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spant (version 1.10.0)

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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1.10.0

License

GPL-3

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Repository

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

Homepage

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

Maintainer

Martin Wilson

Last Published

January 6th, 2021

Functions in spant (1.10.0)

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

Apply Arg operator to an MRS dataset.

Return the number of data points in an MRS dataset.

Apply Mod operator to an MRS dataset.

Apply Conj operator to an MRS dataset.

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

Apply Im operator to 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 the total number of y locations in an MRS dataset.

Simulate pulse sequence acquisition.

Crop an MRSI dataset in the x-y direction

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

Combine a pair of basis set objects.

Calculate the spectral SNR.

Crop mrs_data object data points in the time-domain.

Calculate the sum of squares differences between two mrs_data objects.

Apply Re operator to an MRS dataset.

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

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

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.

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

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.

Return a list of options for an ABfit analysis.

Apply a function over specified array axes.

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

Baseline correction using the ALS method.

Return the default nucleus.

calc_peak_info_vec

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

Return the default transmitter frequency in Hz.

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

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

Frequency-domain convolution based filter.

Extract the fit amplitudes from an object of class fit_result.

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

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.

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

collapse_to_dyns

Collapse MRS data by concatenating spectra along the dynamic dimension.

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

calc_coil_noise_cor

Calculate the noise correlation between coil elements.

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

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

Generate the F product operator.

Return acquisition parameters from a MRS data object.

Transform frequency-domain data to the time-domain.

Return the default sampling frequency in Hz.

Generate a MRSI VOI from an mrs_data object.

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.

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

Return a single slice from a larger MRSI dataset.

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

Arrange spectral plots in a grid.

Extract a subset of MRS data.

gridplot.mrs_data

Arrange spectral plots in a grid.

Generate the Fxy product operator with a specified phase.

Extract a subset of dynamic scans.

Return the default reference value for ppm scale.

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.

comb_csv_results

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

Check LCModel can be run

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

A very simple DICOM reader.

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

Check the TARQUIN binary can be run

Eddy current correction.

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.

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

Apply the max operator to an MRS dataset.

Return a single voxel from a larger mrs dataset.

Grid shift MRSI data in the x/y dimension.

get_guassian_pulse

Generate a gaussian pulse shape.

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

Apply the max operator to an interpolated MRS dataset.

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

Calculate the median dynamic data.

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.

calc_coil_noise_sd

Calculate the noise standard deviation for each coil element.

calc_ed_from_lambda

Calculate the effective dimensions of a spline smoother from lambda.

Combine a list of fit_result objects into a single fit object containing a dynamic series.

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

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

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

Convolve two MRS data objects.

Get a data array from a fit result.

Get a mol_parameters object for a named molecule.

Crop mrs_data object based on a frequency range.

Combine all fitting data points into a single dataframe.

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

downsample_mrs_fd

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

Return the sampling frequency in Hz of an MRS dataset.

decimate_mrs_td

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

Combine a reference and metabolite mrs_data object.

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

Calculate diagnostic information for object of class fit_result.

plot_slice_map_inter

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

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

Read MRS data using the TARQUIN software package.

Display an interactive orthographic projection plot of a nifti object.

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

plot_voi_overlay

Plot a volume as an image overlay.

Write fit results table to a csv file.

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

Generate an affine for nifti generation.

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

Extract the reference component from an mrs_data object.

seq_steam_ideal

STEAM sequence with ideal pulses.

Remove a subset of dynamic scans.

scale_amp_molal_pvc

Apply partial volume correction to a fitting result object.

read_siemens_txt_hdr

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

get_1h_brain_basis_paras_v3

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

Perform a fft and ffshift on a vector.

Convert mrs_data object to a vector.

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

Perform a fit based analysis of MRS data.

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

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

get_voi_seg_psf

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

Image plot method for objects of class mrs_data.

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

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

Generate a MRSI voxel from an mrs_data object.

fp_phase_correct

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

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

get_mrsi_voxel_xy_psf

Generate a MRSI voxel PSF from an mrs_data object.

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

Calculate the mean spectrum from an mrs_data object.

