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.
Imzap                   Complex rounding function taken from
                        complexplus package to reduce the number of
                        spant dependencies.
Mod.mrs_data            Apply Mod operator to 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.
Npts                    Return the number of data points in an MRS
                        dataset.
Nspec                   Return the total number of spectra in an MRS
                        dataset.
Ntrans                  Return the total number of acquired transients
                        for an MRS dataset.
Nx                      Return the total number of x locations in an
                        MRS dataset.
Ny                      Return the total number of y locations in an
                        MRS dataset.
Nz                      Return the total number of z locations in an
                        MRS dataset.
Re.mrs_data             Apply Re operator to an MRS dataset.
abfit_opts              Return a list of options for an ABfit analysis.
abfit_opts_v1_9_0       Return a list of options for an ABfit analysis
                        to maintain comparability with analyses
                        performed with version 1.9.0 (and earlier) of
                        spant.
abfit_reg_opts          Return a list of options for an ABfit analysis
                        with regularision.
acquire                 Simulate pulse sequence acquisition.
add_noise               Add noise to an mrs_data object.
add_noise_spec_snr      Add noise to an mrs_data object to match a
                        given SNR.
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 filter.
append_basis            Combine a pair of basis set objects.
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.
append_regs             Append multiple regressor data frames into a
                        single data frame.
apply_axes              Apply a function over specified array axes.
apply_mrs               Apply a function across given dimensions of a
                        MRS data object.
apply_pulse             Simulate an RF pulse on a single spin.
array2mrs_data          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.
assign_dyns             Overwrite a subset of dynamic scans.
auto_phase              Perform zeroth-order phase correction based on
                        the minimisation of the squared difference
                        between the real and magnitude components of
                        the spectrum.
auto_phase_bl           Perform zeroth-order phase correction based on
                        expected baseline regions.
back_extrap_ar          Back extrapolate time-domain data points using
                        an autoregressive model.
basis2dyn_mrs_data      Convert a basis object to a dynamic mrs_data
                        object.
basis2mrs_data          Convert a basis object to an mrs_data object -
                        where basis signals are spread across the
                        dynamic dimension.
bbase                   Generate a spline basis, slightly adapted from
                        : "Splines, knots, and penalties", Eilers 2010.
bc_als                  Baseline correction using the ALS method.
bc_constant             Remove a constant baseline offset based on a
                        reference spectral region.
bc_gauss                Apply and subtract a Gaussian smoother in the
                        spectral domain.
bc_poly                 Fit and subtract a polynomial to each spectrum
                        in a dataset.
bc_spline               Fit and subtract a smoothing spline to each
                        spectrum in a dataset.
beta2lw                 Covert a beta value in the time-domain to an
                        equivalent linewidth in Hz: x * exp(-i * t * t
                        * beta).
bin_spec                Bin equally spaced spectral regions.
calc_basis_corr_mat     Estimate the correlation matrix for a basis
                        set.
calc_basis_crlbs        Estimate the CRLB for each element in a basis
                        set.
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_design_efficiency
                        Calculate the efficiency of a regressor data
                        frame.
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.
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
circ_mask               Create a logical circular mask spanning the
                        full extent of an n x n matrix.
coherence_filter        Zero all coherence orders other than the one
                        supplied as an argument.
collapse_to_dyns        Collapse MRS data by concatenating spectra
                        along the dynamic dimension.
comb_coils              Combine coil data based on the first data point
                        of a reference signal.
comb_coils_mrsi_gls     Combine MRSI coil data using the GLS method
                        presented by An et al JMRI 37:1445-1450 (2013).
comb_coils_svs_gls      Combine SVS coil data using the GLS method
                        presented by An et al JMRI 37:1445-1450 (2013).
comb_fit_list_dyns      Combine a list of fit results into a single fit
                        result object across the dynamic dimension.
comb_fit_list_fit_tables
                        Combine all fitting data points from a list of
                        fits into a single data frame.
comb_fit_list_result_tables
                        Combine the fit result tables from a list of
                        fit results.
comb_fit_tables         Combine all fitting data points into a single
                        data frame.
comb_metab_ref          Combine a reference and metabolite mrs_data
                        object.
