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spant (version 1.9.0)

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

1.9.0

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 15th, 2020

Functions in spant (1.9.0)

Apply Mod operator to an MRS dataset.

Return the total number of spectra 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.

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

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

Apply Im operator to an MRS dataset.

Apply Arg operator to an MRS dataset.

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

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

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 Conj operator to an MRS dataset.

Calculate the sum of squares differences between two mrs_data objects.

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

Return the default transmitter frequency in Hz.

Return a list of options for an ABfit analysis.

Simulate pulse sequence acquisition.

calc_ed_from_lambda

Calculate the effective dimensions of a spline smoother from lambda.

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

calc_peak_info_vec

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

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

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

Apply Re operator to an MRS dataset.

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

Crop mrs_data object based on a frequency range.

Crop mrs_data object data points in the time-domain.

downsample_mrs_fd

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

Extract the reference component from an mrs_data object.

Extract the metabolite component from an mrs_data object.

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

Generate the F product operator.

Check the TARQUIN binary can be run

A very simple DICOM reader.

Combine a pair of basis set objects.

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

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.

decimate_mrs_td

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

Apply a function over specified array axes.

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

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

Perform an iffshift and ifft on a vector.

Apply the max operator to an interpolated MRS dataset.

Generate the Fxy product operator with a specified phase.

Combine all fitting data points into a single dataframe.

Return the default sampling frequency in Hz.

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

Frequency-domain convolution based filter.

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

Eddy current correction.

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

Generate a MRSI voxel from an mrs_data object.

Return the first time-domain data point.

get_guassian_pulse

Generate a gaussian pulse shape.

mean_dyn_blocks

Calculate the mean of adjacent dynamic scans.

Perform a fft and ffshift on a vector.

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

decimate_mrs_fd

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

HSVD based signal filter.

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

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

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

Perform l2 regularisation artefact suppression.

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

Repeat an array over a given dimension.

Calculate the mean spectrum from an mrs_data object.

get_1h_brain_basis_paras

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

Baseline correction using the ALS method.

seq_pulse_acquire_31p

Simple pulse and acquire sequence with ideal pulses.

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

Calculate the spectral SNR.

Check LCModel can be run

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

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

Calculate the pairwise means across a dynamic data set.

sim_basis_1h_brain

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

Combine a reference and metabolite mrs_data object.

get_1h_brain_basis_paras_v2

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

Return the default nucleus.

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

plot_slice_fit_inter

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

Read an LCModel formatted coord file containing fit information.

Convolve two MRS data objects.

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

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

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

get_1h_brain_basis_paras_v3

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.

plot.fit_result

Plot the fitting results of an object of class fit_result.

Robust Alignment to a Target Spectrum (RATS).

Apply phasing parameters to MRS data.

Get the quantum coherence matrix for a spin system.

seq_spin_echo_ideal_31p

Spin echo sequence with ideal pulses.

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

read_tqn_result

Reader for csv results generated by TARQUIN.

Transform time-domain data to the frequency-domain.

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

Transform frequency-domain data to the time-domain.

Return the frequency scale of an MRS dataset in Hz.

comb_csv_results

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

Generate an affine for nifti generation.

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

Extract a subset of dynamic scans.

seq_steam_ideal

STEAM sequence with ideal pulses.

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

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

Replicate a scan in the dynamic dimension.

Calculate the sum across receiver coil elements.

get_1h_brain_basis_paras_v1

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

Image plot method for objects of class mrs_data.

Generate a MRSI VOI from an mrs_data object.

Extract a subset of MRS data.

calc_coil_noise_cor

Calculate the noise correlation between coil elements.

Generate a SVS acquisition volume from an mrs_data object.

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_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.

HSVD of a complex vector.

Calculate the median dynamic data.

calc_coil_noise_sd

Calculate the noise standard deviation for each coil element.

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

Time-domain convolution based filter.

Normalise mrs_data to a spectral region.

Display an interactive orthographic projection plot of a nifti object.

Display an orthographic projection plot of a nifti object.

