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spant (version 2.20.0)

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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2.20.0

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GPL-3

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Repository

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

Homepage

https://martin3141.github.io/spant/

Maintainer

Martin Wilson

Last Published

May 1st, 2024

Functions in spant (2.20.0)

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

Return a list of options for an ABfit analysis.

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

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

Apply Im operator to an MRS dataset.

Combine a pair of basis set objects.

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

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

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

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

Simulate pulse sequence acquisition.

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

Add noise to an mrs_data object.

Simulate an RF pulse on a single spin.

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

Apply and subtract a Gaussian smoother in the spectral domain.

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

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

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

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

Apply Re operator to an MRS dataset.

Check the TARQUIN binary can be run

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

Baseline correction using the ALS method.

Crop basis_set object based on a frequency range.

Apply a function over specified array axes.

Crop mrs_data object based on a frequency range.

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

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

Crop mrs_data object data points in the time-domain.

coherence_filter

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

Bin equally spaced spectral regions.

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

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

collapse_to_dyns

Collapse MRS data by concatenating spectra along the dynamic dimension.

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

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.

calc_coil_noise_cor

Calculate the noise correlation between coil elements.

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.

elliptical_mask

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

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

Find valid MRS data files recursively from a directory path.

Apply a Gaussian smoother in the spectral domain.

comb_fit_list_fit_tables

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

calc_ed_from_lambda

Calculate the effective dimensions of a spline smoother from lambda.

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.

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

comb_fit_list_result_tables

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

Calculate the sum of squares differences between 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.

Crop an MRSI dataset in the x-y direction

crop_td_pts_end

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

downsample_mrs_fd

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

decimate_mrs_td

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

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

Calculate the spectral SNR.

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

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

Check LCModel can be run

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.

Combine a reference and metabolite mrs_data object.

fit_t1_tr_array

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

fit_t1_ti_array

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

Deconvolve two MRS data objects.

comb_fit_tables

Combine all fitting data points into a single data frame.

Return the default nucleus.

Return the default reference value for ppm scale.

Calculate diagnostic information for object of class fit_result.

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

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

Generate the Fxy product operator with a specified phase.

Extract the fit amplitudes from an object of class fit_result.

decimate_mrs_fd

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

fp_phase_correct

Perform a zeroth order phase correction based on 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.

Eddy current correction.

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

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

Frequency-domain convolution based filter.

Perform a fft and ffshift on a vector.

Transform frequency-domain data to the time-domain.

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

A very simple DICOM reader.

Generate the F product operator.

get_1h_brain_basis_names

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

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

Perform a fit based analysis of MRS data.

Return the sampling frequency in Hz of an MRS dataset.

Write fit results table to a csv file.

get_1h_brain_basis_paras_v3

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

Return the default sampling frequency in Hz.

Return the default transmitter frequency in Hz.

Return acquisition parameters from a MRS data object.

get_1h_brain_basis_paras

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

get_1h_braino_basis_names

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

Apply the Fourier transform over the dynamic dimension.

Generate a BOLD response function.

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

Get a mol_parameters object for a named molecule.

Generate an affine for nifti generation.

Return the first time-domain data point.

Extract a subset of dynamic scans.

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

get_1h_brain_basis_paras_v1

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

get_1h_brain_basis_paras_v2

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

get_guassian_pulse

Generate a gaussian pulse shape.

Extract the metabolite component from an mrs_data object.

Generate a MRSI VOI from an mrs_data object.

Return the first half of a dynamic series.

Generate a trapezoidal response function.

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

Get a data array from a fit result.

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

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

get_1h_spectre_basis_names

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

Generate the I product operator for a single spin.

get_basis_subset

Return a subset of the input basis.

Return the first scans of a dynamic series.

Extract a subset of MRS data.

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

Generate a SVS acquisition volume from an mrs_data object.

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

Generate a MRSI voxel from an mrs_data object.

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

get_uncoupled_mol

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

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

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

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

interleave_dyns

Interleave the first and second half of a dynamic series.

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

get_mrsi_voxel_xy_psf

Generate a MRSI voxel PSF from an mrs_data object.

Extract the reference component from an mrs_data object.

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

Return the second half of a dynamic series.

Image plot method for objects of class mrs_data.

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

get_voi_seg_psf

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

Apply the max operator to an interpolated MRS dataset.

Apply the max operator to an MRS dataset.

Return the last scans of a dynamic series.

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

Grid shift MRSI data in the x/y dimension.

Arrange spectral plots in a grid.

Return a single slice from a larger MRSI dataset.

Return the spin number for a given nucleus.

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

Integrate a spectral region.

Return a single voxel from a larger mrs dataset.

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

Correct linear frequency drift.

Mask an MRSI dataset in the x-y direction

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

make_basis_from_raw

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

gridplot.mrs_data

Arrange spectral plots in a grid.

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

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

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

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

HSVD based signal filter.

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

Convert mrs_data object to a vector.

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

Export a one-page pdf of a single fit result

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.

Perform l2 regularisation artefact suppression.

Display an orthographic projection plot of a nifti object.

Plot the spectral standard deviation.

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.

mean_dyn_blocks

Calculate the mean of adjacent dynamic scans.

HSVD of a complex vector.

Calculate the pairwise means across a dynamic data set.

Return the frequency scale of an MRS dataset in Hz.

Perform an iffshift and ifft on a vector.

HSVD of an mrs_data object.

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

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

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

Calculate the mean spectrum from an mrs_data object.

Calculate the mean spectrum from an mrs_data object.

mask_xy_corners

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

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

scale_amp_molar2molal_pvc

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

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.

Return the mean of a list of mrs_data objects.