conv_mrs                Convolve two MRS data objects.
crop_basis              Crop 'basis_set' object based on a frequency
                        range.
crop_spec               Crop 'mrs_data' object based on a frequency
                        range.
crop_td_pts             Crop 'mrs_data' object data points in the
                        time-domain.
crop_td_pts_end         Crop 'mrs_data' object data points at the end
                        of the FID.
crop_td_pts_pot         Crop 'mrs_data' object data points in the
                        time-domain rounding down to the next smallest
                        power of two (pot). Data that already has a pot
                        length will not be changed.
crop_xy                 Crop an MRSI dataset in the x-y direction
crossprod_3d            Compute the vector cross product between
                        vectors x and y. Adapted from
                        http://stackoverflow.com/questions/15162741/what-is-rs-crossproduct-function
decimate_mrs_fd         Decimate an MRS signal to half the original
                        sampling frequency by filtering in the
                        frequency domain before down sampling.
decimate_mrs_td         Decimate an MRS signal by filtering in the time
                        domain before downsampling.
deconv_mrs              Deconvolve two MRS data objects.
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_nuc                 Return the default nucleus.
def_ref                 Return the default reference value for ppm
                        scale.
dicom_reader            A very simple DICOM reader.
diff_mrs                Apply the diff operator to an MRS dataset in
                        the FID/spectral dimension.
downsample_mrs_fd       Downsample an MRS signal by a factor of 2 using
                        an FFT "brick-wall" 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.
dyn_acq_times           Return a time scale vector of acquisition times
                        for a dynamic MRS scan. The first temporal scan
                        is assigned a value of 0.
ecc                     Eddy current correction.
elliptical_mask         Create an elliptical mask stored as a matrix of
                        logical values.
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.
fd_gauss_smo            Apply a Gaussian smoother in the spectral
                        domain.
find_bids_mrs           Search for MRS data files in a BIDS filesystem
                        structure.
find_mrs_files          Find valid MRS data files recursively from a
                        directory path.
fit_amps                Extract the fit amplitudes from an object of
                        class 'fit_result'.
fit_asy_pvoigt          Fit a single asymmetric pseudo-Voigt resonance
                        in the frequency domain.
fit_diags               Calculate diagnostic information for object of
                        class 'fit_result'.
fit_mrs                 Perform a fit based analysis of MRS data.
fit_res2csv             Write fit results table to a csv file.
fit_svs                 Standard SVS 1H brain analysis pipeline.
fit_svs_edited          Edited SVS 1H brain analysis pipeline.
fit_svs_edited_group_results
                        Combine edited fitting results for group
                        analysis.
fit_svs_group_results   Combine fitting results for group analysis.
fit_svs_gui             GUI interface for the standard SVS 1H brain
                        analysis pipeline, this is a work in progress,
                        and not ready for serious use.
fit_t1_ti_array         Fit a T1 recovery curve, from multiple TIs, to
                        a set of amplitudes.
fit_t1_tr_array         Fit a T1 recovery curve, from multiple TRs, to
                        a set of amplitudes.
fit_t2_te_array         Fit a T2 relaxation curve, from multiple TEs,
                        to a set of amplitudes.
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.
fp_scale                Scale the first time-domain data point in an
                        mrs_data object.
fs                      Return the sampling frequency in Hz of an MRS
                        dataset.
ft_dyns                 Apply the Fourier transform over the dynamic
                        dimension.
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.
gausswin_2d             Create a two dimensional Gaussian window
                        function stored as a matrix.
gen_F                   Generate the F product operator.
gen_F_xy                Generate the Fxy product operator with a
                        specified phase.
gen_I                   Generate the I product operator for a single
                        spin.
gen_baseline_reg        Generate baseline regressor.
gen_bold_reg            Generate BOLD regressors.
gen_conv_reg            Generate regressors by convolving a specified
                        response function with a stimulus.
gen_group_reg           Expand a regressor matrix for a group analysis.
gen_impulse_reg         Generate impulse regressors.
gen_numeric_reg         Generate a regressor from a numeric vector.
gen_poly_reg            Generate polynomial regressors.
gen_trap_reg            Generate trapezoidal regressors.
get_1h_brain_basis_names
                        Return a character vector of common 1H
                        molecules found in healthy human brain.
