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spant (version 2.4.0)

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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2.4.0

License

GPL-3

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Repository

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

Homepage

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

Maintainer

Martin Wilson

Last Published

November 7th, 2022

Functions in spant (2.4.0)

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

Apply Im operator to an MRS dataset.

Apply Mod operator to an MRS dataset.

Return the total number of spectra in an MRS dataset.

Apply Conj operator to an MRS dataset.

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

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

Return a list of options for an ABfit analysis.

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

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.

Add noise to an mrs_data object.

Apply Re operator to an MRS dataset.

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

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

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

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

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

Apply a function over specified array axes.

Calculate the sum of squares differences between two mrs_data objects.

Baseline correction using the ALS method.

calc_coil_noise_sd

Calculate the noise standard deviation for each coil element.

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.

Combine a reference and metabolite mrs_data object.

Bin equally spaced spectral regions.

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.

calc_ed_from_lambda

Calculate the effective dimensions of a spline smoother from lambda.

calc_peak_info_vec

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

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

Convolve two MRS data objects.

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

Combine a pair of basis set objects.

Calculate the spectral SNR.

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

calc_coil_noise_cor

Calculate the noise correlation between coil elements.

Return the default reference value for ppm scale.

Crop an MRSI dataset in the x-y direction

A very simple DICOM reader.

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

Return the default sampling frequency in Hz.

Check LCModel can be run

Check the TARQUIN binary can be run

Return the default nucleus.

Return the default transmitter frequency in Hz.

Calculate diagnostic information for object of class fit_result.

Extract the fit amplitudes from an object of class fit_result.

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

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

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

Generate the F product operator.

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

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

fp_phase_correct

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

Generate the Fxy product operator with a specified phase.

Return the first time-domain data point.

Apply the Fourier transform over the dynamic dimension.

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

Perform a fft and ffshift on a vector.

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

get_guassian_pulse

Generate a gaussian pulse shape.

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

Crop mrs_data object based on a frequency range.

collapse_to_dyns

Collapse MRS data by concatenating spectra along the dynamic dimension.

comb_fit_list_fit_tables

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

comb_fit_list_result_tables

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

comb_fit_tables

Combine all fitting data points into a single data frame.

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

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

Generate a MRSI VOI from an mrs_data object.

Return the last scans of a dynamic series.

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

Eddy current correction.

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

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

Return acquisition parameters from a MRS data object.

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.

Generate a SVS acquisition volume 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.

Return the sampling frequency in Hz of an MRS dataset.

Extract a subset of MRS data.

Return a single slice from a larger MRSI dataset.

Return the first scans of a dynamic series.

Extract the reference component from an mrs_data object.

HSVD of an mrs_data object.

Integrate a spectral region.

Crop mrs_data object data points in the time-domain.

HSVD based signal filter.

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

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

elliptical_mask

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

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

Transform frequency-domain data to the time-domain.

interleave_dyns

Interleave the first and second half of a dynamic series.

Frequency-domain convolution based filter.

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

Arrange spectral plots in a grid.

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

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

Extract the metabolite component from an mrs_data object.

Return the second half of a dynamic series.

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

Calculate the pairwise means across a dynamic data set.

Mask an MRSI dataset in the x-y direction

get_1h_brain_basis_paras_v3

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

mean_dyn_blocks

Calculate the mean of adjacent dynamic scans.

get_1h_brain_basis_paras_v2

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

Calculate the median dynamic data.

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

Image plot method for objects of class mrs_data.

gridplot.mrs_data

Arrange spectral plots in a grid.

Extract a subset of dynamic scans.

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

Get a mol_parameters object for a named molecule.

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).

Perform an iffshift and ifft on a vector.

Generate an affine for nifti generation.

Display an orthographic projection plot of a nifti object.

get_uncoupled_mol

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

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.

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

HSVD of a complex vector.

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

Return the frequency scale of an MRS dataset in Hz.

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

Perform a fit based analysis of MRS data.

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

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

downsample_mrs_fd

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

Write fit results table to a csv file.

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

Read a basis file in LCModel .basis format.

Mask an MRS dataset in the dynamic dimension.

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

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

Return the mean of a list of mrs_data objects.

Calculate the mean dynamic data.

Read MRS data using the TARQUIN software package.

plot_slice_fit_inter

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

Plot a slice from a 7 dimensional array.

Apply a weighting to the FID to enhance spectral resolution.

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.

Read a basis file in LCModel .basis format (for testing only).

get_1h_brain_basis_paras

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

Robust Alignment to a Target Spectrum (RATS).

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.

Apply the max operator to an interpolated MRS dataset.

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

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

Apply the max operator to an MRS dataset.

