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spant (version 2.7.0)

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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2.7.0

License

GPL-3

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Repository

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

Homepage

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

Maintainer

Martin Wilson

Last Published

January 28th, 2023

Functions in spant (2.7.0)

Apply Im operator to an MRS dataset.

Apply Mod operator to an MRS dataset.

Apply Conj operator to an MRS dataset.

Return the total number of spectra in an MRS dataset.

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

Return the number of data points in an MRS dataset.

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

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

Apply Arg operator to an MRS dataset.

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

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

Add noise to an mrs_data object.

Apply Re operator to an MRS dataset.

Return a list of options for an ABfit analysis.

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

Simulate pulse sequence acquisition.

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.

Combine a pair of basis set objects.

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.

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

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

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

Apply a function over specified array axes.

coherence_filter

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

Simulate an RF pulse on a single spin.

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

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

calc_peak_info_vec

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

calc_ed_from_lambda

Calculate the effective dimensions of a spline smoother from lambda.

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

calc_coil_noise_cor

Calculate the noise correlation between coil elements.

calc_coil_noise_sd

Calculate the noise standard deviation for each coil element.

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

collapse_to_dyns

Collapse MRS data by concatenating spectra along the dynamic dimension.

comb_fit_list_result_tables

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

Return the default nucleus.

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

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

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

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

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

Combine a reference and metabolite mrs_data object.

comb_fit_list_fit_tables

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

Calculate the sum of squares differences between two mrs_data objects.

Crop mrs_data object based on a frequency range.

Convolve two MRS data objects.

comb_fit_tables

Combine all fitting data points into a single data frame.

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

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

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.

Return the default reference value for ppm scale.

elliptical_mask

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

Eddy current correction.

Transform frequency-domain data to the time-domain.

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

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

fit_t1_tr_array

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

Baseline correction using the ALS method.

Apply the Fourier transform over the dynamic dimension.

Bin equally spaced spectral regions.

Check the TARQUIN binary 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.

downsample_mrs_fd

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

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

fit_t2_te_array

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

get_1h_brain_basis_paras_v1

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

crop_td_pts_end

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

Calculate the spectral SNR.

Perform a fft and ffshift on a vector.

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

get_1h_brain_basis_paras_v2

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

A very simple DICOM reader.

Generate the I product operator for a single spin.

Crop an MRSI dataset in the x-y direction

Check LCModel can be run

get_1h_brain_basis_paras

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

Return the first scans of a dynamic series.

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.

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

Return the default sampling frequency in Hz.

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

Generate a MRSI voxel from an mrs_data object.

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

Return acquisition parameters from a MRS data object.

get_basis_subset

Return a subset of the input basis.

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

get_mrsi_voxel_xy_psf

Generate a MRSI voxel PSF from an mrs_data object.

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.

Return the sampling frequency in Hz of an MRS dataset.

Perform a fit based analysis of MRS data.

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

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

Extract the metabolite component from an mrs_data object.

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

Return the second half of a dynamic series.

HSVD of an mrs_data object.

HSVD based signal filter.

decimate_mrs_td

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

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.

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

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

Perform an iffshift and ifft on a vector.

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

Return the default transmitter frequency in Hz.

Correct linear frequency drift.

Calculate the pairwise means across a dynamic data set.

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

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

Return the first half of a dynamic series.

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

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

Extract the reference component from an mrs_data object.

Return a single slice from a larger MRSI dataset.

Get a data array from a fit result.

fit_t1_ti_array

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

Extract a subset of MRS data.

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

get_voi_seg_psf

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

Return the first time-domain data point.

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

get_guassian_pulse

Generate a gaussian pulse shape.

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

Get a mol_parameters object for a named molecule.

Calculate the mean dynamic data.

Apply the max operator to an MRS dataset.

Calculate the median dynamic data.

Display an interactive orthographic projection plot of a nifti object.

Generate an affine for nifti generation.

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

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

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

Extract a subset of dynamic scans.

plot_voi_overlay_seg

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

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

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

Generate a MRSI VOI from an mrs_data object.

Frequency-domain convolution based filter.

Extract the fit amplitudes from an object of class fit_result.

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

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

Calculate the mean spectrum from an mrs_data object.

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

Robust Alignment to a Target Spectrum (RATS).

mean_dyn_blocks

Calculate the mean of adjacent dynamic scans.

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

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

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

Apply a weighting to the FID to enhance spectral resolution.

plot_slice_fit_inter

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

Objects exported from other packages

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

get_uncoupled_mol

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

Plot a slice from a 7 dimensional array.

fp_phase_correct

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

Arrange spectral plots in a grid.

Repeat an array over a given dimension.

Return the frequency scale of an MRS dataset in Hz.

HSVD of a complex vector.

gridplot.mrs_data

Arrange spectral plots in a grid.

Image plot method for objects of class mrs_data.

Generate the F product operator.

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

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

Generate the Fxy product operator with a specified phase.

Print a summary of mrs_data parameters.

Get the quantum coherence matrix for a spin system.

Generate a SVS acquisition volume from an mrs_data object.