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

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

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

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

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

Apply a frequency shift to MRS data.

Convert mrs_data object to a vector.

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

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

Get a mol_parameters object for a named molecule.

Return a single voxel from a larger mrs dataset.

get_voi_seg_psf

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

scale_amp_molal_pvc

Apply partial volume correction to a fitting result object.

collapse_to_dyns

Collapse MRS data by concatenating spectra along the dynamic dimension.

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.

stackplot.mrs_data

Stackplot plotting method for objects of class mrs_data.

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

Convert a vector into a mrs_data object.

spant: spectroscopy analysis tools.

interleave_dyns

Interleave the first and second half of a dynamic series.

gridplot.mrs_data

Arrange spectral plots in a grid.

Print fit coordinates from a single index.

Get a data array from a fit result.

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

Print a summary of mrs_data parameters.

Read a basis file in LCModel .basis format.

Mask an MRS dataset in the dynamic dimension.

Return the default reference value for ppm scale.

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

Calculate the mean dynamic data.

plot_voi_overlay_seg

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

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

Reader for csv fit results generated by TARQUIN.

read_siemens_txt_hdr

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

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

CPMG style sequence with ideal pulses.

Integrate a spectral region.

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

Produce a plot with multiple traces.

Return the sampling frequency in Hz of an MRS dataset.

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

stackplot.fit_result

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

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

Zero-fill MRS data in the time domain.

Extract the fit amplitudes from an object of class fit_result.

fp_phase_correct

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

Calculate diagnostic information for object of class fit_result.

Grid shift MRSI data in the x/y dimension.

Simulate a basis file using TARQUIN.

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

plot_voi_overlay

Plot a volume as an image overlay.

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

Read MRS data using the TARQUIN software package.

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

seq_press_ideal

PRESS sequence with ideal pulses.

seq_spin_echo_ideal

Spin echo sequence with ideal pulses.

write_mrs_nifti

Write MRS data object to file in NIFTI format.

print.fit_result

Print a summary of an object of class fit_result.

Read MRS data from a file.

Return the first half of a dynamic series.

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

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

Return a single slice from a larger MRSI dataset.

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

Return the second half of a dynamic series.

HSVD of an mrs_data object.

get_mrsi_voxel_xy_psf

Generate a MRSI voxel PSF from an mrs_data object.

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.

seq_mega_press_ideal

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

Return acquisition parameters from a MRS data object.

set_precomp_verbose

Set the verbosity of the precompute function.

Time-domain spectral registration.

Replicate a scan over a given dimension.

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

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

Mask an MRSI dataset in the x-y direction

Return a list of options for VARPRO based fitting.

scale_amp_ratio

Scale fitted amplitudes to a ratio of signal amplitude.

Plot a slice from a 7 dimensional array.

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

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

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

seq_slaser_ideal

sLASER sequence with ideal pulses.

Simulate a basis set object.

Zero all non-zero-order coherences.

Objects exported from other packages

Calculate the sum of data dynamics.

Calculate the standard deviation spectrum from an mrs_data object.

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

Simulate a mol_parameter object.

Calculate the standard deviation spectrum from an mrs_data object.

Apply the max operator to an MRS dataset.

Apply a weighting to the FID to enhance spectral resolution.

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

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

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

Plotting method for objects of class mrs_data.

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

get_uncoupled_mol

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

Write MRS data object to file.

Arrange spectral plots in a grid.

Remove a subset of dynamic scans.

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.

reson_table2mrs_data

Generate mrs_data from a table of single Lorentzian resonances.

plot_slice_map_inter

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

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.

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

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

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.

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

seq_pulse_acquire

Simple pulse and acquire sequence with ideal pulses.

scale_amp_water_ratio

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

set_def_acq_paras

Set the default acquisition parameters.

Signal space projection method for lipid suppression.

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

Create a spin system object for pulse sequence simulation.

set_precomp_mode

Set the precompute mode.

write_basis_tqn

Generate a basis file using TARQUIN.

spant_mpress_drift

Example MEGA-PRESS data with significant B0 drift.