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spant (version 1.19.0)

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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1.19.0

License

GPL-3

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Repository

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

Homepage

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

Maintainer

Martin Wilson

Last Published

February 14th, 2022

Functions in spant (1.19.0)

Apply Arg operator to an MRS dataset.

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

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

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

Apply Conj operator to an MRS dataset.

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

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

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

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

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

Baseline correction using the ALS method.

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

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

Apply Re operator to an MRS dataset.

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

Calculate the sum of squares differences between two mrs_data objects.

Apply Im operator to an MRS dataset.

Apply Mod operator to an MRS dataset.

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.

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

collapse_to_dyns

Collapse MRS data by concatenating spectra along the dynamic dimension.

Check the TARQUIN binary can be run

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

Simulate pulse sequence acquisition.

Add noise to an mrs_data object.

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

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

calc_ed_from_lambda

Calculate the effective dimensions of a spline smoother from lambda.

decimate_mrs_td

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

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.

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

Combine a pair of basis set objects.

Perform a fft and ffshift on a vector.

Apply the Fourier transform over the dynamic dimension.

Apply a function over specified array axes.

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

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

calc_coil_noise_sd

Calculate the noise standard deviation for each coil element.

calc_coil_noise_cor

Calculate the noise correlation between coil elements.

Crop mrs_data object based on a frequency range.

Convolve two MRS data objects.

Return the number of data points in an MRS dataset.

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

Return the default sampling frequency in Hz.

Return the default reference value for ppm scale.

Calculate the spectral SNR.

Check LCModel can be run

A very simple DICOM reader.

calc_peak_info_vec

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

Return acquisition parameters from a MRS data object.

Extract a subset of dynamic scans.

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

Return the total number of spectra in an MRS dataset.

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

Perform a fit based analysis of MRS data.

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.

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

Return the second half of a dynamic series.

Return a list of options for an ABfit analysis.

comb_fit_tables

Combine all fitting data points into a single data frame.

get_1h_brain_basis_paras_v2

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

get_1h_brain_basis_paras_v3

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.

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.

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

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

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).

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

gridplot.mrs_data

Arrange spectral plots in a grid.

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

Arrange spectral plots in a grid.

Image plot method for objects of class mrs_data.

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

Mask an MRS dataset in the dynamic dimension.

comb_fit_list_fit_tables

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

Get a data array from a fit result.

Return the first half of a dynamic series.

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

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

Perform an iffshift and ifft on a vector.

get_voi_seg_psf

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

Apply phasing parameters to MRS data.

Convert mrs_data object to a vector.

Combine a reference and metabolite mrs_data object.

comb_fit_list_result_tables

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

Return the first scans of a dynamic series.

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

plot.fit_result

Plot the fitting results of an object of class fit_result.

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

decimate_mrs_fd

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

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

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.

fp_phase_correct

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

Get a mol_parameters object for a named molecule.

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

Crop an MRSI dataset in the x-y direction

Crop mrs_data object data points in the time-domain.

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

plot_slice_fit_inter

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

Integrate a spectral region.

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

interleave_dyns

Interleave the first and second half of a dynamic series.

Calculate the mean dynamic data.

Return the mean of a list of mrs_data objects.

Plot a slice from a 7 dimensional array.

Extract the reference component from an mrs_data object.

Generate an affine for nifti generation.

Return the default transmitter frequency in Hz.

Return the default nucleus.

HSVD of a complex vector.

Eddy current correction.

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.

Return the frequency scale of an MRS dataset in Hz.

Extract the fit amplitudes from an object of class fit_result.

HSVD of an mrs_data object.

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_slice_map_inter

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

Read MRS data from a file.

Apply a weighting to the FID to enhance spectral resolution.

HSVD based signal filter.

Calculate diagnostic information for object of class fit_result.

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

get_1h_brain_basis_paras_v1

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

get_1h_brain_basis_paras

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

Transform frequency-domain data to the time-domain.

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

Mask an MRSI dataset in the x-y direction

Apply the max operator to an interpolated MRS dataset.

Return the first time-domain data point.

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

get_guassian_pulse

Generate a gaussian pulse shape.

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

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.

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

Return the sampling frequency in Hz of an MRS dataset.

Frequency-domain convolution based filter.

Calculate the mean spectrum from an mrs_data object.

Generate a MRSI VOI from an mrs_data object.

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

Read a basis file in LCModel .basis format.

Read MRS data using the TARQUIN software package.

Return a single slice from a larger MRSI dataset.

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

Extract a subset of MRS data.

seq_pulse_acquire

Simple pulse and acquire sequence with ideal pulses.

