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spant (version 2.19.0)

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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2.19.0

License

GPL-3

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Repository

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

Homepage

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

Maintainer

Martin Wilson

Last Published

March 22nd, 2024

Functions in spant (2.19.0)

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

Apply Arg 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.

Apply Im operator to an MRS dataset.

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

Apply Mod operator to an MRS dataset.

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

Apply Conj operator to an MRS dataset.

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

Simulate pulse sequence acquisition.

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

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

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.

Return a list of options for an ABfit analysis.

Apply Re operator to an MRS dataset.

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

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

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

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

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.

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

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

Add noise to an mrs_data object.

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

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

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

Apply a function over specified array axes.

Check the TARQUIN binary can be run

Bin equally spaced spectral regions.

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

Apply and subtract a Gaussian smoother in the spectral domain.

coherence_filter

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

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.

Simulate an RF pulse on a single spin.

collapse_to_dyns

Collapse MRS data by concatenating spectra along the dynamic dimension.

calc_coil_noise_cor

Calculate the noise correlation between coil elements.

Calculate the spectral SNR.

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

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

Return the default sampling frequency in Hz.

Crop basis_set object based on a frequency range.

Combine a reference and metabolite mrs_data object.

Convolve two MRS data objects.

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

Check LCModel can be run

Return the default transmitter frequency in Hz.

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

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.

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

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.

decimate_mrs_td

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

Eddy current correction.

Crop an MRSI dataset in the x-y direction

Write fit results table to a csv file.

fit_t1_ti_array

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

calc_coil_noise_sd

Calculate the noise standard deviation for each coil element.

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 mrs_data object based on a frequency range.

Deconvolve two MRS data objects.

elliptical_mask

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

Find valid MRS data files recursively from a directory path.

fp_phase_correct

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

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

comb_fit_tables

Combine all fitting data points into a single data frame.

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

get_1h_brain_basis_names

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

A very simple DICOM reader.

Generate a trapezoidal response function.

get_guassian_pulse

Generate a gaussian pulse shape.

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

Return the first scans of a dynamic series.

Generate an affine for nifti generation.

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

downsample_mrs_fd

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

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

Generate a BOLD response function.

Extract the fit amplitudes from an object of class fit_result.

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

Generate the I product operator for a single spin.

get_mrsi_voxel_xy_psf

Generate a MRSI voxel PSF from an mrs_data object.

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

Return the last scans of a dynamic series.

Generate the F product operator.

Baseline correction using the ALS method.

calc_ed_from_lambda

Calculate the effective dimensions of a spline smoother from lambda.

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.

Return the spin number for a given nucleus.

Return the default nucleus.

Return the first half of a dynamic series.

calc_peak_info_vec

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

Generate the Fxy product operator with a specified phase.

comb_fit_list_fit_tables

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

Generate a SVS acquisition volume from an mrs_data object.

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

Return the default reference value for ppm scale.

get_1h_braino_basis_names

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

decimate_mrs_fd

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

Calculate diagnostic information for object of class fit_result.

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

Extract a subset of MRS data.

Arrange spectral plots in a grid.

Transform frequency-domain data to the time-domain.

fit_t1_tr_array

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

Image plot method for objects of class mrs_data.

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

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

mask_xy_corners

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

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

fit_t2_te_array

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

make_basis_from_raw

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

get_voi_seg_psf

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

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

gridplot.mrs_data

Arrange spectral plots in a grid.

Integrate a spectral region.

get_1h_brain_basis_paras

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

get_basis_subset

Return a subset of the input basis.

get_1h_brain_basis_paras_v1

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

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

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

Generate a MRSI VOI from an mrs_data object.

Extract a subset of dynamic scans.

Generate a MRSI voxel from an mrs_data object.

Apply the Fourier transform over the dynamic dimension.

Perform a fit based analysis of MRS data.

Apply a Gaussian smoother in the spectral domain.

Frequency-domain convolution based filter.

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

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

Perform a fft and ffshift on a vector.

Mask an MRS dataset in the dynamic dimension.

Grid shift MRSI data in the x/y dimension.

Return a single voxel from a larger mrs dataset.

Perform an iffshift and ifft on a vector.

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

get_1h_spectre_basis_names

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

Apply the max operator to an MRS dataset.

Return the sampling frequency in Hz of an MRS dataset.

get_1h_brain_basis_paras_v3

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

Get a data array from a fit result.

Return the first time-domain data point.

get_1h_brain_basis_paras_v2

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

interleave_dyns

Interleave the first and second half of a dynamic series.

Apply the max operator to an interpolated MRS dataset.

Robust Alignment to a Target Spectrum (RATS).

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

Return acquisition parameters from a MRS data object.

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

mean_dyn_blocks

Calculate the mean of adjacent dynamic scans.

Calculate the mean spectrum from an mrs_data object.

mask_xy_ellipse

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

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

plot_slice_fit_inter

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

Convert mrs_data object to a vector.

Resample an image to match a target image space.

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

Extract the metabolite component from an mrs_data object.

HSVD based signal filter.

Resample a basis-set to match a mrs_data acquisition.

Return a single slice from a larger MRSI dataset.

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

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

Return the second half of a dynamic series.

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).

Get the quantum coherence matrix for a spin system.

Print a summary of mrs_data parameters.

Calculate the mean spectrum from an mrs_data object.

read_pulse_bruker

Read a Bruker formatted pulse file

read_pulse_ascii

Read an ASCII formatted pulse file.

Return the mean of a list of mrs_data objects.

print.fit_result

Print a summary of an object of class fit_result.

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

HSVD of an mrs_data object.

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

Return the frequency scale of an MRS dataset in Hz.