Return the second half of a dynamic series.

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

mean_dyn_blocks

Calculate the mean of adjacent dynamic scans.

HSVD of a complex vector.

Integrate a spectral region.

interleave_dyns

Interleave the first and second half of a dynamic series.

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

Return the frequency scale of an MRS dataset in Hz.

plot_voi_overlay_seg

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

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.

Read a basis file in LCModel .basis format.

Generate a SVS acquisition volume from an mrs_data object.

Return the first half of a dynamic series.

Apply phasing parameters to MRS data.

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

scale_amp_molar

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

Resample an image to match a target image space.

scale_amp_ratio

Scale fitted amplitudes to a ratio of signal amplitude.

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

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

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

Display an orthographic projection plot of a nifti object.

set_def_acq_paras

Set the default acquisition parameters.

Normalise mrs_data to a spectral region.

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

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

Extract the metabolite component from an mrs_data object.

get_uncoupled_mol

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

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.

Read an LCModel formatted coord file containing fit information.

Replicate a scan in the dynamic dimension.

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

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

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.

HSVD of an mrs_data object.

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

HSVD based signal filter.

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.

Perform an iffshift and ifft on a vector.

CPMG style sequence with ideal pulses.

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

Mask an MRS dataset in the dynamic dimension.

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

Mask an MRSI dataset in the x-y direction

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

Calculate the mean dynamic data.

Calculate the pairwise means across a dynamic data set.

Print fit coordinates from a single index.

plot_slice_fit_inter

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

Print a summary of mrs_data parameters.

Get the quantum coherence matrix for a spin system.

Simulate a basis file using TARQUIN.

Read MRS data stored in dangerplot (dpt) v3 format.

Read MRS data from a file.

read_tqn_result

Reader for csv results generated by TARQUIN.

Plot a slice from a 7 dimensional array.

Reader for csv fit results generated by TARQUIN.

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_amp_water_ratio

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

Calculate the standard deviation spectrum from an mrs_data object.

Calculate the standard deviation spectrum from an mrs_data object.

seq_pulse_acquire

Simple pulse and acquire sequence with ideal pulses.

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

seq_spin_echo_ideal

Spin echo sequence with ideal pulses.

seq_spin_echo_ideal_31p

Spin echo sequence with ideal pulses.

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

Simulate a mol_parameter object.

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.

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

Time-domain spectral registration.

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.

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

Replicate a scan over a given dimension.

reson_table2mrs_data

Generate mrs_data from a table of single Lorentzian resonances.

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

write_basis_tqn

Generate a basis file using TARQUIN.

set_precomp_verbose

Set the verbosity of the precompute function.

set_precomp_mode

Set the precompute mode.

stackplot.fit_result

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

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.

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

write_mrs_nifti

Write MRS data object to file in NIFTI format.

Transform time-domain data to the frequency-domain.

Time-domain convolution based filter.

Write MRS data object to file.

stackplot.mrs_data

Stackplot plotting method for objects of class mrs_data.

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

Perform l2 regularisation artefact suppression.

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

Plotting method for objects of class mrs_data.

plot.fit_result

Plot the fitting results of an object of class fit_result.

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

Produce a plot with multiple traces.

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

Zero all non-zero-order coherences.

Signal space projection method for lipid suppression.

Simulate a time-domain mrs_data object containing simulated Gaussian noise.

Robust Alignment to a Target Spectrum (RATS).

print.fit_result

Print a summary of an object of class fit_result.

Zero-fill MRS data in the time domain.

seq_slaser_ideal

sLASER sequence with ideal pulses.

Apply a frequency shift to MRS data.

Repeat an array over a given dimension.

Apply a weighting to the FID to enhance spectral resolution.

seq_pulse_acquire_31p

Simple pulse and acquire sequence with ideal pulses.

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

Objects exported from other packages

spant: spectroscopy analysis tools.

spant_mpress_drift

Example MEGA-PRESS data with significant B0 drift.

Calculate the sum across receiver coil elements.

Return a list of options for VARPRO based fitting.

Calculate the sum of data dynamics.

Convert a vector into a mrs_data object.