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spant (version 1.4.0)

MR Spectroscopy Analysis Tools

Description

Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data. .

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Install

install.packages('spant')

Monthly Downloads

692

Version

1.4.0

License

GPL-3

Maintainer

Martin Wilson

Last Published

April 20th, 2020

Functions in spant (1.4.0)

Im.mrs_data

Apply Im operator to an MRS dataset.
Nspec

Return the total number of spectra in an MRS dataset.
Npts

Return the number of data points in an MRS dataset.
Ncoils

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

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

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

Apply Mod operator to an MRS dataset.
Re.mrs_data

Apply Re operator to an MRS dataset.
Ny

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

Return the total number of x locations in an MRS dataset.
beta2lw

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

Calculate the noise correlation between coil elements.
auto_phase

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

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

Apply a function over specified array axes.
acquire

Simulate pulse sequence acquisition.
abfit_opts

Return a list of options for an ABfit analysis.
apply_mrs

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

Combine a pair of basis set objects.
basis2mrs_data

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

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

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

Calculate the sum of squares differences between two mrs_data objects.
collapse_to_dyns

Collapse MRS data by concatenating spectra along the dynamic dimension.
calc_spec_snr

Calculate the spectral SNR.
crop_td_pts

Crop mrs_data object data points in the time-domain.
bbase

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

Back extrapolate time-domain points using the Burg autoregressive model
calc_peak_info_vec

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

Baseline correction using the ALS method.
check_tqn

Check the TARQUIN binary can be run
bc_constant

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

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

Combine coil data following phase correction based on the first data point in the FID.
check_lcm

Check LCModel can be run
comb_fits

Combine a list of fit_result objects into a single fit object containing a dynamic series.
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.
fit_res2csv

Write fit results table to a csv file.
crop_spec

Crop mrs_data object based on a frequency range.
def_ref

Return the default reference value for ppm scale.
conv_mrs

Convolve two MRS data objects.
def_ft

Return the default transmitter frequency in Hz.
decimate_mrs

Downsample an MRS signal by a factor.
calc_sd_poly

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

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

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

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

Combine a reference and metabolite mrs_data object.
def_fs

Return the default sampling frequency in Hz.
fit_diags

Calculate diagnostic information for object of class fit_result.
ecc

Eddy current correction.
ft_shift_mat

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

Perform a fft and ffshift on a vector.
get_even_dyns

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

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

Perform a fit based analysis of MRS data.
get_acq_paras

Return acquisition parameters from a MRS data object.
fp_phase

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

Extract the fit amplitudes from an object of class fit_result.
fd_conv_filt

Frequency-domain convolution based filter.
get_1h_brain_basis_paras_v2

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

Generate the F product operator.
get_dyns

Extract a subset of dynamic scans.
get_fit_map

Get a data array from a fit result.
get_fit_table

Combine all fitting data points into a single dataframe.
gen_F_xy

Generate the Fxy product operator with a specified phase.
get_fh_dyns

Return the first half of a dynamic series.
get_odd_dyns

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

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

Generate a MRSI voxel PSF from an mrs_data object.
crop_xy

Crop an MRSI dataset in the x-y direction
get_voi_cog

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

Return the white matter, gray matter and CSF composition of a volume.
fd2td

Transform frequency-domain data to the time-domain.
ift_shift

Perform an iffshift and ifft on a vector.
hz

Return the frequency scale of an MRS dataset in Hz.
inv_even_dyns

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

Get a mol_parameters object for a named molecule.
hsvd_filt

HSVD based signal filter.
get_svs_voi

Generate a SVS acquisition volume from an mrs_data object.
get_subset

Extract a subset of MRS data.
grid_shift_xy

Grid shift MRSI data in the x/y dimension.
get_mol_names

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

Extract the metabolite component from an mrs_data object.
mask_xy_mat

Mask a 2D MRSI dataset in the x-y dimension.
get_2d_psf

Get the point spread function (PSF) for a 2D phase encoded MRSI scan.
get_mrsi2d_seg

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

Return the first time-domain data point.
fp_phase_correct

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

Return a single slice from a larger MRSI dataset.
get_sh_dyns

Return the second half of a dynamic series.
int_spec

Integrate a spectral region.
interleave_dyns

Interleave the first and second half of a dynamic series.
mat2mrs_data

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

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

Calculate the median dynamic data.
inv_odd_dyns

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

Calculate the mean spectrum from an mrs_data object.
get_guassian_pulse

Generate a gaussian pulse shape.
l2_reg

Perform l2 regularisation artefact suppression using the method proposed by Bilgic et al. JMRI 40(1):181-91 2014.
fs

Return the sampling frequency in Hz of an MRS dataset.
get_1h_brain_basis_paras

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

Extract the reference component from an mrs_data object.
mrs_data2basis

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

Calculate the mean of adjacent dynamic scans.
get_seg_ind

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

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

Apply the max operator to an MRS dataset.
image.mrs_data

Image plot method for objects of class mrs_data.
lw2beta

Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).
mrs_data2mat

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

Mask an MRSI dataset in the x-y direction
get_1h_brain_basis_paras_v1

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

Normalise mrs_data to a spectral region.
plot_slice_map_inter

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

Plot a slice from a 7 dimensional array.
mvifftshift

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

Perform a fftshift on a matrix, with each column replaced by its shifted result.
mrs_data2vec

