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spant (version 3.9.0)

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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3.9.0

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 23rd, 2026

Functions in spant (3.9.0)

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

Return the number of data points in an MRS dataset.

Apply Arg operator to an MRS dataset.

Apply Mod operator to an MRS dataset.

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

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

Simulate pulse sequence acquisition.

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.

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.

add_noise_spec_snr

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

Return a list of options for an ABfit analysis.

Apply Re operator to an MRS dataset.

Combine a pair of basis set objects.

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

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.

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

Convert a 7 dimensional array in into a mrs_data object. The array dimensions should be ordered as : dummy, X, Y, Z, dynamic, coil, FID.

Apply a function over specified array axes.

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

Simulate an RF pulse on a single spin.

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.

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

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.

Append multiple regressor data frames into a single data frame.

Overwrite a subset of dynamic scans.

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.

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

Check the TARQUIN binary can be run

Check LCModel can be run

Bin equally spaced spectral regions.

Baseline correction using the ALS method.

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

collapse_to_dyns

Collapse MRS data by concatenating spectra along the dynamic dimension.

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

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

Crop mrs_data object based on a frequency range.

Crop basis_set object based on a frequency range.

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

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

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

comb_fit_list_dyns

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

Return the default transmitter frequency in Hz.

Apply and subtract a Gaussian smoother in the spectral domain.

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

Return the default sampling frequency in Hz.

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.

Deconvolve two MRS data objects.

downsample_mrs_fd

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

elliptical_mask

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

decimate_mrs_td

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

calc_coil_noise_sd

Calculate the noise standard deviation for each coil element.

calc_peak_info_vec

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

calc_coil_noise_cor

Calculate the noise correlation between coil elements.

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

Combine a reference and metabolite mrs_data object.

Convolve two MRS data objects.

coherence_filter

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

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

Calculate diagnostic information for object of class fit_result.

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

comb_fit_list_fit_tables

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

Standard SVS 1H brain analysis pipeline.

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.

comb_fit_list_result_tables

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

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

comb_fit_tables

Combine all fitting data points into a single data frame.

calc_basis_corr_mat

Estimate the correlation matrix for a basis set.

Calculate the sum of squares differences between two mrs_data objects.

Calculate the spectral SNR.

calc_basis_crlbs

Estimate the CRLB for each element in a basis set.

comb_coils_mrsi_gls

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

A very simple DICOM reader.

Edited SVS 1H brain analysis pipeline.

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

Search for MRS data files in a BIDS filesystem structure.

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

Generate the F product operator.

Write fit results table to a csv file.

Perform a fit based analysis of MRS data.

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.

fit_t1_tr_array

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

Get a data array from a fit result.

get_1h_spectre_basis_names

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

gen_numeric_reg

Generate a regressor from a numeric vector.

Generate polynomial regressors.

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

get_1h_braino_basis_names

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

Generate the Fxy product operator with a specified phase.

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.

comb_coils_svs_gls

Combine SVS 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.

Generate BOLD regressors.

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

get_1h_brain_basis_paras

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

Return the default nucleus.

Get a mol_parameters object for a named molecule.

Generate an affine for nifti generation.

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

Return the first time-domain data point.

Return the sampling frequency in Hz of an MRS dataset.

get_1h_brain_basis_paras_v1

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

Generate a MRSI VOI from an mrs_data object.

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

Extract the metabolite component from an mrs_data object.

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

Extract a subset of MRS data.

Generate a SVS acquisition volume from an mrs_data object.

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

Arrange spectral plots in a grid.

glm_spec_fmrs_fl

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

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

Grid shift MRSI data in the x/y dimension.

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.

Eddy current correction.

HSVD of a complex vector.

HSVD based signal filter.

Integrate a spectral region.

interleave_dyns

Interleave the first and second half of a dynamic series.

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

Extract the fit amplitudes from an object of class fit_result.

Apply the Fourier transform over the dynamic dimension.

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

fit_t1_ti_array

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

Find valid MRS data files recursively from a directory path.

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

Return the default reference value for ppm scale.

Mask an MRS dataset in the dynamic dimension.

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

match_lineshape

Apply Voigt line-broadening to match a reference spectrum.

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

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.

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

Transform frequency-domain data to the time-domain.

fit_svs_edited_group_results

Combine edited fitting results for group analysis.

fit_svs_group_results

Combine fitting results for group analysis.