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_1h_brain_basis_paras_v3
                        Return a list of 'mol_parameter' objects
                        suitable for 1H brain MRS analyses.
get_1h_braino_basis_names
                        Return a character vector of molecules included
                        in the GE BRAINO phantom.
get_1h_spectre_basis_names
                        Return a character vector of molecules included
                        in the Gold Star Phantoms SPECTRE phantom.
get_2d_psf              Get the point spread function (PSF) for a 2D
                        phase encoded MRSI scan.
get_acq_paras           Return acquisition parameters from a MRS data
                        object.
get_basis_subset        Return a subset of the input basis.
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_head_dyns           Return the first scans of a dynamic series.
get_hrf                 Generate a double gamma model of the HRF as
                        used in SPM.
get_lcm_cmd             Print the command to run the LCModel
                        command-line program.
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_mrs_affine          Generate an affine for nifti generation.
get_mrsi2d_seg          Calculate the partial volume estimates for each
                        voxel in a 2D MRSI dataset.
get_mrsi_voi            Generate a MRSI VOI from an 'mrs_data' object.
get_mrsi_voxel          Generate a MRSI voxel from an 'mrs_data'
                        object.
get_mrsi_voxel_xy_psf   Generate a MRSI voxel PSF from an 'mrs_data'
                        object.
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_spin_num            Return the spin number for a given nucleus.
get_subset              Extract a subset of MRS data.
get_svs_voi             Generate a SVS acquisition volume from an
                        'mrs_data' object.
get_tail_dyns           Return the last scans of a dynamic series.
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_tqn_cmd             Print the command to run the TARQUIN
                        command-line program.
get_uncoupled_mol       Generate a 'mol_parameters' object for a simple
                        spin system with one resonance.
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.
get_voi_seg_psf         Return the white matter, gray matter and CSF
                        composition of a volume.
get_voxel               Return a single voxel from a larger mrs
                        dataset.
glm_spec                Perform a GLM analysis of dynamic MRS data in
                        the spectral domain.
glm_spec_fmrs_fl        Perform first-level spectral GLM analysis of an
                        fMRS dataset.
glm_spec_fmrs_group     Perform group-level spectral GLM analysis of an
                        fMRS dataset.
glm_spec_group_linhyp   Test a group-level spectral GLM linear
                        hypothesis.
grid_shift_xy           Grid shift MRSI data in the x/y dimension.
gridplot                Arrange spectral plots in a grid.
gridplot.mrs_data       Arrange spectral plots in a grid.
hsvd                    HSVD of an mrs_data object.
hsvd_filt               HSVD based signal filter.
hsvd_vec                HSVD of a complex vector.
hz                      Return the frequency scale of an MRS dataset in
                        Hz.
ift_shift               Perform an iffshift and ifft on a vector.
ift_shift_mat           Perform an ifft and ifftshift on a matrix with
                        each column replaced by its shifted ifft.
image.mrs_data          Image plot method for objects of class
                        mrs_data.
img2kspace_xy           Transform 2D MRSI data to k-space in the x-y
                        direction.
install_cli             Install the spant command-line interface
                        scripts to a system path.
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.def                  Check if an object is defined, which is the
                        same as being not NULL.
is_fd                   Check if the chemical shift dimension of an MRS
                        data object is in the frequency domain.
kspace2img_xy           Transform 2D MRSI data from k-space to image
                        space in the x-y direction.
l2_reg                  Perform l2 regularisation artefact suppression.
lb                      Apply line-broadening (apodisation) to MRS data
                        or basis object.
lb_renoise              Apply line-broadening to dynamic MRS data and
                        add normally distributed noise (renoise) to
                        reverse any associated improvement in SNR.
lofdc                   Correct linear frequency drift.
