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spant (version 2.15.0)

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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2.15.0

License

GPL-3

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Repository

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

Homepage

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

Maintainer

Martin Wilson

Last Published

September 14th, 2023

Functions in spant (2.15.0)

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

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

Apply Mod operator to an MRS dataset.

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

Apply Re operator to an MRS dataset.

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

Return the number of data points in an MRS dataset.

Combine a pair of basis set objects.

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

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

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.

Return a list of options for an ABfit analysis.

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.

Simulate an RF pulse on a single spin.

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

Apply Arg operator to an MRS dataset.

Apply Conj operator to an MRS dataset.

Baseline correction using the ALS method.

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

calc_coil_noise_cor

Calculate the noise correlation between coil elements.

Return the total number of spectra in an MRS dataset.

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

Check the TARQUIN binary can be run

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.

Calculate the spectral SNR.

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

Check LCModel can be run

Crop basis_set object based on a frequency range.

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

calc_peak_info_vec

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

comb_fit_list_fit_tables

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

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

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.

Simulate pulse sequence acquisition.

Add noise to an mrs_data object.

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

Return the default nucleus.

Crop an MRSI dataset in the x-y direction

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

comb_fit_list_result_tables

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

Apply a function over specified array axes.

Crop mrs_data object based on a frequency range.

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

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

comb_fit_tables

Combine all fitting data points into a single data frame.

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

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

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

Apply and subtract a Gaussian smoother in the spectral domain.

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

Bin equally spaced spectral regions.

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 reference value for ppm scale.

decimate_mrs_fd

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

Find valid MRS data files recursively from a directory path.

Extract the fit amplitudes from an object of class fit_result.

coherence_filter

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

collapse_to_dyns

Collapse MRS data by concatenating spectra along the dynamic dimension.

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

downsample_mrs_fd

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

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.

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

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

Crop mrs_data object data points in the time-domain.

crop_td_pts_end

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

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

Calculate the sum of squares differences between two mrs_data objects.

Frequency-domain convolution based filter.

Apply a Gaussian smoother in the spectral domain.

Return acquisition parameters from a MRS data object.

get_1h_brain_basis_paras_v3

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

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

Return the default sampling frequency in Hz.

Return the default transmitter frequency in Hz.

A very simple DICOM reader.

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

decimate_mrs_td

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

fp_phase_correct

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

get_basis_subset

Return a subset of the input basis.

get_1h_brain_basis_paras

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

Generate the I product operator for a single spin.

Transform frequency-domain data to the time-domain.

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

Deconvolve two MRS data objects.

Combine a reference and metabolite mrs_data object.

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

Calculate diagnostic information for object of class fit_result.

Perform a fit based analysis of MRS data.

Convolve two MRS data objects.

Get a mol_parameters object for a named molecule.

Write fit results table to a csv file.

Return a single slice from a larger MRSI dataset.

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

Extract a subset of MRS data.

Return the first scans of a dynamic series.

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

Generate an affine for nifti generation.

fit_t1_ti_array

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

Extract the metabolite component from an mrs_data object.

Generate a SVS acquisition volume from an mrs_data object.

Return the second half of a dynamic series.

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

Return the last scans of a dynamic series.

Return the sampling frequency in Hz of an MRS dataset.

Return a single voxel from a larger mrs dataset.

Eddy current correction.

HSVD of an mrs_data object.

elliptical_mask

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

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

fit_t1_tr_array

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

Grid shift MRSI data in the x/y dimension.

get_1h_brain_basis_paras_v1

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

HSVD based signal filter.

Generate the F product operator.

get_1h_brain_basis_paras_v2

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

Return the mean of a list of mrs_data objects.

fit_t2_te_array

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

Perform a fft and ffshift on a vector.

Apply the Fourier transform over the dynamic dimension.

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

Generate the Fxy product operator with a specified phase.

Extract a subset of dynamic scans.

Calculate the median dynamic data.

HSVD of a complex vector.

Correct linear frequency drift.

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

Return the first half of a dynamic series.

Generate a MRSI voxel from an mrs_data object.

Generate a MRSI VOI from an mrs_data object.

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

Get a data array from a fit result.

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

Return the first time-domain data point.

get_mrsi_voxel_xy_psf

Generate a MRSI voxel PSF from an mrs_data object.

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

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

get_uncoupled_mol

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

get_guassian_pulse

Generate a gaussian pulse shape.

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.

Return the frequency scale of an MRS dataset in Hz.

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

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

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.

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

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

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

mean_dyn_blocks

Calculate the mean of adjacent dynamic scans.

Arrange spectral plots in a grid.

Perform an iffshift and ifft on a vector.

Convert mrs_data object to a vector.

get_voi_seg_psf

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

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

mean_vec_blocks

Calculate the mean of adjacent blocks in a vector.

Apply phasing parameters to MRS data.

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

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

Print a summary of mrs_data parameters.

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

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

Calculate the mean spectrum from an mrs_data object.

Apply the max operator to an interpolated MRS dataset.

scale_amp_ratio_value

Scale fitted amplitudes to a ratio of signal amplitude.

mask_xy_corners

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

gridplot.mrs_data

Arrange spectral plots in a grid.

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

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

Objects exported from other packages

Perform l2 regularisation artefact suppression.

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

Extract the reference component from an mrs_data object.