Return the last scans of a dynamic series.

Return a single voxel from a larger mrs dataset.

Mask an MRSI dataset in the x-y direction

recon_twix_2d_mrsi

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

Grid shift MRSI data in the x/y dimension.

Integrate a spectral region.

Print fit coordinates from a single index.

plot_slice_map_inter

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

plot_voi_overlay

Plot a volume as an image overlay.

Read a basis file in LCModel .basis format.

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

rectangular_mask

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

Return the mean of a list of mrs_data objects.

mask_xy_corners

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

mask_xy_ellipse

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

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

Scale mrs_data to a spectral region.

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

Replicate a scan in the dynamic dimension.

Create a spin system object for pulse sequence simulation.

Replicate a scan over a given dimension.

Calculate the standard deviation spectrum from an mrs_data object.

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

seq_spin_echo_ideal

Spin echo sequence with ideal pulses.

make_basis_from_raw

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

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

Simulate an mrs_data object containing complex zero valued samples.

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

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.

Reader for csv fit results generated by TARQUIN.

Simulate a mol_parameter object.

Mask an MRS dataset in the dynamic dimension.

mean_vec_blocks

Calculate the mean of adjacent blocks in a vector.

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.

Simulate an mrs_data object containing simulated Gaussian noise.

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

seq_spin_echo_ideal_31p

Spin echo sequence with ideal pulses.

Simulate a basis file using TARQUIN.

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

read_tqn_result

Reader for csv results generated by TARQUIN.

Calculate the mean spectrum from an mrs_data object.

Display an orthographic projection plot of a nifti object.

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

Apply phasing parameters to MRS data.

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

Smooth data across the dynamic dimension with a Gaussian kernel.

zero_higher_orders

Zero all coherences including and above a given order.

Perform a mathematical operation on a spectral region.

print.fit_result

Print a summary of an object of class fit_result.

sim_th_excit_profile

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

interleave_dyns

Interleave the first and second half of a dynamic series.

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

zero_td_pts_end

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

Calculate the standard deviation spectrum from an mrs_data object.

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).

Read an LCModel formatted coord file containing fit information.

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.

Perform l2 regularisation artefact suppression.

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

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

Time-domain spectral registration.

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

read_siemens_txt_hdr

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

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).

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

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

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.

Resample a basis-set to match a mrs_data acquisition.

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

Resample an image to match a target image space.

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

scale_amp_ratio_value

Scale fitted amplitudes to a ratio of signal amplitude.

Convert mrs_data object to a vector.

seq_pulse_acquire_31p

Simple pulse and acquire sequence with ideal pulses.

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

seq_slaser_ideal

sLASER sequence with ideal pulses.

Sum two mrs_data objects.

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

varpro_3_para_opts

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

spant_abfit_benchmark

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

spant_mpress_drift

Example MEGA-PRESS data with significant B0 drift.

plot.fit_result

Plot the fitting results of an object of class fit_result.

Plotting method for objects of class mrs_data.

CPMG style sequence with ideal pulses.

scale_amp_water_ratio

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

Calculate the sum across receiver coil elements.

Return the sum of a list of mrs_data objects.

seq_press_ideal

PRESS sequence with ideal pulses.

Read MRS data from a file.

seq_mega_press_ideal

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

set_precomp_verbose

Set the verbosity of the precompute function.

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

Read MRS data using the TARQUIN software package.

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

Zero-fill MRS data in the time domain.

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

Calculate the sum of data dynamics.

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).

reson_table2mrs_data

Generate mrs_data from a table of single Lorentzian resonances.

seq_pulse_acquire

Simple pulse and acquire sequence with ideal pulses.

set_def_acq_paras

Set the default acquisition parameters.

Remove a subset of dynamic scans.

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.

Simulate a basis set object.

Apply frequency shifts to basis set signals.

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

Apply a frequency shift to MRS data.

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.

sim_basis_1h_brain

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

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.

write_mrs_nifti

Write MRS data object to file in NIFTI format.

seq_steam_ideal

STEAM sequence with ideal pulses.

svs_1h_brain_analysis

Standard SVS 1H brain analysis pipeline.

svs_1h_brain_batch_analysis

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

set_mask_xy_mat

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

seq_steam_ideal_cof

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

Decompose an mrs_data object into white and gray matter spectra.

spant_simulation_benchmark

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

set_precomp_mode

Set the precompute mode.

sim_basis_1h_brain_press

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

sim_basis_mm_lip_lcm

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

stackplot.mrs_data

Stackplot plotting method for objects of class mrs_data.

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.

Subtract the mean dynamic spectrum from a dynamic series.

Transform time-domain data to the frequency-domain.

Write MRS data object to file.

Time-domain convolution based filter.

write_basis_tqn

Generate a basis file using TARQUIN.

Sort the basis-set elements alphabetically.

spant: spectroscopy analysis tools.

Signal space projection method for lipid suppression.

Return a list of options for VARPRO based fitting.

varpro_basic_opts

Return a list of options for a basic VARPRO analysis.

Convert a vector into a mrs_data object.

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