HSVD of a complex vector.

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

Repeat an array over a given dimension.

Calculate the median dynamic data.

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

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

Apply a weighting to the FID to enhance spectral resolution.

Correct linear frequency drift.

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

mean_vec_blocks

Calculate the mean of adjacent blocks in a vector.

Export a one-page pdf of a single fit result

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

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

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

Plotting method for objects of class mrs_data.

Set the repetition time of an MRS dataset.

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

scale_basis_from_singlet

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

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_molal

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

Reader for csv fit results generated by TARQUIN.

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

read_tqn_result

Reader for csv results generated by TARQUIN.

Apply phasing parameters to MRS data.

Calculate the pairwise means across a dynamic data set.

Mask an MRSI dataset in the x-y direction

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

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

Calculate the mean dynamic data.

scale_amp_ratio

Scale fitted amplitudes to a ratio of signal amplitude.

Apply a frequency shift to MRS data.

Plot the spectral standard deviation.

spant_abfit_benchmark

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

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

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

Print fit coordinates from a single index.

Replicate a scan in the dynamic dimension.

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

read_siemens_txt_hdr

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

spant: spectroscopy analysis tools.

Simulate an mrs_data object containing simulated Gaussian noise.

CPMG style sequence with ideal pulses.

plot_voi_overlay

Plot a volume as an image overlay.

recon_twix_2d_mrsi

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

seq_mega_press_ideal

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

plot_voi_overlay_seg

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

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

plot.fit_result

Plot the fitting results of an object of class fit_result.

seq_pulse_acquire

Simple pulse and acquire sequence with ideal pulses.

seq_steam_ideal_cof

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

rectangular_mask

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

Objects exported from other packages

scale_amp_molar

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

Read MRS data from a file.

Replicate a scan over a given dimension.

Get a mol_parameters object for a named molecule.

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).

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

set_precomp_verbose

Set the verbosity of the precompute function.

scale_basis_amp

Scale a basis object by a scalar.

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

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

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...).

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

Extract the reference component from an mrs_data object.

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

Produce a plot with multiple traces.

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

Signal space projection method for lipid suppression.

scale_amp_ratio_value

Scale fitted amplitudes to a ratio of signal amplitude.

set_precomp_mode

Set the precompute mode.

Read MRS data using the TARQUIN software package.

set_mask_xy_mat

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

Simulate an mrs_data object containing complex zero valued samples.

seq_press_ideal

PRESS sequence with ideal pulses.

write_mrs_nifti

Write MRS data object to file in NIFTI format.

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

Calculate the sum of data dynamics.

scale_amp_molar2molal_pvc

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

seq_press_2d_shaped

PRESS sequence with shaped refocusing pulses.

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

sim_basis_mm_lip_lcm

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

Simulate a basis file using TARQUIN.

Convert a vector into a mrs_data object.

svs_1h_brain_analysis

Standard SVS 1H brain analysis pipeline.

Return the sum of a list of mrs_data objects.

Perform l2 regularisation artefact suppression.

Display an interactive orthographic projection plot of a nifti object.

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

Display an orthographic projection plot of a nifti object.

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

Plot a slice from a 7 dimensional array.

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

plot_slice_map_inter

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

Read a basis file in LCModel .basis format.

sim_basis_1h_brain

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

Subtract the first dynamic spectrum from a dynamic series.

seq_steam_ideal

STEAM sequence with ideal pulses.

scale_amp_water_ratio

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

seq_spin_echo_ideal

Spin echo sequence with ideal pulses.

Time-domain spectral registration.

varpro_basic_opts

Return a list of options for a basic VARPRO analysis.

Calculate the sum across receiver coil elements.

Apply frequency shifts to basis set signals.

Simulate a basis set object.

Sum two mrs_data objects.

svs_1h_brain_batch_analysis

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

write_pulse_ascii

Write an ASCII formatted pulse file.

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

Sort the basis-set elements alphabetically.

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.

svs_1h_brain_analysis_dev

Standard SVS 1H brain analysis pipeline.

Smooth data across the dynamic dimension with a Gaussian kernel.

sub_median_dyns

Subtract the median dynamic spectrum from a dynamic series.

Scale mrs_data to a spectral region.

Calculate the standard deviation spectrum from an mrs_data object.

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.

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_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.

reson_table2mrs_data

Generate mrs_data from a table of single Lorentzian resonances.

Read an LCModel formatted coord file containing fit information.

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.

Return a list of options for VARPRO based fitting.

spant_simulation_benchmark

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

spant_mpress_drift

Example MEGA-PRESS data with significant B0 drift.

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

Calculate the standard deviation spectrum from an mrs_data object.

Remove a subset of dynamic scans.

seq_slaser_ideal

sLASER sequence with ideal pulses.

stackplot.mrs_data

Stackplot plotting method for objects of class mrs_data.

set_def_acq_paras

Set the default acquisition parameters.

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

Set the number of transients for an mrs_data object.

sim_th_excit_profile

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

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

Create a spin system object for pulse sequence simulation.

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

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

Decompose an mrs_data object into white and gray matter spectra.

Return the repetition time of an MRS dataset.

Simulate a mol_parameter object.

Perform a mathematical operation on a spectral region.

Write MRS data object to file.

write_basis_tqn

Generate a basis file using TARQUIN.

zero_higher_orders

Zero all coherences including and above a given order.

Transform time-domain data to the frequency-domain.

Zero-fill MRS data in the time domain.

zero_td_pts_end

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

Time-domain convolution based filter.

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.

Return the echo time of an MRS dataset.

Subtract the mean dynamic spectrum from a dynamic series.