse sequence simulation.

CPMG style sequence with ideal pulses.

read_basis_niidir

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

Resample a basis-set to match a mrs_data acquisition.

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.

read_pulse_ascii

Read an ASCII formatted pulse file.

Write MRS data object to file.

Return the sum of a list of mrs_data objects.

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.

Repeat an array over a given dimension.

Smooth data across the dynamic dimension with a Gaussian kernel.

seq_press_ideal

PRESS sequence with ideal pulses.

Calculate the sum across receiver coil elements.

Replicate a scan in the dynamic dimension.

gridplot.mrs_data

Arrange spectral plots in a grid.

Perform a t-test on spectral data points.

write_mrs_nifti

Write MRS data object to file in NIFTI format.

Time-domain spectral registration.

seq_pulse_acquire

Simple pulse and acquire sequence with ideal pulses.

scale_amp_ratio_value

Scale fitted amplitudes to a ratio of signal amplitude.

Apply a frequency shift to MRS data.

Apply frequency shifts to basis set signals.

seq_steam_ideal

STEAM sequence with ideal pulses.

Signal space projection method for lipid suppression.

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

sim_th_excit_profile

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

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

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

Convert a vector into a mrs_data object.

scale_amp_molar2molal_pvc

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

Simulate a basis set object.

seq_steam_ideal_cof

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

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.

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

stackplot.mrs_data

Stackplot plotting method for objects of class mrs_data.

Simulate an mrs_data object containing complex zero valued samples.

Time-domain convolution based filter.

Sort the basis-set elements alphabetically.

sim_basis_1h_brain

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

sim_basis_1h_brain_press

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

Calculate the sum of data dynamics.

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.

sub_odd_from_even_dyns

Subtract the odd dynamic scans from the even dynamic scans.

Transform time-domain data to the frequency-domain.

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

zero_higher_orders

Zero all coherences including and above a given order.

zero_td_pts_end

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

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

Zero-fill MRS data in the time domain.

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

interleave_dyns

Interleave the first and second half of a dynamic series.

Integrate a spectral region.

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

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

mask_xy_corners

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

Mask an MRSI dataset in the x-y direction

print.fit_result

Print a summary of an object of class fit_result.

Scale mrs_data to a spectral region.

Calculate the standard deviation spectrum from an mrs_data object.

Split paths into parts based on backslash, forwardslash and dot characters and return a data frame of these parts.

plot.fit_result

Plot the fitting results of an object of class fit_result.

phase_ref_1h_brain

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

Simulate a mol_parameter object.

seq_spin_echo_ideal

Spin echo sequence with ideal pulses.

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

read_tqn_result

Reader for csv results generated by TARQUIN.

scale_amp_legacy

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

Print a summary of mrs_data parameters.

seq_slaser_ideal

sLASER sequence with ideal pulses.

rectangular_mask

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

Remove a subset of dynamic scans.

Objects exported from other packages

spant_sim_fmrs_dataset

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

Return a list of options for VARPRO based fitting.

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

spant_simulation_benchmark

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

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 repetition time of an MRS dataset.

Subtract the first dynamic spectrum from a dynamic series.

sub_even_from_odd_dyns

Subtract the even dynamic scans from the odd dynamic scans.

varpro_basic_opts

Return a list of options for a basic VARPRO analysis.

write_pulse_ascii

Write an ASCII formatted pulse file.

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

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

Apply Im 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.

Apply Conj 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.