Image plot method for objects of class mrs_data.

plot_slice_map_inter

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

plot_slice_fit_inter

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

Integrate a spectral region.

interleave_dyns

Interleave the first and second half of a dynamic series.

make_basis_from_raw

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

Mask an MRS dataset in the dynamic dimension.

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).

reson_table2mrs_data

Generate mrs_data from a table of single Lorentzian resonances.

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

seq_pulse_acquire_31p

Simple pulse and acquire sequence with ideal pulses.

Apply the max operator to an MRS dataset.

Export a one-page pdf of a single fit result

mask_xy_ellipse

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

Display an orthographic projection plot of a nifti object.

plot.fit_result

Plot the fitting results of an object of class fit_result.

Calculate the pairwise means across a dynamic data set.

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

Mask an MRSI dataset in the x-y direction

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

Calculate the mean dynamic data.

Read MRS data from a file.

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

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

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

Plot the spectral standard deviation.

Get the quantum coherence matrix for a spin system.

scale_amp_water_ratio

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

plot_voi_overlay

Plot a volume as an image overlay.

Plotting method for objects of class mrs_data.

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

Print fit coordinates from a single index.

Replicate a scan over a given dimension.

Display an interactive orthographic projection plot of a nifti object.

Transform time-domain data to the frequency-domain.

Repeat an array over a given dimension.

scale_amp_ratio

Scale fitted amplitudes to a ratio of signal amplitude.

seq_slaser_ideal

sLASER sequence with ideal pulses.

set_mask_xy_mat

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

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

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

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).

scale_amp_molar

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

Resample a basis-set to match a mrs_data acquisition.

Replicate a scan in the dynamic dimension.

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

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

Read a basis file in LCModel .basis format.

zero_higher_orders

Zero all coherences including and above a given order.

seq_press_ideal

PRESS sequence with ideal pulses.

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

Read an LCModel formatted coord file containing fit information.

Resample an image to match a target image space.

read_siemens_txt_hdr

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

set_precomp_mode

Set the precompute mode.

seq_pulse_acquire

Simple pulse and acquire sequence with ideal pulses.

print.fit_result

Print a summary of an object of class fit_result.

Robust Alignment to a Target Spectrum (RATS).

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.

Apply a weighting to the FID to enhance spectral resolution.

Apply a frequency shift to MRS data.

set_precomp_verbose

Set the verbosity of the precompute function.

Plot a slice from a 7 dimensional array.

Reader for csv fit results generated by TARQUIN.

recon_twix_2d_mrsi

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

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

plot_voi_overlay_seg

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

Scale mrs_data to a spectral region.

rectangular_mask

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

scale_amp_molar2molal_pvc

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

set_def_acq_paras

Set the default acquisition parameters.

zero_td_pts_end

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

Read MRS data using the TARQUIN software package.

Apply frequency shifts to basis set signals.

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

svs_1h_brain_batch_analysis

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

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.

Signal space projection method for lipid suppression.

Calculate the standard deviation spectrum from an mrs_data object.

Remove a subset of dynamic scans.

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

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

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

read_tqn_result

Reader for csv results generated by TARQUIN.

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

sim_th_excit_profile

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

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_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_abfit_benchmark

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

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

Calculate the standard deviation spectrum from an mrs_data object.

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.

Set the repetition time of an MRS dataset.

CPMG style sequence with ideal pulses.

Subtract the mean dynamic spectrum from a dynamic series.

Simulate a mol_parameter object.

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

Simulate an mrs_data object containing simulated Gaussian noise.

Convert a vector into a mrs_data object.

seq_mega_press_ideal

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

seq_spin_echo_ideal

Spin echo sequence with ideal pulses.

Return the sum of a list of mrs_data objects.

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

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_spin_echo_ideal_31p

Spin echo sequence with ideal pulses.

Time-domain spectral registration.

Simulate an mrs_data object containing complex zero valued samples.

sim_basis_mm_lip_lcm

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

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

Simulate a basis set object.

write_basis_tqn

Generate a basis file using TARQUIN.

Calculate the sum of data dynamics.

Sort the basis-set elements alphabetically.

Set the number of transients for an mrs_data object.

Simulate a basis file using TARQUIN.

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

varpro_basic_opts

Return a list of options for a basic VARPRO analysis.

stackplot.mrs_data

Stackplot plotting method for objects of class mrs_data.

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: spectroscopy analysis tools.

svs_1h_brain_analysis

Standard SVS 1H brain analysis pipeline.

spant_mpress_drift

Example MEGA-PRESS data with significant B0 drift.

Decompose an mrs_data object into white and gray matter spectra.

Sum two mrs_data objects.

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.

Calculate the sum across receiver coil elements.

Subtract the first dynamic spectrum from a dynamic series.

Write MRS data object to file.

Produce a plot with multiple traces.

Return the repetition time of an MRS dataset.

Time-domain convolution based filter.

Smooth data across the dynamic dimension with a Gaussian kernel.

seq_steam_ideal_cof

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

seq_steam_ideal

STEAM sequence with ideal pulses.

Create a spin system object for pulse sequence simulation.

stackplot.fit_result

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

Zero-fill MRS data in the time domain.

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 a basis object to an LCModel .basis formatted file.

varpro_3_para_opts

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

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

Perform a mathematical operation on a spectral region.

write_mrs_nifti

Write MRS data object to file in NIFTI format.

Apply Im operator to an MRS dataset.