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spant (version 1.13.0)

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

1.13.0

License

GPL-3

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Repository

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

Homepage

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

Maintainer

Martin Wilson

Last Published

June 9th, 2021

Functions in spant (1.13.0)

Apply Im operator to an MRS dataset.

Return the total number of spectra in an MRS dataset.

Apply Arg operator to an MRS dataset.

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

Apply Conj operator to an MRS dataset.

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

Apply Mod operator to an MRS dataset.

Return the number of data points in an MRS dataset.

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

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

Combine a pair of basis set objects.

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

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.

Add noise to an mrs_data object.

Simulate pulse sequence acquisition.

Return the total number of z locations in 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.

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

Apply Re operator to an MRS dataset.

Calculate the spectral SNR.

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

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

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

Return a list of options for an ABfit analysis.

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

Calculate the sum of squares differences between two mrs_data objects.

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

Apply a function over specified array axes.

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.

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

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

collapse_to_dyns

Collapse MRS data by concatenating spectra along the dynamic dimension.

downsample_mrs_fd

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

Check the TARQUIN binary can be run

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.

Baseline correction using the ALS method.

Return the default sampling frequency in Hz.

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

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 ffshift on a vector.

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

Return the default transmitter frequency in Hz.

Eddy current correction.

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

calc_coil_noise_sd

Calculate the noise standard deviation for each coil element.

calc_coil_noise_cor

Calculate the noise correlation between coil elements.

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

Generate an affine for nifti generation.

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

HSVD of an mrs_data object.

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

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

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

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

Generate the F product operator.

Return the sampling frequency in Hz of an MRS dataset.

Check LCModel can be run

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 a reference and metabolite mrs_data object.

Crop an MRSI dataset in the x-y direction

Return the default nucleus.

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

Convolve two MRS data objects.

Generate the Fxy product operator with a specified phase.

Return the first half of a dynamic series.

fp_phase_correct

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

Return the default reference value for ppm scale.

HSVD based signal filter.

Extract a subset of dynamic scans.

comb_fit_tables

Combine all fitting data points into a single data frame.

comb_fit_list_result_tables

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

Crop mrs_data object based on a frequency range.

Generate a MRSI VOI from an mrs_data object.

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

Generate a MRSI voxel from an mrs_data object.

Return a single slice from a larger MRSI dataset.

Return the second half of a dynamic series.

Get a data array from a fit result.

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

comb_csv_results

Combine the results from multiple csv format files into a table.

get_1h_brain_basis_paras

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

get_voi_seg_psf

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

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

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

Image plot method for objects of class mrs_data.

Invert 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.

Transform frequency-domain data to the time-domain.

comb_fit_list_fit_tables

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

decimate_mrs_td

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

Arrange spectral plots in a grid.

Apply the max operator to an interpolated MRS dataset.

Crop mrs_data object data points in the time-domain.

A very simple DICOM reader.

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

Extract the fit amplitudes from an object of class fit_result.

Frequency-domain convolution based filter.

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

Perform l2 regularisation artefact suppression.

gridplot.mrs_data

Arrange spectral plots in a grid.

Mask an MRSI dataset in the x-y direction

Calculate the mean spectrum from an mrs_data object.

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

get_1h_brain_basis_paras_v1

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

Perform a fit based analysis of MRS data.

Write fit results table to a csv file.

Display an orthographic projection plot of a nifti object.

plot_slice_fit_inter

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

Display an interactive orthographic projection plot of a nifti object.

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

plot_voi_overlay

Plot a volume as an image overlay.

Calculate diagnostic information for object of class fit_result.

plot_voi_overlay_seg

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

Print fit coordinates from a single index.

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

print.fit_result

Print a summary of an object of class fit_result.

Objects exported from other packages

Return acquisition parameters from a MRS data object.

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 metabolite component from an mrs_data object.

get_mrsi_voxel_xy_psf

Generate a MRSI voxel PSF from an mrs_data object.

get_uncoupled_mol

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

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

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

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

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

Repeat an array over a given dimension.

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

Return the first time-domain data point.

Plotting method for objects of class mrs_data.

Apply the max operator to an MRS dataset.

Integrate a spectral region.

interleave_dyns

Interleave the first and second half of a dynamic series.

mean_dyn_blocks

Calculate the mean of adjacent dynamic scans.

