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spant (version 2.5.0)

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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Version

2.5.0

License

GPL-3

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Repository

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

Homepage

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

Maintainer

Martin Wilson

Last Published

December 6th, 2022

Functions in spant (2.5.0)

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

Apply Conj operator to an MRS dataset.

Apply Arg operator to an MRS dataset.

Apply Im operator to an MRS dataset.

Return the number of data points in an MRS dataset.

Return the total number of x locations in 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 a list of options for an ABfit analysis.

Apply Re operator to an MRS dataset.

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

Apply Mod operator to an MRS dataset.

Simulate pulse sequence acquisition.

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

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

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

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.

Combine a pair of basis set objects.

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

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

Add noise to an mrs_data object.

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

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

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

Calculate the spectral SNR.

collapse_to_dyns

Collapse MRS data by concatenating spectra along the dynamic dimension.

Calculate the sum of squares differences between two mrs_data objects.

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

Baseline correction using the ALS method.

Check the TARQUIN binary can be run

Bin equally spaced spectral regions.

calc_coil_noise_cor

Calculate the noise correlation between coil elements.

Check LCModel can be run

comb_fit_list_fit_tables

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

calc_peak_info_vec

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

decimate_mrs_td

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

downsample_mrs_fd

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

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

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

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

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

Apply a function over specified array axes.

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

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

calc_coil_noise_sd

Calculate the noise standard deviation for each coil element.

Apply the Fourier transform over the dynamic dimension.

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

fp_phase_correct

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

calc_ed_from_lambda

Calculate the effective dimensions of a spline smoother from lambda.

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

Return the default nucleus.

Return the default transmitter frequency in Hz.

Return the default sampling frequency in Hz.

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.

comb_fit_list_result_tables

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

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

Frequency-domain convolution based filter.

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

Crop an MRSI dataset in the x-y direction

Transform frequency-domain data to the time-domain.

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

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

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).

Crop mrs_data object data points in the time-domain.

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.

Generate the Fxy product operator with a specified phase.

Generate a MRSI VOI from an mrs_data object.

Perform a fft and ffshift on a vector.

Generate the F product operator.

Crop mrs_data object based on a frequency range.

Eddy current correction.

comb_fit_tables

Combine all fitting data points into a single data frame.

Extract a subset of MRS data.

get_voi_seg_psf

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

Extract the fit amplitudes from an object of class fit_result.

Generate a SVS acquisition volume from an mrs_data object.

Return a single slice from a larger MRSI dataset.

Calculate diagnostic information for object of class fit_result.

get_guassian_pulse

Generate a gaussian pulse shape.

Generate a MRSI voxel from an mrs_data object.

Generate an affine for nifti generation.

Return acquisition parameters from a MRS data object.

Return the second half of a dynamic series.

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

Return a single voxel from a larger mrs dataset.

Return the first scans of a dynamic series.

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.

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.

get_basis_subset

Return a subset of the input basis.

Extract a subset of dynamic scans.

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

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

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

interleave_dyns

Interleave the first and second half of a dynamic series.

HSVD of an mrs_data object.

gridplot.mrs_data

Arrange spectral plots in a grid.

Mask an MRSI dataset in the x-y direction

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

Integrate a spectral region.

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

Combine a reference and metabolite mrs_data object.

Convolve two MRS data objects.

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

decimate_mrs_fd

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

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.

A very simple DICOM reader.

Return the default reference value for ppm scale.

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

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

Calculate the mean dynamic data.

Calculate the pairwise means across a dynamic data set.

get_1h_brain_basis_paras_v3

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

get_1h_brain_basis_paras_v2

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

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

Return the sampling frequency in Hz of an MRS dataset.

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

Print fit coordinates from a single index.

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).

HSVD based signal filter.

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

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

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

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

HSVD of a complex vector.

Mask an MRS dataset in the dynamic dimension.

Calculate the mean spectrum from an mrs_data object.

Apply the max operator to an interpolated MRS dataset.

Calculate the mean spectrum from an mrs_data object.

Image plot method for objects of class mrs_data.

Display an orthographic projection plot of a nifti object.

Display an interactive orthographic projection plot of a nifti object.

Apply the max operator to an MRS dataset.

print.fit_result

Print a summary of an object of class fit_result.

Print a summary of mrs_data parameters.

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

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.

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

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

plot.fit_result

Plot the fitting results of an object of class fit_result.

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

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.

read_tqn_result

Reader for csv results generated by TARQUIN.

Resample a basis-set to match a mrs_data acquisition.

read_siemens_txt_hdr

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

mean_dyn_blocks

Calculate the mean of adjacent dynamic scans.

Resample an image to match a target image space.

Apply phasing parameters to MRS data.

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

Read MRS data using the TARQUIN software package.

