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spant (version 3.1.0)

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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3.1.0

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GPL-3

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Repository

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

Homepage

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

Maintainer

Martin Wilson

Last Published

December 17th, 2024

Functions in spant (3.1.0)

Apply Re operator to an MRS dataset.

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.

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

Simulate an RF pulse on a single spin.

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

Apply a function over specified array axes.

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

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

Apply and subtract a Gaussian smoother in the spectral domain.

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

calc_design_efficiency

Calculate the efficiency of a regressor data frame.

calc_coil_noise_cor

Calculate the noise correlation between coil elements.

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

calc_ed_from_lambda

Calculate the effective dimensions of a spline smoother from lambda.

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

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.

Combine a pair of basis set objects.

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.

Calculate the spectral SNR.

calc_basis_corr_mat

Estimate the correlation matrix for a basis set.

basis2dyn_mrs_data

Convert a basis object to a dynamic mrs_data object.

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

Append multiple regressor data frames into a single data frame.

calc_basis_crlbs

Estimate the CRLB for each element in a basis set.

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

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

comb_coils_mrsi_gls

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

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).

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

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

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.

Bin equally spaced spectral regions.

comb_fit_list_result_tables

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

comb_fit_list_fit_tables

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

Check the TARQUIN binary can be run

Deconvolve two MRS data objects.

calc_coil_noise_sd

Calculate the noise standard deviation for each coil element.

Crop basis_set object based on a frequency range.

Calculate the sum of squares differences between two mrs_data objects.

crop_td_pts_end

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

coherence_filter

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

Crop mrs_data object data points in the time-domain.

Crop mrs_data object based on a frequency range.

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

comb_fit_tables

Combine all fitting data points into a single data frame.

Check LCModel can be run

Search for MRS data files in a BIDS filesystem structure.

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.

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.

Convolve two MRS data objects.

Transform frequency-domain data to the time-domain.

calc_peak_info_vec

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

Calculate diagnostic information for object of class fit_result.

Extract the fit amplitudes from an object of class fit_result.

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

Crop an MRSI dataset in the x-y direction

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.

Find valid MRS data files recursively from a directory path.

collapse_to_dyns

Collapse MRS data by concatenating spectra along the dynamic dimension.

Perform a fit based analysis of MRS data.

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

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

decimate_mrs_td

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

gen_baseline_reg

Generate baseline regressor.

Return the default nucleus.

Apply a Gaussian smoother in the spectral domain.

Frequency-domain convolution based filter.

Write fit results table to a csv file.

Return the default transmitter frequency in Hz.

Return the sampling frequency in Hz of an MRS dataset.

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

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

Return the default reference value for ppm scale.

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

fit_t1_tr_array

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

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

fit_t1_ti_array

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

Apply the Fourier transform over the dynamic dimension.

downsample_mrs_fd

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

Return the first half of a dynamic series.

Expand a regressor matrix for a group analysis.

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

Combine a reference and metabolite mrs_data object.

get_guassian_pulse

Generate a gaussian pulse shape.

gen_impulse_reg

Generate impulse regressors.

A very simple DICOM reader.

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

Generate the F product operator.

Return the last scans of a dynamic series.

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

Get a data array from a fit result.

get_1h_brain_basis_paras_v3

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

Generate BOLD regressors.

Perform a fft and ffshift on a vector.

get_1h_brain_basis_paras_v2

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

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

Return the second half of a dynamic series.

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

Standard SVS 1H brain analysis pipeline.

Generate polynomial regressors.

Generate an affine for nifti generation.

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

fp_phase_correct

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

Return the default sampling frequency in Hz.

Return a single voxel from a larger mrs dataset.

Return the first scans of a dynamic series.

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

get_1h_braino_basis_names

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

Apply the max operator to an MRS dataset.

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

Extract the reference component from an mrs_data object.

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

Calculate the mean dynamic data.

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

Apply the max operator to an interpolated MRS dataset.

Calculate the mean spectrum from an mrs_data object.

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

Return the spin number for a given nucleus.

Extract a subset of MRS data.

Perform l2 regularisation artefact suppression.

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

Return acquisition parameters from a MRS data object.

