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spant (version 2.14.0)

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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2.14.0

License

GPL-3

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Repository

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

Homepage

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

Maintainer

Martin Wilson

Last Published

July 19th, 2023

Functions in spant (2.14.0)

Apply Mod operator to an MRS dataset.

Apply Conj operator to an MRS dataset.

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

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.

Return the total number of spectra in an MRS dataset.

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

Apply Arg operator to an MRS dataset.

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

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

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

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

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.

Simulate pulse sequence acquisition.

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

Add noise to an mrs_data object.

Combine a pair of basis set objects.

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.

Apply a function over specified array axes.

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.

calc_ed_from_lambda

Calculate the effective dimensions of a spline smoother from lambda.

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.

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.

Baseline correction using the ALS method.

Apply Re operator to an MRS dataset.

coherence_filter

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

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

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

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

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

Convolve two MRS data objects.

Combine a reference and metabolite mrs_data object.

Calculate the sum of squares differences between two mrs_data objects.

calc_coil_noise_sd

Calculate the noise standard deviation for each coil element.

calc_coil_noise_cor

Calculate the noise correlation between coil elements.

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

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

Return the default sampling frequency in Hz.

Bin equally spaced spectral regions.

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

Simulate an RF pulse on a single spin.

comb_fit_list_result_tables

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

Deconvolve two MRS data objects.

comb_fit_tables

Combine all fitting data points into a single data frame.

Write fit results table to a csv file.

Perform a fit based analysis of MRS data.

A very simple DICOM reader.

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

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

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.

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

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

fp_phase_correct

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

Transform frequency-domain data to the time-domain.

Frequency-domain convolution based filter.

Apply a Gaussian smoother in the spectral domain.

Check LCModel can be run

Calculate the spectral SNR.

Crop mrs_data object data points in the time-domain.

Generate the F product operator.

Perform a fft and ffshift on a vector.

Return the default transmitter 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.

downsample_mrs_fd

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

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

Get a mol_parameters object for a named molecule.

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

Return the first half of a dynamic series.

Eddy current correction.

fit_t1_tr_array

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

elliptical_mask

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

fit_t1_ti_array

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

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.

Perform an iffshift and ifft on a vector.

Generate a MRSI VOI from an mrs_data object.

Return the frequency scale of an MRS dataset in Hz.

Generate a MRSI voxel from an mrs_data object.

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

Extract a subset of MRS data.

Return the first scans of a dynamic series.

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.

Integrate a spectral region.

Generate a SVS acquisition volume from an mrs_data object.

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

Grid shift MRSI data in the x/y dimension.

Arrange spectral plots in a grid.

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

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

Apply and subtract a Gaussian smoother in the spectral domain.

interleave_dyns

Interleave the first and second half of a dynamic series.

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

Generate an affine for nifti generation.

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

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

HSVD of an mrs_data object.

Crop basis_set object based on a frequency range.

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

gridplot.mrs_data

Arrange spectral plots in a grid.

get_1h_brain_basis_paras_v1

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

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

Check the TARQUIN binary can be run

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

mean_dyn_blocks

Calculate the mean of adjacent dynamic scans.

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

get_1h_brain_basis_paras_v2

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

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

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.

Mask an MRS dataset in the dynamic dimension.

mask_xy_ellipse

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

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

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

Crop mrs_data object based on a frequency range.

fit_t2_te_array

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

Generate the Fxy product operator with a specified phase.

Generate the I product operator for a single spin.

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

get_1h_brain_basis_paras_v3

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

Return the second half of a dynamic series.

Return a single slice from a larger MRSI dataset.

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

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

Export a one-page pdf of a single fit result

Plot a slice from a 7 dimensional array.

Calculate the pairwise means across a dynamic data set.

Get the quantum coherence matrix for a spin system.

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

Return acquisition parameters from a MRS data object.

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

Read MRS data using the TARQUIN software package.

plot_slice_fit_inter

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

Display an orthographic projection plot of a nifti object.

Robust Alignment to a Target Spectrum (RATS).

Return the default nucleus.

Return the default reference value for ppm scale.

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.

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

Calculate the mean spectrum from an mrs_data object.

Calculate the mean spectrum from an mrs_data object.

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

get_uncoupled_mol

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

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

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.

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

Get a data array from a fit result.

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

Image plot method for objects of class mrs_data.

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

Return the first time-domain data point.

Extract the reference component from an mrs_data object.

Return the mean of a list of mrs_data objects.

Perform l2 regularisation artefact suppression.

HSVD based signal filter.

Calculate the mean dynamic data.

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

Return a single voxel from a larger mrs dataset.

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

recon_twix_2d_mrsi

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

Calculate diagnostic information for object of class fit_result.

reson_table2mrs_data

Generate mrs_data from a table of single Lorentzian resonances.

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

plot.fit_result

Plot the fitting results of an object of class fit_result.

Plotting method for objects of class mrs_data.

HSVD of a complex vector.

Display an interactive orthographic projection plot of a nifti object.

Convert mrs_data object to a vector.

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

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

mask_xy_corners

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

get_basis_subset

Return a subset of the input basis.

Extract a subset of dynamic scans.

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

Apply the Fourier transform over the dynamic dimension.

