MR Spectroscopy Analysis Tools


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Documentation for package ‘spant’ version 0.13.0

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A B C D E F G H I L M N P Q R S T V W Z

spant-package spant: spectroscopy analysis tools.

-- A --

acquire Simulate pulse sequence acquisition.
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.
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.
apply_mrs Apply a function across given dimensions of a MRS data object.
apply_pvc Convert default LCM/TARQUIN concentration scaling to molal units with partial volume correction.
Arg.mrs_data Apply Arg operator to an MRS dataset.

-- B --

basis2mrs_data Convert a basis object to an mrs_data object - where basis signals are spread across the dynamic dimension.
beta2lw Covert a beta value in the time-domain to an equivalent linewidth in Hz: x * exp(-i * t * t * beta).

-- C --

calc_coil_noise_cor Calculate the noise correlation between coil elements.
calc_coil_noise_sd Calculate the noise standard deviation for each coil element.
calc_sd_poly Perform a polynomial fit, subtract and return the standard deviation of the residuals.
calc_spec_diff Calculate the sum of squares differences between two mrs_data objects.
calc_spec_snr Calculate the spectral SNR.
check_lcm Check LCModel can be run
check_tqn Check the TARQUIN binary can be run
comb_coils Combine coil data based on the first data point of a reference signal.
comb_csv_results Combine the results from multiple csv format files into a table.
comb_metab_ref Combine a reference and metabolite mrs_data object.
conj Conjugate MRS data.
Conj.mrs_data Apply Conj operator to an MRS dataset.
conv_mrs Convolve two MRS data objects.
crop_spec Crop 'mrs_data' object based on a frequency range.
crop_td_pts Crop 'mrs_data' object data points in the time-domain.

-- D --

def_acq_paras Return (and optionally modify using the input arguments) a list of the default acquisition parameters.
def_fs Return the default sampling frequency in Hz.
def_ft Return the default transmitter frequency in Hz.
def_N Return the default number of data points in the spectral dimension.
def_ref Return the default reference value for ppm scale.
diff_mrs Apply the diff operator to an MRS dataset in the FID/spectral dimension.
dyns Return the number of dynamic scans in an MRS dataset.

-- E --

ecc Eddy current correction.
est_noise_sd Estimate the standard deviation of the noise from a segment of an mrs_data object.

-- F --

fd2td Transform frequency-domain data to the time-domain.
fd_conv_filt Frequency-domain convolution based filter.
fit_diags Calculate diagnostic information for object of class 'fit_result'.
fit_mrs Perform a fit based analysis of MRS data.
fit_tab2csv Write fit results table to a csv file.
fp_phase Return the phase of the first data point in the time-domain.
fp_phase_correct Perform a zeroth order phase correction based on the phase of the first data point in the time-domain.
fs Return the sampling frequency in Hz of an MRS dataset.
ft_shift Perform a fft and ffshift on a vector.
ft_shift_mat Perform a fft and fftshift on a matrix with each column replaced by its shifted fft.

-- G --

gen_F Generate the F product operator.
gen_F_xy Generate the Fxy product operator with a specified phase.
get_1h_brain_basis_paras 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.
get_1h_brain_basis_paras_v2 Return a list of 'mol_parameter' objects suitable for 1H brain MRS analyses.
get_acq_paras Return acquisition parameters from a MRS data object.
get_dyns Extract a subset of dynamic scans.
get_even_dyns Return even numbered dynamic scans starting from 1 (2,4,6...).
get_fh_dyns Return the first half of a dynamic series.
get_fit_map Get a data array from a fit result.
get_fp Return the first time-domain data point.
get_guassian_pulse Generate a gaussian pulse shape.
get_metab Extract the metabolite component from an mrs_data object.
get_mol_names Return a character array of names that may be used with the 'get_mol_paras' function.
get_mol_paras Get a 'mol_parameters' object for a named molecule.
get_odd_dyns Return odd numbered dynamic scans starting from 1 (1,3,5...).
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).
get_sh_dyns Return the second half of a dynamic series.
get_slice Return a single slice from a larger MRSI dataset.
get_svs_voi Generate a SVS acquisition volume from an 'mrs_data' object.
get_td_amp Return an array of amplitudes derived from fitting the initial points in the time domain and extrapolating back to t=0.
get_uncoupled_mol Generate a 'mol_parameters' object for a simple spin system with one resonance.
get_voi_seg Return the white matter, gray matter and CSF composition of a volume.
get_voxel Return a single voxel from a larger mrs dataset.

-- H --

hsvd_filt HSVD based signal filter.

-- I --

ift_shift Perform an iffshift and ifft on a vector.
Im.mrs_data Apply Im operator to an MRS dataset.
image.mrs_data Image plot method for objects of class mrs_data.
interleave_dyns Interleave the first and second half of a dynamic series.
int_spec Integrate a spectral region.
inv_even_dyns Invert even numbered dynamic scans starting from 1 (2,4,6...).
inv_odd_dyns Invert odd numbered dynamic scans starting from 1 (1,3,5...).
is_fd Check if the chemical shift dimension of an MRS data object is in the frequency domain.

-- L --

lb Apply line-broadening (apodisation) to MRS data or basis object.
lb.basis_set Apply line-broadening (apodisation) to MRS data or basis object.
lb.mrs_data 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).
lw2beta Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-t * t * beta).