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

Apply phasing parameters to MRS data.

get_voi_seg_psf

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

reson_table2mrs_data

Generate mrs_data from a table of single Lorentzian resonances.

recon_twix_2d_mrsi

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

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

rectangular_mask

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

Return the first half of a dynamic series.

Generate a MRSI voxel from an mrs_data object.

Get a data array from a fit result.

get_mrsi_voxel_xy_psf

Generate a MRSI voxel PSF from an mrs_data object.

get_1h_brain_basis_paras_v1

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

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

Calculate the mean spectrum from an mrs_data object.

plot_slice_map_inter

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

Calculate the mean spectrum from an mrs_data object.

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

Print fit coordinates from a single index.

Display an interactive orthographic projection plot of a nifti object.

plot.fit_result

Plot the fitting results of an object of class fit_result.

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

Replicate a scan in the dynamic dimension.

Replicate a scan over a given dimension.

Plotting method for objects of class mrs_data.

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

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

Return a single voxel from a larger mrs dataset.

set_def_acq_paras

Set the default acquisition parameters.

CPMG style sequence with ideal pulses.

plot_voi_overlay

Plot a volume as an image overlay.

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

read_siemens_txt_hdr

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

Objects exported from other packages

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

Repeat an array over a given dimension.

seq_slaser_ideal

sLASER sequence with ideal pulses.

seq_spin_echo_ideal

Spin echo sequence with ideal pulses.

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

Scale mrs_data to a spectral region.

Grid shift MRSI data in the x/y dimension.

Print a summary of mrs_data parameters.

print.fit_result

Print a summary of an object of class fit_result.

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

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

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

Resample an image to match a target image space.

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

Get the quantum coherence matrix for a spin system.

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

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

Perform l2 regularisation artefact suppression.

Convert mrs_data object to a vector.

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

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

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

Reader for csv fit results generated by TARQUIN.

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.

sim_basis_1h_brain

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

Sum two mrs_data objects.

set_precomp_verbose

Set the verbosity of the precompute function.

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.

set_precomp_mode

Set the precompute mode.

Signal space projection method for lipid suppression.

Calculate the standard deviation spectrum from an mrs_data object.

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

Simulate a mol_parameter object.

Simulate an mrs_data object containing simulated Gaussian noise.

Calculate the standard deviation spectrum from an mrs_data object.

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

Apply a frequency shift to MRS data.

spant_simulation_benchmark

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

Decompose an mrs_data object into white and gray matter spectra.

stackplot.mrs_data

Stackplot plotting method for objects of class mrs_data.

Return the sum of a list of mrs_data objects.

Sort the basis-set elements alphabetically.

spant: spectroscopy analysis tools.

Zero all non-zero-order coherences.

Subtract the mean dynamic spectrum from a dynamic series.

Zero-fill MRS data in the time domain.

scale_amp_ratio

Scale fitted amplitudes to a ratio of signal amplitude.

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

scale_amp_molar

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

Apply frequency shifts to basis set signals.

seq_pulse_acquire

Simple pulse and acquire sequence with ideal pulses.

Simulate a basis set object.

seq_pulse_acquire_31p

Simple pulse and acquire sequence with ideal pulses.

stackplot.fit_result

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

varpro_basic_opts

Return a list of options for a basic VARPRO analysis.

Simulate an mrs_data object containing complex zero valued samples.

Produce a plot with multiple traces.

Return a list of options for VARPRO based fitting.

scale_amp_ratio_value

Scale fitted amplitudes to a ratio of signal amplitude.

scale_amp_water_ratio

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

seq_mega_press_ideal

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

Perform a mathematical operation on a spectral region.

plot_voi_overlay_seg

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

write_mrs_nifti

Write MRS data object to file in NIFTI format.

write_basis_tqn

Generate a basis file using TARQUIN.

Transform time-domain data to the frequency-domain.

Time-domain convolution based filter.

Create a spin system object for pulse sequence simulation.

Write MRS data object to file.

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

Calculate the sum across receiver coil elements.

seq_press_ideal

PRESS sequence with ideal pulses.

set_mask_xy_mat

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

Calculate the sum of data dynamics.

varpro_3_para_opts

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

Read an LCModel formatted coord file containing fit information.

Remove a subset of dynamic scans.

Read MRS data from a file.

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

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

Time-domain spectral registration.

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.

scale_amp_molal_pvc

Apply partial volume correction to a fitting result object.

seq_steam_ideal

STEAM sequence with ideal pulses.

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

spant_abfit_benchmark

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

seq_spin_echo_ideal_31p

Spin echo sequence with ideal pulses.

Simulate a basis file using TARQUIN.

spant_mpress_drift

Example MEGA-PRESS data with significant B0 drift.

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.

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

Convert a vector into a mrs_data object.