Scale mrs_data to a spectral region.

read_siemens_txt_hdr

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

seq_pulse_acquire_31p

Simple pulse and acquire sequence with ideal pulses.

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

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

Calculate the median dynamic data.

seq_spin_echo_ideal_31p

Spin echo sequence with ideal pulses.

seq_steam_ideal

STEAM sequence with ideal pulses.

scale_amp_molal_pvc

Apply partial volume correction to a fitting result object.

Reader for csv fit results generated by TARQUIN.

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

Calculate the standard deviation spectrum from an mrs_data object.

Simulate a mol_parameter object.

scale_amp_molar

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

Generate the F product operator.

Generate the Fxy product operator with a specified phase.

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

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

Generate a MRSI voxel from an mrs_data object.

Extract the metabolite component from an mrs_data object.

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

Simulate an mrs_data object containing simulated Gaussian noise.

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).

print.fit_result

Print a summary of an object of class fit_result.

Calculate the standard deviation 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.

Print a summary of mrs_data parameters.

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

set_mask_xy_mat

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

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 the max operator to an MRS dataset.

Simulate a basis file using TARQUIN.

mean_dyn_blocks

Calculate the mean of adjacent dynamic scans.

Get the quantum coherence matrix for a spin system.

get_mrsi_voxel_xy_psf

Generate a MRSI voxel PSF from an mrs_data object.

spant_abfit_benchmark

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

rectangular_mask

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

Robust Alignment to a Target Spectrum (RATS).

Objects exported from other packages

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

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

spant_mpress_drift

Example MEGA-PRESS data with significant B0 drift.

Return a list of options for VARPRO based fitting.

Repeat an array over a given dimension.

Convert a vector into a mrs_data object.

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

scale_amp_water_ratio

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

scale_amp_ratio

Scale fitted amplitudes to a ratio of signal amplitude.

CPMG style sequence with ideal pulses.

Replicate a scan in the dynamic dimension.

Calculate the pairwise means across a dynamic data set.

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

Generate a SVS acquisition volume from an mrs_data object.

Simulate an mrs_data object containing complex zero valued samples.

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

Calculate the sum across receiver coil elements.

svs_1h_brain_batch_analysis

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

Subtract the mean dynamic spectrum from a dynamic series.

Plotting method for objects of class mrs_data.

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

seq_press_ideal

PRESS sequence with ideal pulses.

seq_mega_press_ideal

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

set_def_acq_paras

Set the default acquisition parameters.

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

plot_voi_overlay

Plot a volume as an image overlay.

Transform time-domain data to the frequency-domain.

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

Return the last scans of a dynamic series.

Read an LCModel formatted coord file containing fit information.

read_tqn_result

Reader for csv results generated by TARQUIN.

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.

plot_voi_overlay_seg

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

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

sim_basis_1h_brain

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

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_simulation_benchmark

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

Perform a mathematical operation on a spectral region.

set_precomp_verbose

Set the verbosity of the precompute function.

recon_twix_2d_mrsi

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

set_precomp_mode

Set the precompute mode.

Apply frequency shifts to basis set signals.

Simulate a basis set object.

stackplot.fit_result

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

spant: spectroscopy analysis tools.

svs_1h_brain_analysis

Standard SVS 1H brain analysis pipeline.

Sort the basis-set elements alphabetically.

Return the sum of a list of mrs_data objects.

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

stackplot.mrs_data

Stackplot plotting method for objects of class mrs_data.

write_basis_tqn

Generate a basis file using TARQUIN.

Zero all non-zero-order coherences.

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.

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

Perform l2 regularisation artefact suppression.

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

Grid shift MRSI data in the x/y dimension.

Return a single voxel from a larger mrs dataset.

Write MRS data object to file.

write_mrs_nifti

Write MRS data object to file in NIFTI format.

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

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

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

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

Display an orthographic projection plot of a nifti object.

Apply a frequency shift to MRS data.

Sum two mrs_data objects.

Calculate the sum of data dynamics.

varpro_3_para_opts

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

zero'th order phase correction
global damping
global frequency shift.

varpro_basic_opts

Return a list of options for a basic VARPRO analysis.

Display an interactive orthographic projection plot of a nifti object.

Resample an image to match a target image space.

Replicate a scan over a given dimension.

reson_table2mrs_data

Generate mrs_data from a table of single Lorentzian resonances.

Create a spin system object for pulse sequence simulation.

seq_spin_echo_ideal

Spin echo sequence with ideal pulses.

Remove a subset of dynamic scans.

seq_slaser_ideal

sLASER sequence with ideal pulses.

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.

Produce a plot with multiple traces.

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

Time-domain convolution based filter.

Time-domain spectral registration.

Zero-fill MRS data in the time domain.