A B C D E F G H I L M N P R S T V W Z
spant-package | spant: spectroscopy analysis tools. |
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_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_peak_info | Search for the highest peak in a spectral region and return the frequency, height and FWHM. |
calc_sd_poly | Perform a polynomial fit, subtract and return the standard deviation of the residuals. |
calc_spec_snr | Calculate the spectral SNR. |
check_lcm | Check LCModel can be run |
check_tqn | Check the TARQUIN binary can be run |
combine_metab_ref | Combine a reference and metabolite mrs_data object. |
comb_coils | Combine coil data based on the first data point of a reference signal. |
conj | Conjugate MRS data. |
crop_spec | Crop 'mrs_data' object based on a frequency range. |
def_acq_paras | Return 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. |
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. |
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. |
get_1h_brain_basis_paras | 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_fit_map | Get a data array from a fit result |
get_fp | Return the first time-domain data point. |
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_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. |
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...). |
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. |
lw2beta | Covert a linewidth in Hz to an equivalent beta value in the time-domain ie: x * exp(-i * 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. |
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. |
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. |
mvfftshift | Perform a fftshift on a matrix, with each column replaced by its shifted result. |
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. |
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. |
press_ideal | PRESS sequence with ideal pulses. |
print.fit_result | Print a summary of an object of class 'fit_result'. |
print.mrs_data | Print a summary of mrs_data parameters. |
pulse_acquire | Simple pulse and acquire sequence with ideal pulses. |
pulse_acquire_31p | Simple pulse and acquire sequence with ideal pulses. |
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_dyn | Replicate a scan in the dynamic 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. |
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_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_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_echo_ideal | Spin echo sequence with ideal pulses. |
spin_echo_ideal_31p | Spin echo sequence with ideal pulses. |
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. |
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. |
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. |
zf | Zero-fill MRS data in the time domain. |
zf_xy | Zero-fill MRSI data in the k-space x-y direction. |