Apply phasing parameters to MRS data.

Read MRS data from a file.

Print a summary of mrs_data parameters.

scale_amp_ratio

Scale fitted amplitudes to a ratio of signal amplitude.

print.fit_result

Print a summary of an object of class fit_result.

read_ima_dyn_dir

Read a directory containing Siemens MRS IMA files and combine along the dynamic dimension. Note that the coil ID is inferred from the sorted file name and should be checked when consistency is required.

Read an LCModel formatted coord file containing fit information.

Calculate the mean dynamic data.

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

plot_voi_overlay

Plot a volume as an image overlay.

Print fit coordinates from a single index.

Resample a basis-set to match a mrs_data acquisition.

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).

Replicate a scan over a given dimension.

Set the number of transients for an mrs_data object.

CPMG style sequence with ideal pulses.

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

set_precomp_verbose

Set the verbosity of the precompute function.

Apply frequency shifts to basis set signals.

set_precomp_mode

Set the precompute mode.

Apply a frequency shift to 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).

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

Reader for csv fit results generated by TARQUIN.

Mask an MRS dataset in the dynamic dimension.

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

read_siemens_txt_hdr

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

Replicate a scan in the dynamic dimension.

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).

plot_voi_overlay_seg

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

Read MRS data using the TARQUIN software package.

Repeat an array over a given dimension.

read_pulse_ascii

Read an ASCII formatted pulse file.

recon_twix_2d_mrsi

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

spant_abfit_benchmark

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

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

scale_amp_molar

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

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

mean_vec_blocks

Calculate the mean of adjacent blocks in a vector.

Calculate the median dynamic data.

spant_mpress_drift

Example MEGA-PRESS data with significant B0 drift.

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

Display an interactive orthographic projection plot of a nifti object.

plot_slice_fit_inter

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

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

Resample an image to match a target image space.

scale_basis_from_singlet

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

seq_mega_press_ideal

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

scale_basis_amp

Scale a basis object by a scalar.

Subtract the mean dynamic spectrum from a dynamic series.

sub_median_dyns

Subtract the median dynamic spectrum from a dynamic series.

Calculate the sum across receiver coil elements.

Calculate the standard deviation spectrum from an mrs_data object.

set_def_acq_paras

Set the default acquisition parameters.

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

Plot a slice from a 7 dimensional array.

Get the quantum coherence matrix for a spin system.

Simulate a basis file using TARQUIN.

seq_press_2d_shaped

PRESS sequence with shaped refocusing pulses.

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

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

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

read_pulse_bruker

Read a Bruker formatted pulse file

Robust Alignment to a Target Spectrum (RATS).

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

read_tqn_result

Reader for csv results generated by TARQUIN.

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

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

Subtract the first dynamic spectrum from a dynamic series.

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.

Sum two mrs_data objects.

Return the sum of a list of mrs_data objects.

Calculate the sum of data dynamics.

Calculate the standard deviation spectrum from an mrs_data object.

seq_slaser_ideal

sLASER sequence with ideal pulses.

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

Apply a weighting to the FID to enhance spectral resolution.

Plotting method for objects of class mrs_data.

plot.fit_result

Plot the fitting results of an object of class fit_result.

spant: spectroscopy analysis tools.

Simulate an mrs_data object containing complex zero valued samples.

Sort the basis-set elements alphabetically.

seq_spin_echo_ideal

Spin echo sequence with ideal pulses.

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.

rectangular_mask

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

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

Read a basis file in LCModel .basis format.

Objects exported from other packages

Remove a subset of dynamic scans.

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

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_ideal

PRESS sequence with ideal pulses.

Scale mrs_data to a spectral region.

Perform a mathematical operation on a spectral region.

Smooth data across the dynamic dimension with a Gaussian kernel.

Signal space projection method for lipid suppression.

Write MRS data object to file.

write_mrs_nifti

Write MRS data object to file in NIFTI format.

Create a spin system object for pulse sequence simulation.

Time-domain convolution based filter.

Time-domain spectral registration.

seq_pulse_acquire

Simple pulse and acquire sequence with ideal pulses.

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.

seq_steam_ideal

STEAM sequence with ideal pulses.

scale_amp_ratio_value

Scale fitted amplitudes to a ratio of signal amplitude.

seq_steam_ideal_cof

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

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

Simulate a basis set object.

sim_basis_1h_brain

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

set_mask_xy_mat

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

Return the echo time of an MRS dataset.

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

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

Set the repetition time of an MRS dataset.

svs_1h_brain_batch_analysis

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

Return a list of options for VARPRO based fitting.

Transform time-domain data to the frequency-domain.

Return the repetition time of an MRS dataset.

Simulate a mol_parameter object.

spant_simulation_benchmark

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

Simulate an mrs_data object containing simulated Gaussian noise.

Zero-fill MRS data in the time domain.

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

Convert a vector into a mrs_data object.

sim_th_excit_profile

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

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.

Decompose an mrs_data object into white and gray matter spectra.

svs_1h_brain_analysis

Standard SVS 1H brain analysis pipeline.

Produce a plot with multiple traces.

stackplot.fit_result

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

varpro_3_para_opts

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

svs_1h_brain_analysis_dev

Standard SVS 1H brain analysis pipeline.

write_basis_tqn

Generate a basis file using TARQUIN.

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

varpro_basic_opts

Return a list of options for a basic VARPRO analysis.

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.

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

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

Apply Mod operator to an MRS dataset.

Return the number of data points in an MRS dataset.

Apply Conj operator to an MRS dataset.

Return the total number of spectra in an MRS dataset.

Apply Arg operator to an MRS dataset.