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spant (version 1.14.0)

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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1.14.0

License

GPL-3

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Repository

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

Homepage

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

Maintainer

Martin Wilson

Last Published

July 23rd, 2021

Functions in spant (1.14.0)

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

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

Return the number of data points in an MRS dataset.

Apply Arg operator to an MRS dataset.

Apply Im operator to an MRS dataset.

Return the total number of spectra in an MRS dataset.

Apply Mod 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.

Apply Conj operator to an MRS dataset.

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

Combine a pair of basis set objects.

Simulate pulse sequence acquisition.

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

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

collapse_to_dyns

Collapse MRS data by concatenating spectra along the dynamic dimension.

Crop an MRSI dataset in the x-y direction

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

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

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

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

Apply Re operator to an MRS dataset.

Return a list of options for an ABfit analysis.

downsample_mrs_fd

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

Append MRS data across the coil 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.

Check LCModel can be run

Baseline correction using the ALS method.

Add noise to an 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.

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

Calculate the spectral SNR.

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

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

comb_fit_list_result_tables

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

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

comb_fit_tables

Combine all fitting data points into a single data frame.

Crop mrs_data object based on a frequency range.

calc_ed_from_lambda

Calculate the effective dimensions of a spline smoother from lambda.

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

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

Convolve two MRS data objects.

Combine a reference and metabolite mrs_data object.

Transform frequency-domain data to the time-domain.

Calculate diagnostic information for object of class fit_result.

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

Perform a fit based analysis of MRS data.

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.

Apply a function over specified array axes.

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

A very simple DICOM reader.

calc_peak_info_vec

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

comb_csv_results

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

Return the default transmitter frequency in Hz.

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

comb_fit_list_fit_tables

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

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 sampling frequency in Hz.

Perform a fft and ffshift on a vector.

Apply a function across given dimensions of 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.

get_uncoupled_mol

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

Return the first time-domain data point.

Get a data array from a fit result.

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

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

Crop mrs_data object data points in the time-domain.

Return the default nucleus.

Return the default reference value for ppm scale.

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

Generate the Fxy product operator with a specified phase.

Integrate a spectral region.

Perform an iffshift and ifft on a vector.

Return the frequency scale of an MRS dataset in Hz.

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

calc_coil_noise_sd

Calculate the noise standard deviation for each coil element.

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

calc_coil_noise_cor

Calculate the noise correlation between coil elements.

get_1h_brain_basis_paras

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

Calculate the sum of squares differences between two mrs_data objects.

get_1h_brain_basis_paras_v2

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

get_1h_brain_basis_paras_v1

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

Return acquisition parameters from a MRS data object.

Return the sampling frequency in Hz of an MRS dataset.

Apply the Fourier transform over the dynamic dimension.

Calculate the mean spectrum from an mrs_data object.

Get a mol_parameters object for a named molecule.

Return the mean of a list of mrs_data objects.

Extract a subset of dynamic scans.

mean_dyn_blocks

Calculate the mean of adjacent dynamic scans.

decimate_mrs_fd

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

Generate an affine for nifti generation.

Return the first half of a dynamic series.

Return the second half of a dynamic series.

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

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

Generate a SVS acquisition volume from an mrs_data object.

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

Eddy current correction.

Check the TARQUIN binary can be run

Return a single slice from a larger MRSI dataset.

Write fit results table to a csv file.

elliptical_mask

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

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

Generate a MRSI voxel from an mrs_data object.

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

Extract the metabolite component from an mrs_data object.

Generate the F product operator.

Extract a subset of MRS data.

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

Extract the reference component from an mrs_data object.

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

Grid shift MRSI data in the x/y dimension.

get_mrsi_voxel_xy_psf

Generate a MRSI voxel PSF from an mrs_data object.

HSVD based signal filter.

HSVD of a complex vector.

Arrange spectral plots in a grid.

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

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

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

Perform l2 regularisation artefact suppression.

decimate_mrs_td

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

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

Extract the fit amplitudes from an object of class fit_result.

Frequency-domain convolution based filter.

get_1h_brain_basis_paras_v3

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

Calculate the median dynamic data.

Convert mrs_data object to a vector.

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

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

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

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

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

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

interleave_dyns

Interleave the first and second half of a dynamic series.

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

Print a summary of mrs_data parameters.

Calculate the pairwise means across a dynamic data set.

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

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

Image plot method for objects of class mrs_data.