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

Frequency-domain convolution based filter.

gen_baseline_reg

Generate baseline regressor.

Perform a fft and ffshift on a vector.

Generate the I product operator for a single spin.

Expand a regressor matrix for a group analysis.

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

Generate trapezoidal regressors.

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

Calculate the median dynamic data.

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

Convert mrs_data object to a vector.

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

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

Plotting method for objects of class mrs_data.

Return acquisition parameters from a MRS data object.

get_1h_brain_basis_paras_v2

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

get_1h_brain_basis_paras_v3

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

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

gen_impulse_reg

Generate impulse regressors.

Calculate the mean dynamic data.

mean_dyns_scheme

Average sets of dynamics according to a scheme vector.

Return the first half of a dynamic series.

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

get_1h_brain_basis_names

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

Return the second half of a dynamic series.

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

get_basis_subset

Return a subset of the input basis.

Return the last scans of a dynamic series.

HSVD of 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.

Return the frequency scale of an MRS dataset in Hz.

gridplot.mrs_data

Arrange spectral plots in a grid.

Perform an iffshift and ifft on a vector.

Extract a subset of dynamic scans.

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

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

get_guassian_pulse

Generate a gaussian pulse shape.

Return the first scans of a dynamic series.

Generate a MRSI voxel from an mrs_data object.

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

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

Return a single slice from a larger MRSI dataset.

Extract the reference component from an mrs_data object.

Get the quantum coherence matrix for a spin system.

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

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

Return the spin number for a given nucleus.

read_tqn_result

Reader for csv results generated by TARQUIN.

Robust Alignment to a Target Spectrum (RATS).

preproc_svs_dataset

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

get_voi_seg_psf

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

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.

Image plot method for objects of class mrs_data.

rectangular_mask

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

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

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

get_mrsi_voxel_xy_psf

Generate a MRSI voxel PSF from an mrs_data object.

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

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

mean_dyn_blocks

Calculate the mean of adjacent dynamic scans.

Calculate the pairwise means across a dynamic data set.

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

get_uncoupled_mol

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

glm_spec_fmrs_group

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

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

glm_spec_group_linhyp

Test a group-level spectral GLM linear hypothesis.

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

Objects exported from other packages

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).

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

Export a one-page pdf of a single fit result

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).

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).

Apply phasing parameters to MRS data.

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

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.

Perform l2 regularisation artefact suppression.

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

scale_basis_from_singlet

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

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

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

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.

Calculate the mean 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.

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.

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

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

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

Print fit coordinates from a single index.

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.

mask_xy_ellipse

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

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

plot_slice_fit_inter

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

recon_twix_2d_mrsi

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

scale_amp_ratio_value

Scale fitted amplitudes to a ratio of signal amplitude.

reson_table2mrs_data

Generate mrs_data from a table of single Lorentzian resonances.

scale_amp_ratio

Scale fitted amplitudes to a ratio of signal amplitude.

Calculate the standard deviation spectrum from an mrs_data object.

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

Read MRS data from the filesystem.

Plot the spectral standard deviation.

Plot regressors as an image.

plot_slice_map_inter

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

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

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

Replicate a scan in the dynamic dimension.

Read an LCModel formatted coord file containing fit information.

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).

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

read_pulse_bruker

Read a Bruker formatted pulse file

Set the number of transients for an mrs_data object.

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

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.

Set the repetition time of an MRS dataset.

sim_basis_1h_brain

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

Smooth data across the dynamic dimension with a Gaussian kernel.

Print a summary of mrs_data parameters.

Read a basis file in LCModel .basis format.

Apply a weighting to the FID to enhance spectral resolution.

Plot a slice from a 7 dimensional array.

read_siemens_txt_hdr

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

print.fit_result

Print a summary of an object of class fit_result.

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

scale_amp_water_ratio

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

Repeat an array over a given dimension.

Sort the basis-set elements alphabetically.

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

Produce a plot with multiple traces.

varpro_3_para_opts

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

Signal space projection method for lipid suppression.

sub_odd_from_even_dyns

Subtract the odd dynamic scans from the even dynamic scans.

seq_press_ideal

PRESS sequence with ideal pulses.

Remove a subset of dynamic scans.

Reader for csv fit results generated by TARQUIN.