Convert mrs_data object to a vector.
get_mrsi_voi

Generate a MRSI VOI from an mrs_data object.
get_mrsi_voxel

Generate a MRSI voxel from an mrs_data object.
plot_bc

Convenience function to plot a baseline estimate with the original data.
ortho3

Display an orthographic projection plot of a nifti object.
plot.mrs_data

Plotting method for objects of class mrs_data.
print.mrs_data

Print a summary of mrs_data parameters.
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.
peak_info

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

Apply the max operator to an interpolated MRS dataset.
ortho3_int

Display an interactive orthographic projection plot of a nifti object.
phase

Apply phasing parameters to MRS data.
plot.fit_result

Plot the fitting results of an object of class fit_result.
get_uncoupled_mol

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

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

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

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

Return a single voxel from a larger mrs dataset.
rats

Robust Alignment to a Target Spectrum (RATS).
mean_dyn_pairs

Calculate the pairwise means across a dynamic data set.
lw2alpha

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

Calculate the mean dynamic data.
read_lcm_coord

Read an LCModel formatted coord file containing fit information.
re_weighting

Apply a weighting to the FID to enhance spectral resolution.
rep_dyn

Replicate a scan in the dynamic dimension.
reexports

Objects exported from other packages
qn_states

Get the quantum coherence matrix for a spin system.
mrsi2d_img2kspace

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

Reader for csv fit results generated by TARQUIN.
rep_array_dim

Repeat an array over a given dimension.
read_tqn_result

Reader for csv results generated by TARQUIN.
rep_mrs

Replicate a scan over a given dimension.
resample_img

Resample an image to match a target image space.
resample_voi

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

Plot a 2D slice from an MRSI fit result object.
n2coord

Print fit coordinates from a single index.
plot_slice_fit

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

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).
sd

Standard Deviation
seq_cpmg_ideal

CPMG style sequence with ideal pulses.
seconds

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

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

Calculate the standard deviation spectrum from an mrs_data object.
seq_steam_ideal

STEAM sequence with ideal pulses.
set_def_acq_paras

Set the default acquisition parameters.
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.
seq_spin_echo_ideal_31p

Spin echo sequence with ideal pulses.
read_basis

Read a basis file in LCModel .basis format.
scale_amp_ratio

Scale fitted amplitudes to a ratio of signal amplitude.
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.

read_mrs

Read MRS data from a file.
shift

Apply a frequency shift to MRS data.
tdsr

Time-domain spectral registration.
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.
sim_basis

Simulate a basis set object.
stackplot

Produce a plot with multiple traces.
write_basis

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

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

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

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

Simulate a basis file using TARQUIN.
scale_amp_water_ratio

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

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

Apply partial volume correction to a fitting result object.
seq_pulse_acquire

Simple pulse and acquire sequence with ideal pulses.
seq_pulse_acquire_31p

Simple pulse and acquire sequence with ideal pulses.
scale_amp_molar

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

spant: spectroscopy analysis tools.
seq_slaser_ideal

sLASER sequence with ideal pulses.
mrsi2d_kspace2img

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

Return a list of options for VARPRO based fitting.
vec2mrs_data

Convert a vector into a mrs_data object.
sim_brain_1h

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

Calculate the sum across receiver coil elements.
write_mrs_dpt_v2

Write MRS data object to file in dangerplot (dpt) v2 format.
seq_spin_echo_ideal

Spin echo sequence with ideal pulses.
write_mrs_lcm_raw

Write MRS data object to file in a RAW format compatible with LCModel.
sum_dyns

Calculate the sum of data dynamics.
zf

Zero-fill MRS data in the time domain.
plot_voi_overlay

Plot a volume as an image overlay.
plot_voi_overlay_seg

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

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

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

Create a spin system object for pulse sequence simulation.
stackplot.fit_result

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

Print a summary of an object of class fit_result.
read_mrs_tqn

Read MRS data using the TARQUIN software package.
write_basis_tqn

Generate a basis file using TARQUIN.
spant_mpress_drift

Example MEGA-PRESS data with significant B0 drift.
stackplot.mrs_data

Stackplot plotting method for objects of class mrs_data.
write_mrs_rda

Write MRS data object to file in rds format.
read_siemens_txt_hdr

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

Zero all non-zero-order coherences.
reslice_to_mrs

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

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

PRESS sequence with ideal pulses.
rm_dyns

Remove a subset of dynamic scans.
seq_mega_press_ideal

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

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

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

Simulate a mol_parameter object.
td_conv_filt

Time-domain convolution based filter.
td2fd

Transform time-domain data to the frequency-domain.
Arg.mrs_data

Apply Arg operator to an MRS dataset.
Conj.mrs_data

Apply Conj operator to an MRS dataset.
align

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

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