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spant (version 1.1.0)

MR Spectroscopy Analysis Tools

Description

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

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install.packages('spant')

Monthly Downloads

605

Version

1.1.0

License

GPL-3

Maintainer

Martin Wilson

Last Published

March 1st, 2020

Functions in spant (1.1.0)

Mod.mrs_data

Apply Mod operator to an MRS dataset.
N

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

Return the total number of spectra in an MRS dataset.
Arg.mrs_data

Apply Arg operator to an MRS dataset.
Im.mrs_data

Apply Im operator to an MRS dataset.
Npts

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

Combine a pair of basis set objects.
Ndyns

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

Apply Conj operator to an MRS dataset.
apodise_xy

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

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

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

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

Simulate pulse sequence acquisition.
Nx

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

Return the total number of coil elements 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_spec_snr

Calculate the spectral SNR.
back_extrap

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

Align spectra to a reference frequency using a convolution based method.
basis2mrs_data

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

Check LCModel can be run
calc_coil_noise_sd

Calculate the noise standard deviation for each coil element.
calc_coil_noise_cor

Calculate the noise correlation between coil elements.
conv_mrs

Convolve two MRS data objects.
apply_pvc

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

Crop mrs_data object based on a frequency range.
def_acq_paras

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

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

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

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

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

Check the TARQUIN binary can be run
def_fs

Return the default sampling frequency in Hz.
crop_xy

Crop an MRSI dataset in the x-y direction
ft_shift

Perform a fft and ffshift on a vector.
get_1h_brain_basis_paras_v1

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

Return the total number of y locations in an MRS dataset.
get_1h_brain_basis_paras_v2

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

Get a data array from a fit result.
get_slice

Return a single slice from a larger MRSI dataset.
get_voi_seg

Return the white matter, gray matter and CSF composition of a volume.
lw2beta

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

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

Return the first half of a dynamic series.
get_sh_dyns

Return the second half of a dynamic series.
def_ft

Return the default transmitter frequency in Hz.
def_ref

Return the default reference value for ppm scale.
comb_coils

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

Return the total number of z locations in an MRS dataset.
mrs_data2mat

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

Calculate the median dynamic data.
mask_xy

Mask an MRSI dataset in the x-y direction
mrs_data2basis

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

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

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

Combine coil data following phase correction based on the first data point in the FID.
mrs_data2vec

Convert mrs_data object to a vector.
apply_mrs

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

Apply a function over specified array axes.
fd2td

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

Frequency-domain convolution based filter.
Re.mrs_data

Apply Re operator to an MRS dataset.
calc_sd_poly

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

Baseline correction using the ALS method.
abfit_opts

Return a list of options for an ABfit analysis.
calc_spec_diff

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

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

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

Perform a fit based analysis of MRS data.
comb_fits

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

Plot a slice from a 7 dimensional array.
calc_ed_from_lambda

Calculate the effective dimensions of a spline smoother from lambda.
calc_peak_info_vec

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

Robust Alignment to a Target Spectrum (RATS).
re_weighting

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

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

Conjugate MRS data.
def_N

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

Combine a reference and metabolite mrs_data object.
fp_phase

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

Downsample an MRS signal by a factor.
ft_shift_mat

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

Generate the F product operator.
read_mrs_tqn

Read MRS data using the TARQUIN software package.
ecc

Eddy current correction.
l2_reg

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

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

Generate a MRSI voxel from an mrs_data object.
hsvd_filt

HSVD based signal filter.
get_mrsi_voi

Generate a MRSI VOI from an mrs_data object.
is_fd

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

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

Grid shift MRSI data in the x/y dimension.
mean.mrs_data

Calculate the mean spectrum from an mrs_data object.
fit_tab2csv

Write fit results table to a csv file.
read_siemens_txt_hdr

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

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

Perform a fftshift on a matrix, with each column replaced by its shifted result.
ortho3_int

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

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

Return the ppm scale of an MRS dataset.
mean_dyn_blocks

Calculate the mean of adjacent dynamic scans.
peak_info

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

Print a summary of an object of class fit_result.
rm_dyns

Remove a subset of dynamic scans.
reslice_to_mrs

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

Extract a subset of dynamic scans.
fit_amps

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

Calculate diagnostic information for object of class fit_result.
est_noise_sd

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

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

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

Extract the metabolite component from an mrs_data object.
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.
gen_F_xy

Generate the Fxy product operator with a specified phase.
get_subset

Extract a subset of MRS data.
get_svs_voi

Generate a SVS acquisition volume from an mrs_data object.
hz

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

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

Return the first time-domain data point.
read_lcm_coord

Read an LCModel formatted coord file containing fit information.
get_1h_brain_basis_paras