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).
make_basis_from_raw     Make a basis-set object from a directory
                        containing LCModel formatted RAW files.
mask_dyns               Mask an MRS dataset in the dynamic dimension.
mask_fit_res            Mask fit result spectra depending on a vector
                        of bool values.
mask_xy                 Mask an MRSI dataset in the x-y direction
mask_xy_corners         Mask the four corners of an MRSI dataset in the
                        x-y plane.
mask_xy_ellipse         Mask the voxels outside an elliptical region
                        spanning the MRSI dataset in the x-y plane.
mask_xy_mat             Mask a 2D MRSI dataset in the x-y dimension.
mat2mrs_data            Convert a matrix (with spectral points in the
                        column dimension and dynamics in the row
                        dimensions) into a mrs_data object.
match_files             Match files based on a vector of input paths
                        and a glob pattern. The glob pattern is
                        appended to each path and should match one file
                        only.
match_lineshape         Apply Voigt line-broadening to match a
                        reference spectrum.
matexp                  Matrix exponential function taken from
                        complexplus package to reduce the number of
                        spant dependencies.
max_mrs                 Apply the max operator to an MRS dataset.
max_mrs_interp          Apply the max operator to an interpolated MRS
                        dataset.
mean.list               Calculate the mean spectrum from an mrs_data
                        object.
mean.mrs_data           Calculate the mean spectrum from an mrs_data
                        object.
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.
mean_dyns_scheme        Average sets of dynamics according to a scheme
                        vector.
mean_mrs_list           Return the mean of a list of mrs_data objects.
mean_vec_blocks         Calculate the mean of adjacent blocks in a
                        vector.
median_dyns             Calculate the median dynamic data.
mod_td                  Apply the Modulus operator to the time-domain
                        MRS signal.
mr_data2bids            Create a BIDS file structure from a vector of
                        data paths or list of mri/mrs data objects.
mrs_data2basis          Convert an mrs_data object to basis object -
                        where basis signals are spread across the
                        dynamic dimension in the MRS data.
mrs_data2bids           Create a BIDS file structure from a vector of
                        MRS data paths or list of mrs_data objects.
mrs_data2list           Split MRS data containing multiple spectra into
                        a list of single spectra datasets.
mrs_data2mat            Convert mrs_data object to a matrix, with
                        spectral points in the column dimension and
                        dynamics in the row dimension.
mrs_data2spec_mat       Convert mrs_data object to a matrix, with
                        spectral points in the column dimension and
                        dynamics in the row 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.
mvifftshift             Perform an ifftshift on a matrix, with each
                        column replaced by its shifted result.
n2coord                 Print fit coordinates from a single index.
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).
one_page_pdf            Export a one-page pdf of a single fit result
ortho3                  Display an orthographic projection plot of a
                        nifti object.
ortho3_inter            Display an interactive orthographic projection
                        plot of a nifti object.
paths2df                Split paths into parts based on backslash,
                        forwardslash and dot characters and return a
                        data frame of these parts.
peak_info               Search for the highest peak in a spectral
                        region and return the frequency, height and
                        FWHM.
pg_extrap_xy            Papoulis-Gerchberg (PG) algorithm method for
                        k-space extrapolation.
phase                   Apply phasing parameters to MRS data.
phase_ref_1h_brain      Corrected zero order phase and chemical shift
                        offset in 1H MRS data from the brain.
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_bc                 Convenience function to plot a baseline
                        estimate with the original data.
plot_reg                Plot regressors as an image.
plot_slice_fit          Plot a 2D slice from an MRSI fit result object.
plot_slice_fit_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_spec_sd            Plot the spectral standard deviation.
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 or fit
                        result.
precomp                 Save function results to file and load on
                        subsequent calls to avoid repeat computation.
preproc_svs             Preprocess and perform quality assessment of a
                        single SVS data set.
preproc_svs_dataset     Preprocess and perform quality assessment of
                        one or more SVS data sets.
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).
re_weighting            Apply a weighting to the FID to enhance
                        spectral resolution.
read_basis              Read a basis file in LCModel .basis format.
read_basis_niidir       Read a basis folder containing one NIfTI MRS
                        file for each basis element.
read_dkd_moco_log       Read the log from Dinesh's MoCo sLASER
                        sequence.