Calculate the pairwise means across a dynamic data set.

Eddy current correction.

elliptical_mask

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

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

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

glm_spec_fmrs_fl

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

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

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

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

get_1h_spectre_basis_names

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

Generate trapezoidal regressors.

glm_spec_fmrs_group

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

glm_spec_group_linhyp

Test a group-level spectral GLM linear hypothesis.

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

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

Return the first time-domain data point.

Generate a MRSI VOI from an mrs_data object.

Arrange spectral plots in a grid.

Generate a MRSI voxel from an mrs_data object.

Read an LCModel formatted coord file containing fit information.

Grid shift MRSI data in the x/y dimension.

preproc_svs_dataset

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

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.

Display an orthographic projection plot of a nifti object.

Generate a SVS acquisition volume from an mrs_data object.

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

get_1h_brain_basis_paras_v1

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

Generate the Fxy product operator with a specified phase.

Objects exported from other packages

Image plot method for objects of class mrs_data.

mrs_data2spec_mat

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

scale_amp_ratio_value

Scale fitted amplitudes to a ratio of signal amplitude.

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

scale_amp_molar2molal_pvc

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

scale_amp_ratio

Scale fitted amplitudes to a ratio of signal amplitude.

Repeat an array over a given dimension.

Apply phasing parameters to MRS data.

reson_table2mrs_data

Generate mrs_data from a table of single Lorentzian resonances.

Generate the I product operator for a single spin.

get_1h_brain_basis_paras

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

seq_steam_ideal_cof

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

Calculate the median dynamic data.

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

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

gridplot.mrs_data

Arrange spectral plots in a grid.

Perform an iffshift and ifft on a vector.

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

Calculate the standard deviation spectrum from an mrs_data object.

Calculate the standard deviation spectrum from an mrs_data object.

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

Display an interactive orthographic projection plot of a nifti object.

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

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

seq_steam_ideal

STEAM sequence with ideal pulses.

Simulate a basis file using TARQUIN.

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

plot_slice_fit_inter

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

Mask an MRSI dataset in the x-y direction

HSVD of a complex vector.

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

Return the frequency scale of an MRS dataset in Hz.

seq_press_ideal

PRESS sequence with ideal pulses.

Extract the metabolite component from an mrs_data object.

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

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

Simulate an mrs_data object containing complex zero valued samples.

mask_xy_corners

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

get_1h_brain_basis_names

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

get_basis_subset

Return a subset of the input basis.

Smooth data across the dynamic dimension with a Gaussian kernel.

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

Replicate a scan in the dynamic dimension.

read_tqn_result

Reader for csv results generated by TARQUIN.

Read MRS data using the TARQUIN software package.

Read MRS data from the filesystem.

Subtract the first dynamic spectrum from a dynamic series.

Subtract the mean dynamic spectrum from a dynamic series.

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

svs_1h_brain_batch_analysis

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

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

plot_slice_map_inter

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

get_mrsi_voxel_xy_psf

Generate a MRSI voxel PSF from an mrs_data object.

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

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.

Extract a subset of dynamic scans.

Return the mean of a list of mrs_data objects.

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

Resample a basis-set to match a mrs_data acquisition.

Perform a t-test on spectral data points.

Replicate a scan over a given dimension.

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

Convert a vector into a mrs_data object.

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

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

mean_vec_blocks

Calculate the mean of adjacent blocks in a vector.

Convert mrs_data object to a vector.

plot_voi_overlay_seg

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

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

Simulate a basis set object.

plot.fit_result

Plot the fitting results of an object of class fit_result.

Plotting method for objects of class mrs_data.

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

Return a single slice from a larger MRSI dataset.

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.

seq_mega_press_ideal

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

HSVD based signal filter.

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

get_uncoupled_mol

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

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

Get a mol_parameters object for a named molecule.

scale_amp_water_ratio

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

HSVD of an mrs_data object.

Plot the spectral standard deviation.

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).

spant_simulation_benchmark

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

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

sub_median_dyns

Subtract the median dynamic spectrum from a dynamic series.

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

plot_voi_overlay

Plot a volume as an image overlay.