Calculate the pairwise means across a dynamic data set.

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

Convert mrs_data object to a vector.

Apply phasing parameters to MRS data.

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

Remove a subset of dynamic scans.

get_1h_brain_basis_paras_v2

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

read_siemens_txt_hdr

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

Read MRS data using the TARQUIN software package.

plot.fit_result

Plot the fitting results of an object of class fit_result.

Extract the reference component from an mrs_data object.

Perform an iffshift and ifft on a vector.

get_guassian_pulse

Generate a gaussian pulse shape.

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

get_1h_brain_basis_paras_v3

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

scale_amp_molal_pvc

Apply partial volume correction to a fitting result object.

scale_amp_ratio

Scale fitted amplitudes to a ratio of signal amplitude.

seq_mega_press_ideal

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

scale_amp_molar

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

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

seq_press_ideal

PRESS sequence with ideal pulses.

seq_pulse_acquire_31p

Simple pulse and acquire sequence with ideal pulses.

Simulate a mol_parameter object.

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

seq_pulse_acquire

Simple pulse and acquire sequence with ideal pulses.

seq_slaser_ideal

sLASER sequence with ideal pulses.

Simulate a basis set object.

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

Spin echo 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.

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

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

Return a single voxel from a larger mrs dataset.

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

Extract a subset of MRS data.

HSVD of a complex vector.

Get a mol_parameters object for a named molecule.

Generate a SVS acquisition volume from an mrs_data object.

Grid shift MRSI data in the x/y dimension.

Return the frequency scale of an MRS dataset in Hz.

Signal space projection method for lipid suppression.

Get the quantum coherence matrix for a spin system.

spant: spectroscopy analysis tools.

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

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

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

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

spant_abfit_benchmark

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

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

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.

Time-domain spectral registration.

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

Read a basis file in LCModel .basis format.

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.

Transform time-domain data to the frequency-domain.

Time-domain convolution based filter.

Mask an MRS dataset in the dynamic dimension.

Replicate a scan in the dynamic dimension.

Replicate a scan over a given 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.

Print a summary of mrs_data parameters.

Calculate the mean dynamic data.

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).

Calculate the median dynamic data.

scale_amp_water_ratio

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

Plot a slice from a 7 dimensional array.

Normalise mrs_data to a spectral region.

Read MRS data from a file.

Robust Alignment to a Target Spectrum (RATS).

Read an LCModel formatted coord file containing fit information.

Resample an image to match a target image space.

Reader for csv fit results generated by TARQUIN.

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.

plot_slice_map_inter

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

Scale an mrs_data object by a constant.

read_tqn_result

Reader for csv results generated by TARQUIN.

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

set_precomp_verbose

Set the verbosity of the precompute function.

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

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

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

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

set_def_acq_paras

Set the default acquisition parameters.

Simulate an mrs_data object containing simulated Gaussian noise.

Calculate the sum across receiver coil elements.

stackplot.mrs_data

Stackplot plotting method for objects of class mrs_data.

Return a list of options for VARPRO based fitting.

CPMG style sequence with ideal pulses.

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

seq_spin_echo_ideal_31p

Spin echo sequence with ideal pulses.

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

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

Convert a vector into a mrs_data object.

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.

Calculate the standard deviation spectrum from an mrs_data object.

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

Calculate the standard deviation spectrum from an mrs_data object.

set_precomp_mode

Set the precompute mode.

reson_table2mrs_data

Generate mrs_data from a table of single Lorentzian resonances.

Simulate a basis file using TARQUIN.

Apply frequency shifts to basis set signals.

seq_steam_ideal

STEAM sequence with ideal pulses.

Apply a frequency shift to MRS data.

Calculate the sum of data dynamics.

Zero all non-zero-order coherences.

Sum two mrs_data objects.

Zero-fill MRS data in the time domain.

Create a spin system object for pulse sequence simulation.

write_basis_tqn

Generate a basis file using TARQUIN.

spant_mpress_drift

Example MEGA-PRESS data with significant B0 drift.

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

Produce a plot with multiple traces.

svs_1h_brain_analysis

Standard SVS 1H brain analysis pipeline.

stackplot.fit_result

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

svs_1h_brain_batch_analysis

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

Write MRS data object to file.

write_mrs_nifti

Write MRS data object to file in NIFTI format.