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.
read_lcm_coord          Read an LCModel formatted coord file containing
                        fit information.
read_mrs                Read MRS data from the filesystem.
read_mrs_tqn            Read MRS data using the TARQUIN software
                        package.
read_pulse_ascii        Read an ASCII formatted pulse file.
read_pulse_bruker       Read a Bruker formatted pulse file
read_pulse_pta          Read a .pta formatted pulse file compatible
                        with Siemens PulseTool.
read_siemens_txt_hdr    Read the text format header found in Siemens
                        IMA and TWIX data files.
read_tqn_fit            Reader for csv fit results generated by
                        TARQUIN.
read_tqn_result         Reader for csv results generated by TARQUIN.
recon_imag              Reconstruct complex time-domain data from the
                        real part of frequency-domain data.
recon_imag_vec          Reconstruct complex time-domain data from the
                        real part of frequency-domain data.
recon_twix_2d_mrsi      Reconstruct 2D MRSI data from a twix file
                        loaded with read_mrs.
rectangular_mask        Create a rectangular mask stored as a matrix of
                        logical values.
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_basis          Resample a basis-set to match a mrs_data
                        acquisition.
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.
reslice_to_mrs          Reslice a nifti object to match the orientation
                        of mrs data.
reson_table2mrs_data    Generate mrs_data from a table of single
                        Lorentzian resonances.
rm_dyns                 Remove a subset of dynamic scans.
scale_amp_legacy        Apply water reference scaling to a fitting
                        results object to yield metabolite quantities
                        in units of "mmol per Kg wet weight".
scale_amp_molal         Apply water reference scaling to a fitting
                        results object to yield metabolite quantities
                        in millimolar (mM) units (mol / kg of tissue
                        water).
scale_amp_molal_pvc     Apply water reference scaling to a fitting
                        results object to yield metabolite quantities
                        in millimolar (mM) units (mol / kg of tissue
                        water).
scale_amp_molar         Apply water reference scaling to a fitting
                        results object to yield metabolite quantities
                        in millimolar (mM) units (mol / Litre of
                        tissue). This function is depreciated, please
                        use scale_amp_legacy instead.
scale_amp_molar2molal_pvc
                        Convert default LCM/TARQUIN concentration
                        scaling to molal units with partial volume
                        correction.
scale_amp_ratio         Scale fitted amplitudes to a ratio of signal
                        amplitude.
scale_amp_ratio_value   Scale fitted amplitudes to a ratio of signal
                        amplitude.
scale_amp_water_ratio   Scale metabolite amplitudes as a ratio to the
                        unsuppressed water amplitude.
scale_basis_amp         Scale a basis object by a scalar.
scale_basis_from_singlet
                        Scale a basis-set to be consistent with spant
                        assumptions for water scaling.
scale_mrs_amp           Scale an mrs_data object by a scalar or vector
                        or amplitudes.
scale_spec              Scale mrs_data to a spectral region.
sd.list                 Calculate the standard deviation spectrum from
                        an mrs_data object.
sd.mrs_data             Calculate the standard deviation spectrum from
                        an mrs_data object.
seconds                 Return a time scale vector to match the FID of
                        an MRS data object.
segment_t1_fsl          Segment T1 weighted MRI data using FSL FAST and
                        write to file. Runs deface and bet as
                        preprocessing steps by default.
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_2d_shaped     PRESS sequence with shaped refocusing pulses.
seq_press_ideal         PRESS sequence with ideal pulses.
seq_pulse_acquire       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_steam_ideal         STEAM sequence with ideal pulses.
seq_steam_ideal_cof     STEAM sequence with ideal pulses and coherence
                        order filtering to simulate gradient crushers.
seq_steam_ideal_young   STEAM sequence with ideal pulses using the
                        z-rotation gradient simulation method described
                        by Young et al JMR 140, 146-152 (1999).
set_Ntrans              Set the number of transients for an mrs_data
                        object.
set_def_acq_paras       Set the default acquisition parameters.
set_lcm_cmd             Set the command to run the LCModel command-line
                        program.
set_lw                  Apply line-broadening to an mrs_data object to
                        achieve a specified linewidth.
set_mask_xy_mat         Set the masked voxels in a 2D MRSI dataset to
                        given spectrum.
set_precomp_mode        Set the precompute mode.
set_precomp_verbose     Set the verbosity of the precompute function.
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.
set_tr                  Set the repetition time of an MRS dataset.
shift                   Apply a frequency shift to MRS data.
shift_basis             Apply frequency shifts to basis set signals.
sim_asy_pvoigt          Generate an asymmetric pseudo-Voigt resonance
                        in the frequency domain.