Write fit results table to a csv file.

Perform a fit based analysis of MRS data.

reson_table2mrs_data

Generate mrs_data from a table of single Lorentzian resonances.

Calculate the standard deviation spectrum from an mrs_data object.

Remove a subset of dynamic scans.

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

Get a data array from a fit result.

Return the first time-domain data point.

get_1h_brain_basis_paras

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

seq_slaser_ideal

sLASER sequence with ideal pulses.

Scale mrs_data to a spectral region.

seq_spin_echo_ideal

Spin echo sequence with ideal pulses.

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

Extract the metabolite component from an mrs_data object.

Return the first half of a dynamic series.

get_1h_brain_basis_paras_v1

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

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

Plotting method for objects of class mrs_data.

Convert mrs_data object to a vector.

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

Robust Alignment to a Target Spectrum (RATS).

Get the quantum coherence matrix for a spin system.

Return the mean of a list of mrs_data objects.

Calculate the median dynamic data.

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

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

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

Return the last scans of a dynamic series.

Arrange spectral plots in a grid.

Perform l2 regularisation artefact suppression.

Grid shift MRSI data in the x/y dimension.

seq_pulse_acquire

Simple pulse and acquire sequence with ideal pulses.

set_def_acq_paras

Set the default acquisition parameters.

Calculate the standard deviation spectrum from an mrs_data object.

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

seq_pulse_acquire_31p

Simple pulse and acquire sequence with ideal pulses.

Apply frequency shifts to basis set signals.

Simulate a basis set object.

Produce a plot with multiple traces.

Signal space projection method for lipid suppression.

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.

Create a spin system object for pulse sequence simulation.

recon_twix_2d_mrsi

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

rectangular_mask

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

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

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

Extract the reference component from an mrs_data object.

Replicate a scan in the dynamic dimension.

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

Replicate a scan over a given dimension.

scale_amp_ratio_value

Scale fitted amplitudes to a ratio of signal amplitude.

scale_amp_ratio

Scale fitted amplitudes to a ratio of signal amplitude.

Subtract the mean dynamic spectrum from a dynamic series.

CPMG style sequence with ideal pulses.

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

Perform an ifftshift 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.

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

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

Apply a frequency shift to MRS data.

Simulate an mrs_data object containing complex zero valued samples.

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

write_basis_tqn

Generate a basis file using TARQUIN.

plot_voi_overlay

Plot a volume as an image overlay.

Simulate a basis file using TARQUIN.

Decompose an mrs_data object into white and gray matter spectra.

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

Simulate a mol_parameter object.

Sort the basis-set elements alphabetically.

Calculate the sum of data dynamics.

plot_voi_overlay_seg

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

set_mask_xy_mat

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

sim_basis_mm_lip_lcm

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

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

stackplot.mrs_data

Stackplot plotting method for objects of class mrs_data.

Return a list of options for VARPRO based fitting.

Perform a mathematical operation on a spectral region.

stackplot.fit_result

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

Convert a vector into a mrs_data object.

Calculate the sum across receiver coil elements.

Sum two mrs_data objects.

write_mrs_nifti

Write MRS data object to file in NIFTI format.

Write MRS data object to file.

Objects exported from other packages

Repeat an array over a given dimension.

Zero-fill MRS data in the time domain.

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

Read an LCModel formatted coord file containing fit information.

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.

varpro_basic_opts

Return a list of options for a basic VARPRO analysis.

varpro_3_para_opts

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

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).

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

seq_spin_echo_ideal_31p

Spin echo sequence with ideal pulses.

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

Perform an iffshift and ifft on a vector.

Return the frequency scale of an MRS dataset in Hz.

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

set_precomp_verbose

Set the verbosity of the precompute function.

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_steam_ideal

STEAM sequence with ideal pulses.

set_precomp_mode

Set the precompute mode.

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

spant: spectroscopy analysis tools.

Return the sum of a list of mrs_data objects.

spant_abfit_benchmark

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

Plot a slice from a 7 dimensional array.

plot_slice_map_inter

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

scale_amp_water_ratio

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

Read a basis file in LCModel .basis format.

Apply a weighting to the FID to enhance spectral resolution.

seq_mega_press_ideal

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

seq_press_ideal

PRESS sequence with ideal pulses.

scale_basis_from_singlet

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

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

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

Simulate an mrs_data object containing simulated Gaussian noise.

svs_1h_brain_analysis

Standard SVS 1H brain analysis pipeline.

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

spant_simulation_benchmark

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

Time-domain convolution based filter.

spant_mpress_drift

Example MEGA-PRESS data with significant B0 drift.

svs_1h_brain_batch_analysis

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

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.

Zero all non-zero-order coherences.

Transform time-domain data to the frequency-domain.