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

Generate a gaussian pulse shape.
rep_dyn

Replicate a scan in the dynamic dimension.
seq_cpmg_ideal

CPMG style sequence with ideal pulses.
set_ref

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

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

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

Replicate a scan over a given dimension.
get_2d_psf

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

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

Perform an iffshift and ifft on a vector.
inv_even_dyns

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

Return acquisition parameters from a MRS data object.
seq_press_ideal

PRESS sequence with ideal pulses.
sim_basis_tqn

Simulate a basis file using TARQUIN.
seq_spin_echo_ideal_31p

Spin echo sequence with ideal pulses.
seq_steam_ideal

STEAM sequence with ideal pulses.
get_ref

Extract the reference component from an mrs_data object.
get_seg_ind

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

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

Simulate a mol_parameter object.
norm_mrs

Normalise mrs_data to a spectral region.
mat2mrs_data

Convert a matrix (with spectral points in the row dimension and dynamics in the column dimensions) into a mrs_data object.
sim_brain_1h

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

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

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

Image plot method for objects of class mrs_data.
lb

Apply line-broadening (apodisation) to MRS data or basis object.
lw2alpha

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

Calculate the pairwise means across a dynamic data set.
plot_voi_overlay

Plot a volume as an image overlay.
read_mrs

Read MRS data from a file.
mean_dyns

Calculate the mean dynamic data.
plot_slice_fit_inter

Plot a 2D slice from an MRSI fit result object.
mrsi2d_img2kspace

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

Plot a 2D slice from an MRSI fit result object.
mrsi2d_kspace2img

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

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

Get a mol_parameters object for a named molecule.
sum_coils

Calculate the sum across receiver coil elements.
ortho3

Display an orthographic projection plot of a nifti object.
set_def_acq_paras

Set the default acquisition parameters.
seq_pulse_acquire_31p

Simple pulse and acquire sequence with ideal pulses.
resample_voi

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

Resample an image to match a target image space.
read_mrs_dpt

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

Simple pulse and acquire sequence with ideal pulses.
stackplot

Produce a plot with multiple traces.
vec2mrs_data

Convert a vector into a mrs_data object.
varpro_opts

Return a list of options for VARPRO based fitting.
set_lcm_cmd

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

Plotting method for objects of class mrs_data.
sum_dyns

Calculate the sum of data dynamics.
spant-package

spant: spectroscopy analysis tools.
stackplot.mrs_data

Stackplot plotting method for objects of class mrs_data.
sim_resonances

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

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

Reader for csv fit results generated by TARQUIN.
read_basis

Read a basis file in LCModel .basis format.
get_mrsi2d_seg

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

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

Generate a basis file using TARQUIN.
zero_nzoc

Zero all non-zero-order coherences.
write_basis

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

Apply partial volume correction to a fitting result object.
scale_amp_molar

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

Generate a MRSI voxel PSF from an mrs_data object.
read_tqn_result

Reader for csv results generated by TARQUIN.
get_odd_dyns

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

sLASER sequence with ideal pulses.
get_voxel

Return a single voxel from a larger mrs dataset.
seq_spin_echo_ideal

Spin echo sequence with ideal pulses.
interleave_dyns

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

Integrate a spectral region.
sim_basis

Simulate a basis set object.
zf

Zero-fill MRS data in the time domain.
get_voi_seg_psf

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

Apply a frequency shift to MRS data.
max_mrs

Apply the max operator to an MRS dataset.
n2coord

Print fit coordinates from a single index.
max_mrs_interp

Apply the max operator to an interpolated MRS dataset.
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.
td_conv_filt

Time-domain convolution based filter.
zf_xy

Zero-fill MRSI data in the k-space x-y direction.
td2fd

Transform time-domain data to the frequency-domain.
sim_basis_1h_brain

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

Apply phasing parameters to MRS data.
rep_array_dim

Repeat an array over a given dimension.
reexports

Objects exported from other packages
print.mrs_data

Print a summary of mrs_data parameters.
plot.fit_result

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

Scale fitted amplitudes to a ratio of signal amplitude.
sd.mrs_data

Calculate the standard deviation spectrum from an mrs_data object.
scale_amp_water_ratio

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

Standard Deviation
qn_states

Get the quantum coherence matrix for a spin system.
set_td_pts

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

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

Example MEGA-PRESS data with significant B0 drift.
tdsr

Time-domain spectral registration.
write_mrs_dpt_v2

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

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

Create a spin system object for pulse sequence simulation.
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.