-- M --

mat2mrs_data Convert a matrix (with spectral points in the row dimension and dynamics in the column dimensions) into a mrs_data object.
max_mrs Apply the max operator to an MRS dataset.
max_mrs_interp Apply the max operator to an interpolated MRS dataset.
mean_dyns Calculate the mean dynamic data.
mean_dyn_blocks Calculate the mean of adjacent dynamic scans.
mean_dyn_pairs Calculate the pairwise means across a dynamic data set.
median_dyns Calculate the median dynamic data.
Mod.mrs_data Apply Mod operator to an MRS dataset.
mrs_data2basis Convert an mrs_data object to basis object - where basis signals are spread across the dynamic dimension in the MRS data.
mrs_data2mat Convert mrs_data object to a matrix, with spectral points in the row dimension and dynamics in the column dimension.
mrs_data2vec Convert mrs_data object to a vector.
mvfftshift Perform a fftshift on a matrix, with each column replaced by its shifted result.

-- N --

N Return the number of data points in an MRS dataset.
n2coord Print fit coordinates from a single index.
Nspec Return the total number of spectra in an MRS dataset.

-- P --

peak_info Search for the highest peak in a spectral region and return the frequency, height and FWHM.
phase Apply phasing parameters to MRS data.
plot.fit_result Plot the fitting results of an object of class 'fit_result'.
plot.mrs_data Plotting method for objects of class mrs_data.
plot_fit_slice Plot a 2D slice from an MRSI fit result object.
plot_fit_slice_inter Plot a 2D slice from an MRSI fit result object.
plot_slice_map Plot a slice from a 7 dimensional array.
plot_slice_map_inter Plot an interactive slice map from a data array where voxels can be selected to display a corresponding spectrum.
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.
ppm Return the ppm scale of an MRS dataset.
print.fit_result Print a summary of an object of class 'fit_result'.
print.mrs_data Print a summary of mrs_data parameters.

-- Q --

qn_states Get the quantum coherence matrix for a spin system.

-- R --

rats Robust Alignment to a Target Spectrum (RATS).
Re.mrs_data Apply Re operator to an MRS dataset.
read_basis Read a basis file in LCModel .basis format.
read_lcm_coord Read an LCModel formatted coord file containing fit information.
read_mrs Read MRS data from a file.
read_mrs_dpt Read MRS data stored in dangerplot (dpt) v3 format.
read_mrs_tqn Read MRS data using the TARQUIN software package.
read_tqn_fit Reader for csv fit results generated by TARQUIN.
read_tqn_result Reader for csv results generated by TARQUIN.
rep_array_dim Repeat an array over a given dimension.
rep_dyn Replicate a scan in the dynamic dimension.
rep_mrs Replicate a scan over a given dimension.
resample_voi Resample a VOI to match a target image space.
rm_dyns Remove a subset of dynamic scans.

-- S --

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).
scale_amp_ratio Scale fitted amplitudes to a ratio of signal amplitude.
scale_amp_water_ratio Scale metabolite amplitudes as a ratio to the unsupressed water amplitude.
seconds Return a time scale vector to match the FID of an MRS data object.
seq_cpmg_ideal CPMG style sequence with ideal pulses.
seq_mega_press_ideal MEGA-PRESS sequence with ideal localisation pulses and Gaussian shaped editing pulse.
seq_press_ideal PRESS sequence with ideal pulses.
seq_pulse_acquire Simple pulse and acquire sequence with ideal pulses.
seq_pulse_acquire_31p Simple pulse and acquire sequence with ideal pulses.
seq_slaser_ideal sLASER sequence with ideal pulses.
seq_spin_echo_ideal Spin echo sequence with ideal pulses.
seq_spin_echo_ideal_31p Spin echo sequence with ideal pulses.
seq_steam_ideal STEAM sequence with ideal pulses.
set_def_acq_paras Set the default acquisition parameters.
set_lcm_cmd Set the command to run the LCModel command-line program.
set_ref Set the ppm reference value (eg ppm value at 0Hz).
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.
shift Apply a frequency shift to MRS data.
sim_basis 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.
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.
sim_basis_tqn Simulate a basis file using TARQUIN.
sim_brain_1h Simulate MRS data with a similar appearance to normal brain (by default).
sim_mol Simulate a 'mol_parameter' object.
sim_noise Simulate a time-domain mrs_data object containing simulated Gaussian noise.
sim_resonances Simulate a MRS data object containing a set of simulated resonances.
spant spant: spectroscopy analysis tools.
spant_mpress_drift Example MEGA-PRESS data with significant B0 drift.
spin_sys Create a spin system object for pulse sequence simulation.
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.
stackplot 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.
stackplot.mrs_data Stackplot plotting method for objects of class mrs_data.
sum_coils Calculate the sum across receiver coil elements.
sum_dyns Calculate the sum of data dynamics.

-- T --

td2fd Transform time-domain data to the frequency-domain.
tdsr Time-domain spectral registration.
td_conv_filt Time-domain convolution based filter.

-- V --

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.
varpro_opts Return a list of options for VARPRO based fitting.
vec2mrs_data Convert a vector into a mrs_data object.

-- W --

write_basis Write a basis object to an LCModel .basis formatted file.
write_basis_tqn Generate a basis file using TARQUIN.
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.

-- Z --

zero_nzoc Zero all non-zero-order coherences.
zf Zero-fill MRS data in the time domain.
zf.basis_set Zero-fill MRS data in the time domain.
zf.mrs_data Zero-fill MRS data in the time domain.
zf_xy Zero-fill MRSI data in the k-space x-y direction.