Calculate the standard deviation spectrum from an mrs_data object.

scale_amp_legacy

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

Resample a basis-set to match a mrs_data acquisition.

Replicate a scan over a given dimension.

Scale mrs_data to a spectral region.

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

seq_pulse_acquire

Simple pulse and acquire sequence with ideal pulses.

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

Apply the max operator to an MRS dataset.

set_def_acq_paras

Set the default acquisition parameters.

Apply the max operator to an interpolated MRS dataset.

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

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

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

Simulate a basis set object.

sim_th_excit_profile

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

Return the sum of a list of mrs_data objects.

seq_steam_ideal

STEAM sequence with ideal pulses.

seq_mega_press_ideal

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

seq_steam_ideal_cof

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

seq_press_2d_shaped

PRESS sequence with shaped refocusing pulses.

scale_basis_amp

Scale a basis object by a scalar.

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

Apply a frequency shift to MRS data.

Apply frequency shifts to basis set signals.

Simulate an mrs_data object containing simulated Gaussian noise.

Perform a mathematical operation on a spectral region.

stackplot.fit_result

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

Decompose an mrs_data object into white and gray matter spectra.

Return the mean of a list of mrs_data objects.

spant_sim_fmrs_dataset

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

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

set_mask_xy_mat

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

Simulate a mol_parameter object.

mean_vec_blocks

Calculate the mean of adjacent blocks in a vector.

Trim a vector of filesystem paths.

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.

Write MRS data object to file.

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

svs_1h_brain_analysis

Standard SVS 1H brain analysis pipeline.

write_mrs_nifti

Write MRS data object to file in NIFTI format.

Return the repetition time of an MRS dataset.

zero_td_pts_end

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

Subtract the mean dynamic spectrum from a dynamic series.

sub_median_dyns

Subtract the median dynamic spectrum from a dynamic series.

Simulate an mrs_data object containing complex zero valued samples.

spant_simulation_benchmark

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

Display an orthographic projection plot of a nifti object.

Display an interactive orthographic projection plot of a nifti object.

stackplot.mrs_data

Stackplot plotting method for objects of class mrs_data.

phase_ref_1h_brain

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

plot.fit_result

Plot the fitting results of an object of class fit_result.

Read MRS data using the TARQUIN software package.

read_dkd_moco_log

Read the log from Dinesh's MoCo sLASER sequence.

plot_voi_overlay_seg

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

plot_voi_overlay

Plot a volume as an image overlay.

read_basis_niidir

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

Return the echo time of an MRS dataset.

zero_higher_orders

Zero all coherences including and above a given order.

Sum two mrs_data objects.

Convert a vector into a mrs_data object.

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

Zero-fill MRS data in the time domain.

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

Transform time-domain data to the frequency-domain.

Perform a t-test on spectral data points.

Return a list of options for VARPRO based fitting.

Subtract the first dynamic spectrum from a dynamic series.

varpro_basic_opts

Return a list of options for a basic VARPRO analysis.

sub_even_from_odd_dyns

Subtract the even dynamic scans from the odd dynamic scans.

write_basis_niidir

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

seq_slaser_ideal

sLASER sequence with ideal pulses.

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.

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

scale_amp_molar2molal_pvc

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

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

CPMG style sequence with ideal pulses.

read_pulse_ascii

Read an ASCII formatted pulse file.

Resample an image to match a target image space.

seq_spin_echo_ideal

Spin echo sequence with ideal pulses.

set_precomp_mode

Set the precompute mode.

svs_1h_brain_analysis_dev

Standard SVS 1H brain analysis pipeline.

set_precomp_verbose

Set the verbosity of the precompute function.

write_basis_tqn

Generate a basis file using TARQUIN.

svs_1h_brain_batch_analysis

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

sim_basis_mm_lip_lcm

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

Create a spin system object for pulse sequence simulation.

Time-domain convolution based filter.

spant: spectroscopy analysis tools.

Simulate a basis file using TARQUIN.

Calculate the sum across receiver coil elements.

spant_abfit_benchmark

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

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.

Calculate the sum of data dynamics.

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.

write_pulse_ascii

Write an ASCII formatted pulse file.

Time-domain spectral registration.

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

Return the total number of spectra in an MRS dataset.

Apply Conj operator to an MRS dataset.

Apply Im operator to an MRS dataset.