Mask an MRSI dataset in the x-y direction

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

Extract the metabolite component from an mrs_data object.

Return the sampling frequency in Hz of an MRS dataset.

Repeat an array over a given dimension.

read_siemens_txt_hdr

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

Reader for csv fit results generated by TARQUIN.

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_result

Print a summary of an object of class fit_result.

scale_basis_amp

Scale a basis object by a scalar.

Print a summary of mrs_data parameters.

scale_basis_from_singlet

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

seq_steam_ideal_cof

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

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.

get_mrsi_voxel_xy_psf

Generate a MRSI voxel PSF from an mrs_data object.

Return the last scans of a dynamic series.

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

Correct linear frequency drift.

mean_vec_blocks

Calculate the mean of adjacent blocks in a vector.

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

Calculate the median dynamic data.

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

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

make_basis_from_raw

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

Print fit coordinates from a single index.

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

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.

Remove a subset of dynamic scans.

scale_amp_molal

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

Scale mrs_data to a spectral region.

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).

Apply the max operator to an MRS dataset.

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).

Apply the max operator to an interpolated MRS dataset.

Plot the spectral standard deviation.

plot_slice_map_inter

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

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

rectangular_mask

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

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

sim_basis_1h_brain

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

seq_pulse_acquire

Simple pulse and acquire sequence with ideal pulses.

seq_pulse_acquire_31p

Simple pulse and acquire sequence with ideal pulses.

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

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

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.

Sort the basis-set elements alphabetically.

Return the repetition time of an MRS dataset.

Time-domain spectral registration.

varpro_3_para_opts

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

Smooth data across the dynamic dimension with a Gaussian kernel.

Read a basis file in LCModel .basis format.

plot_voi_overlay

Plot a volume as an image overlay.

plot_voi_overlay_seg

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

Apply phasing parameters to MRS data.

Apply a weighting to the FID to enhance spectral resolution.

Replicate a scan over a given dimension.

varpro_basic_opts

Return a list of options for a basic VARPRO analysis.

scale_amp_molar2molal_pvc

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

Resample a basis-set to match a mrs_data acquisition.

Replicate a scan in the dynamic dimension.

Objects exported from other packages

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

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).

scale_amp_molar

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

scale_amp_ratio

Scale fitted amplitudes to a ratio of signal amplitude.

seq_steam_ideal

STEAM sequence with ideal pulses.

scale_amp_ratio_value

Scale fitted amplitudes to a ratio of signal amplitude.

Create a spin system object for pulse sequence simulation.

Apply a frequency shift to MRS data.

Set the repetition time of an MRS dataset.

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

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

seq_spin_echo_ideal_31p

Spin echo sequence with ideal pulses.

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

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

set_precomp_verbose

Set the verbosity of the precompute function.

read_tqn_result

Reader for csv results generated by TARQUIN.

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.

svs_1h_brain_analysis

Standard SVS 1H brain analysis pipeline.

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

Read MRS data from a file.

Resample an image to match a target image space.

sim_basis_mm_lip_lcm

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

Read an LCModel formatted coord file containing fit information.

CPMG style sequence with ideal pulses.

scale_amp_water_ratio

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

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

seq_slaser_ideal

sLASER sequence with ideal pulses.

seq_spin_echo_ideal

Spin echo sequence with ideal pulses.

Simulate a basis file using TARQUIN.

Simulate an mrs_data object containing simulated Gaussian noise.

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

Return a list of options for VARPRO based fitting.

Simulate a basis set object.

Apply frequency shifts to basis set signals.

Simulate an mrs_data object containing complex zero valued samples.

set_def_acq_paras

Set the default acquisition parameters.

Subtract the first dynamic spectrum from a dynamic series.

Zero-fill MRS data in the time domain.

Subtract the mean dynamic spectrum from a dynamic series.

sim_th_excit_profile

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

Set the number of transients for an mrs_data object.

Convert a vector into a mrs_data object.

zero_td_pts_end

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

Write MRS data object to file.

spant: spectroscopy analysis tools.

Calculate the standard deviation spectrum from an mrs_data object.

svs_1h_brain_batch_analysis

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

spant_abfit_benchmark

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

Decompose an mrs_data object into white and gray matter spectra.

write_mrs_nifti

Write MRS data object to file in NIFTI format.

stackplot.fit_result

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

Time-domain convolution based filter.

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

Transform time-domain data to the frequency-domain.

Perform a mathematical operation on a spectral region.

Return the sum of a list of mrs_data objects.

Sum two mrs_data objects.

stackplot.mrs_data

Stackplot plotting method for objects of class mrs_data.

zero_higher_orders

Zero all coherences including and above a given order.

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_mask_xy_mat

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

Calculate the standard deviation spectrum from an mrs_data object.

set_precomp_mode

Set the precompute mode.

seq_press_ideal

PRESS sequence with ideal pulses.

seq_mega_press_ideal

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

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

spant_simulation_benchmark

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

Produce a plot with multiple traces.

Simulate a mol_parameter object.

Signal space projection method for lipid suppression.

spant_mpress_drift

Example MEGA-PRESS data with significant B0 drift.

write_basis_tqn

Generate a basis file using TARQUIN.

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

Calculate the sum of data dynamics.

Calculate the sum across receiver coil elements.