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

Get the quantum coherence matrix for a spin system.

get_guassian_pulse

Generate a gaussian pulse shape.

plot_voi_overlay_seg

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

Calculate the mean dynamic data.

Display an interactive orthographic projection plot of a nifti object.

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

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

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

read_siemens_txt_hdr

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

Reader for csv fit results generated by TARQUIN.

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

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

reson_table2mrs_data

Generate mrs_data from a table of single Lorentzian resonances.

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

Generate a MRSI VOI from an mrs_data object.

get_voi_seg_psf

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

Read MRS data from a file.

seq_spin_echo_ideal

Spin echo sequence with ideal pulses.

Replicate a scan in the dynamic dimension.

Replicate a scan over a given dimension.

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

seq_spin_echo_ideal_31p

Spin echo sequence with ideal pulses.

Return a single voxel from a larger mrs dataset.

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

gridplot.mrs_data

Arrange spectral plots in a grid.

Apply the max operator to an MRS dataset.

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.

Apply the max operator to an interpolated MRS dataset.

plot.fit_result

Plot the fitting results of an object of class fit_result.

Scale mrs_data to a spectral region.

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.

HSVD of an mrs_data object.

Simulate an mrs_data object containing complex zero valued samples.

Plotting method for objects of class mrs_data.

spant: spectroscopy analysis tools.

Read MRS data using the TARQUIN software package.

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

plot_slice_fit_inter

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

Plot a slice from a 7 dimensional array.

seq_steam_ideal

STEAM sequence with ideal pulses.

Apply a frequency shift to MRS data.

set_def_acq_paras

Set the default acquisition parameters.

Objects exported from other packages

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.

Apply frequency shifts to basis set signals.

stackplot.mrs_data

Stackplot plotting method for objects of class mrs_data.

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

Apply phasing parameters to MRS data.

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

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

Simulate a basis set object.

print.fit_result

Print a summary of an object of class fit_result.

svs_1h_brain_batch_analysis

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

Subtract the mean dynamic spectrum from a dynamic series.

Repeat an array over a given dimension.

scale_amp_water_ratio

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

sim_basis_1h_brain

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

Transform time-domain data to the frequency-domain.

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

scale_amp_molar

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

scale_amp_ratio

Scale fitted amplitudes to a ratio of signal amplitude.

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.

Mask an MRS dataset in the dynamic dimension.

seq_press_ideal

PRESS sequence with ideal pulses.

CPMG style sequence with ideal pulses.

Mask an MRSI dataset in the x-y direction

seq_mega_press_ideal

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

seq_pulse_acquire

Simple pulse and acquire sequence with ideal pulses.

Read an LCModel formatted coord file containing fit information.

Simulate a basis file using TARQUIN.

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.

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.

seq_slaser_ideal

sLASER sequence with ideal pulses.

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

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

seq_pulse_acquire_31p

Simple pulse and acquire sequence with ideal pulses.

Resample an image to match a target image space.

Calculate the standard deviation spectrum from an mrs_data object.

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

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

Print fit coordinates from a single index.

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

Display an orthographic projection plot of a nifti object.

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).

Time-domain spectral registration.

Time-domain convolution based filter.

Zero-fill MRS data in the time domain.

plot_slice_map_inter

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

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

plot_voi_overlay

Plot a volume as an image overlay.

Simulate a mol_parameter object.

set_mask_xy_mat

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

set_precomp_mode

Set the precompute mode.

Robust Alignment to a Target Spectrum (RATS).

Apply a weighting to the FID to enhance spectral resolution.

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.

read_tqn_result

Reader for csv results generated by TARQUIN.

rectangular_mask

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

Remove a subset of dynamic scans.

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

Simulate an mrs_data object containing simulated Gaussian noise.

scale_amp_molal_pvc

Apply partial volume correction to a fitting result object.

Signal space projection method for lipid suppression.

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

svs_1h_brain_analysis

Standard SVS 1H brain analysis pipeline.

Sum two mrs_data objects.

Perform a mathematical operation on a spectral region.

write_mrs_nifti

Write MRS data object to file in NIFTI format.

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

set_precomp_verbose

Set the verbosity of the precompute function.

Zero all non-zero-order coherences.

Create a spin system object for pulse sequence simulation.

Calculate the sum across receiver coil elements.

Calculate the sum of data dynamics.

Convert a vector into a mrs_data object.

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

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.

Return a list of options for VARPRO based fitting.

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.

write_basis_tqn

Generate a basis file using TARQUIN.

Write MRS data object to file.