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

Set the number of transients for an mrs_data object.

Return the echo 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.

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

sim_th_excit_profile

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

Reader for csv fit results generated by TARQUIN.

Get the quantum coherence matrix for a spin system.

Print a summary of mrs_data parameters.

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

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

Resample an image to match a target image space.

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).

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.

seq_pulse_acquire

Simple pulse and acquire sequence with ideal pulses.

seq_press_2d_shaped

PRESS sequence with shaped refocusing pulses.

zero_higher_orders

Zero all coherences including and above a given order.

spant: spectroscopy analysis tools.

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

Correct linear frequency drift.

get_voi_seg_psf

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

Mask an MRS dataset in the dynamic dimension.

interleave_dyns

Interleave the first and second half of a dynamic series.

Integrate a spectral region.

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).

make_basis_from_raw

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

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

Calculate the mean spectrum from an mrs_data object.

mean_dyn_blocks

Calculate the mean of adjacent dynamic scans.

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.

Apply a frequency shift to MRS data.

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

Apply frequency shifts to basis set signals.

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

Print fit coordinates from a single index.

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

Plot regressors as an image.

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

spant_sim_fmrs_dataset

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

write_pulse_ascii

Write an ASCII formatted pulse file.

Calculate the sum across receiver coil elements.

Set the repetition time of an MRS dataset.

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

Simulate an mrs_data object containing simulated Gaussian noise.

Simulate a mol_parameter object.

CPMG style sequence with ideal pulses.

Create a spin system object for pulse sequence simulation.

Transform time-domain data to the frequency-domain.

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

Time-domain convolution based filter.

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

zero_td_pts_end

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

Calculate the sum of data dynamics.

Export a one-page pdf of a single fit result

Plot a slice from a 7 dimensional array.

Sum two mrs_data objects.

Return the repetition time of an MRS dataset.

varpro_3_para_opts

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

phase_ref_1h_brain

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

Scale mrs_data to a spectral region.

Read a basis file in LCModel .basis format.

Remove a subset of dynamic scans.

write_mrs_nifti

Write MRS data object to file in NIFTI format.

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.

Sort the basis-set elements alphabetically.

write_basis_tqn

Generate a basis file using TARQUIN.

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.

Time-domain spectral registration.

Return the sum of a list of mrs_data objects.

Robust Alignment to a Target Spectrum (RATS).

Apply a weighting to the FID to enhance spectral resolution.

set_def_acq_paras

Set the default acquisition parameters.

recon_twix_2d_mrsi

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

read_pulse_ascii

Read an ASCII formatted pulse file.

rectangular_mask

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

read_pulse_bruker

Read a Bruker formatted pulse file

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

set_mask_xy_mat

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

Signal space projection method for lipid suppression.

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

Perform a mathematical operation on a spectral region.

Decompose an mrs_data object into white and gray matter spectra.

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).

seq_slaser_ideal

sLASER sequence with ideal pulses.

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_spin_echo_ideal

Spin echo sequence with ideal pulses.

set_precomp_verbose

Set the verbosity of the precompute function.

spant_abfit_benchmark

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

stackplot.fit_result

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

set_precomp_mode

Set the precompute mode.

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.

stackplot.mrs_data

Stackplot plotting method for objects of class mrs_data.

sim_basis_mm_lip_lcm

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

spant_mpress_drift

Example MEGA-PRESS data with significant B0 drift.

Write MRS data object to file.

Produce a plot with multiple traces.

Zero-fill MRS data in the time domain.

svs_1h_brain_analysis

Standard SVS 1H brain analysis pipeline.

varpro_basic_opts

Return a list of options for a basic VARPRO analysis.

svs_1h_brain_analysis_dev

Standard SVS 1H brain analysis pipeline.

Return a list of options for VARPRO based fitting.

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

Apply Conj operator to an MRS dataset.

Apply Mod operator to an MRS dataset.

Return the number of data points in an MRS dataset.

Apply Arg operator to an MRS dataset.

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

Return the total number of spectra in an MRS dataset.

Apply Im 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 a list of options for an ABfit analysis.

Simulate pulse sequence acquisition.

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

Add noise to an mrs_data object.

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