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. |
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. |
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. |
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. |
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. |
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. |
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. |
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. |
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. |