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_mm_lip_lcm    Simulate a macromolecular and lipid basis-set
                        suitable for 1H brain MRS analysis.
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 an mrs_data object containing
                        simulated Gaussian noise.
sim_resonances          Simulate a MRS data object containing a set of
                        simulated resonances.
sim_th_excit_profile    Simulate an ideal pulse excitation profile by
                        smoothing a top-hat function with a Gaussian.
sim_zero                Simulate an mrs_data object containing complex
                        zero valued samples.
smooth_dyns             Smooth data across the dynamic dimension with a
                        Gaussian kernel.
sort_basis              Sort the basis-set elements alphabetically.
spant-package           spant: spectroscopy analysis tools.
spant_abfit_benchmark   Simulate and fit some spectra with ABfit for
                        benchmarking purposes. Basic timing and
                        performance metrics will be printed.
spant_sim_fmrs_dataset
                        Simulate an example fMRS dataset for a block
                        design fMRS experiment and export a BIDS
                        structure.
spant_simulation_benchmark
                        Simulate a typical metabolite basis set for
                        benchmarking. Timing metrics will be printed on
                        completion.
spec_decomp             Decompose an mrs_data object into white and
                        gray matter spectra.
spec_op                 Perform a mathematical operation on a spectral
                        region.
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.
ssp                     Signal space projection method for lipid
                        suppression.
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.
sub_even_from_odd_dyns
                        Subtract the even dynamic scans from the odd
                        dynamic scans.
sub_first_dyn           Subtract the first dynamic spectrum from a
                        dynamic series.
sub_mean_dyns           Subtract the mean dynamic spectrum from a
                        dynamic series.
sub_median_dyns         Subtract the median dynamic spectrum from a
                        dynamic series.
sub_odd_from_even_dyns
                        Subtract the odd dynamic scans from the even
                        dynamic scans.
subtract_rest_task      Subtract mean rest spectrum from mean task
                        spectrum after applying optimal linebroadening
                        to the mean task spectrum. Usually used to
                        correct for the BOLD lineshape narrowing effect
                        in 1H fMRS data.
sum_coils               Calculate the sum across receiver coil
                        elements.
sum_dyns                Calculate the sum of data dynamics.
sum_mrs                 Sum two mrs_data objects.
sum_mrs_list            Return the sum of a list of mrs_data objects.
sv_res_table            Output a table of fit amplitudes and error
                        estimates for a single-voxel fit.
svs_1h_brain_analysis   Standard SVS 1H brain analysis pipeline.
svs_1h_brain_analysis_dev
                        Standard SVS 1H brain analysis pipeline.
svs_1h_brain_batch_analysis
                        Batch interface to the standard SVS 1H brain
                        analysis pipeline.
t_test_spec             Perform a t-test on spectral data points.
td2fd                   Transform time-domain data to the
                        frequency-domain.
td_conv_filt            Time-domain convolution based filter.
tdsr                    Time-domain spectral registration.
te                      Return the echo time of an MRS dataset.
tr                      Return the repetition time of an MRS dataset.
trim_paths              Trim a vector of filesystem paths.
varpro_3_para_opts      Return a list of options for VARPRO based
                        fitting with 3 free parameters.
varpro_basic_opts       Return a list of options for a basic VARPRO
                        analysis.
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_niidir      Write a basis object to folder containing one
                        NIfTI MRS file for each basis element.
write_basis_tqn         Generate a basis file using TARQUIN.
write_mrs               Write MRS data object to file.
write_mrs_nifti         Write MRS data object to file in NIFTI format.
write_pulse_ascii       Write an ASCII formatted pulse file.
zero_fade_spec          Fade a spectrum to zero by frequency domain
                        multiplication with a tanh function. Note this
                        operation distorts data points at the end of
                        the FID.
zero_higher_orders      Zero all coherences including and above a given
                        order.
zero_td_pts_end         Set 'mrs_data' object data points at the end of
                        the FID to zero.
zf                      Zero-fill MRS data in the time domain.
zf_xy                   Zero-fill MRSI data in the k-space x-y
                        direction.
