Arg.mrs_data            Apply Arg operator to an MRS dataset.
Conj.mrs_data           Apply Conj operator to an MRS dataset.
Im.mrs_data             Apply Im operator to an MRS dataset.
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.
Re.mrs_data             Apply Re operator to an MRS dataset.
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.
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).
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.
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.
def_N                   Return the default number of data points in the
                        spectral dimension.
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_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.
ecc                     Eddy current correction.
est_noise_sd            Estimate the standard deviation of the noise
                        from a segment of an mrs_data object.
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.
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.
hsvd_filt               HSVD based signal filter.
ift_shift               Perform an iffshift and ifft on a vector.
image.mrs_data          Image plot method for objects of class
                        mrs_data.
int_spec                Integrate a spectral region.
interleave_dyns         Interleave the first and second half of a
                        dynamic series.
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.
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).
lw2beta                 Covert a linewidth in Hz to an equivalent beta
                        value in the time-domain ie: x * exp(-t * t *
                        beta).
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_dyn_blocks         Calculate the mean of adjacent dynamic scans.
mean_dyn_pairs          Calculate the pairwise means across a dynamic
                        data set.
mean_dyns               Calculate the mean dynamic data.
median_dyns             Calculate the median dynamic data.
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.
n2coord                 Print fit coordinates from a single index.
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.
qn_states               Get the quantum coherence matrix for a spin
                        system.
rats                    Robust Alignment to a Target Spectrum (RATS).
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.
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-package           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.
td2fd                   Transform time-domain data to the
                        frequency-domain.
td_conv_filt            Time-domain convolution based filter.
tdsr                    Time-domain spectral registration.
varpro_3_para_opts      Return a list of options for VARPRO based
                        fitting with 3 free parameters: <U+0095> zero'th order
                        phase correction <U+0095> global damping <U+0095> global
                        frequency shift.
varpro_opts             Return a list of options for VARPRO based
                        fitting.
vec2mrs_data            Convert a vector into a mrs_data object.
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.
zero_nzoc               Zero all non-zero-order coherences.
zf                      Zero-fill MRS data in the time domain.
zf_xy                   Zero-fill MRSI data in the k-space x-y
                        direction.
