Man pages for spant
MR Spectroscopy Analysis Tools

abfit_optsReturn a list of options for an ABfit analysis.
acquireSimulate pulse sequence acquisition.
alignAlign spectra to a reference frequency using a convolution...
apodise_xyApodise MRSI data in the x-y direction with a k-space filter.
append_basisCombine a pair of basis set objects.
append_coilsAppend MRS data across the coil dimension, assumes they...
append_dynsAppend MRS data across the dynamic dimension, assumes they...
apply_axesApply a function over specified array axes.
apply_mrsApply a function across given dimensions of a MRS data...
apply_pvcConvert default LCM/TARQUIN concentration scaling to molal...
Arg.mrs_dataApply Arg operator to an MRS dataset.
array2mrs_dataConvert a 7 dimensional array in into a mrs_data object. The...
auto_phasePerform zeroth-order phase correction based on the...
back_extrap_arBack extrapolate time-domain data points using an...
basis2mrs_dataConvert a basis object to an mrs_data object - where basis...
bbaseGenerate a spline basis, slightly adapted from : "Splines,...
bc_alsBaseline correction using the ALS method.
bc_constantRemove a constant baseline offset based on a reference...
beta2lwCovert a beta value in the time-domain to an equivalent...
calc_coil_noise_corCalculate the noise correlation between coil elements.
calc_coil_noise_sdCalculate the noise standard deviation for each coil element.
calc_ed_from_lambdaCalculate the effective dimensions of a spline smoother from...
calc_peak_info_vecCalculate the FWHM of a peak from a vector of intensity...
calc_sd_polyPerform a polynomial fit, subtract and return the standard...
calc_spec_diffCalculate the sum of squares differences between two mrs_data...
calc_spec_snrCalculate the spectral SNR.
check_lcmCheck LCModel can be run
check_tqnCheck the TARQUIN binary can be run
circ_maskCreate a logical circular mask spanning the full extent of an...
collapse_to_dynsCollapse MRS data by concatenating spectra along the dynamic...
comb_coilsCombine coil data based on the first data point of a...
comb_csv_resultsCombine the results from multiple csv format files into a...
comb_fitsCombine a list of fit_result objects into a single fit object...
comb_metab_refCombine a reference and metabolite mrs_data object.
Conj.mrs_dataApply Conj operator to an MRS dataset.
conv_mrsConvolve two MRS data objects.
crop_specCrop 'mrs_data' object based on a frequency range.
crop_td_ptsCrop 'mrs_data' object data points in the time-domain.
crop_xyCrop an MRSI dataset in the x-y direction
crossprod_3dCompute the vector cross product between vectors x and y....
decimate_mrs_fdDecimate an MRS signal to half the original sampling...
decimate_mrs_tdDecimate an MRS signal by filtering in the time domain before...
def_acq_parasReturn (and optionally modify using the input arguments) a...
def_fsReturn the default sampling frequency in Hz.
def_ftReturn the default transmitter frequency in Hz.
def_NReturn the default number of data points in the spectral...
def_nucReturn the default nucleus.
def_refReturn the default reference value for ppm scale.
diff_mrsApply the diff operator to an MRS dataset in the FID/spectral...
downsample_mrs_fdDownsample an MRS signal by a factor of 2 using an FFT...
downsample_mrs_tdDownsample an MRS signal by a factor of 2 by removing every...
eccEddy current correction.
est_noise_sdEstimate the standard deviation of the noise from a segment...
fd2tdTransform frequency-domain data to the time-domain.
fd_conv_filtFrequency-domain convolution based filter.
fit_ampsExtract the fit amplitudes from an object of class...
fit_diagsCalculate diagnostic information for object of class...
fit_mrsPerform a fit based analysis of MRS data.
fit_res2csvWrite fit results table to a csv file.
fp_phaseReturn the phase of the first data point in the time-domain.
fp_phase_correctPerform a zeroth order phase correction based on the phase of...
fp_scaleScale the first time-domain data point in an mrs_data object.
fsReturn the sampling frequency in Hz of an MRS dataset.
ft_shiftPerform a fft and ffshift on a vector.
ft_shift_matPerform a fft and fftshift on a matrix with each column...
gen_FGenerate the F product operator.
gen_F_xyGenerate the Fxy product operator with a specified phase.
get_1h_brain_basis_parasReturn a list of 'mol_parameter' objects suitable for 1H...
get_1h_brain_basis_paras_v1Return a list of 'mol_parameter' objects suitable for 1H...
get_1h_brain_basis_paras_v2Return a list of 'mol_parameter' objects suitable for 1H...
get_1h_brain_basis_paras_v3Return a list of 'mol_parameter' objects suitable for 1H...
get_2d_psfGet the point spread function (PSF) for a 2D phase encoded...
get_acq_parasReturn acquisition parameters from a MRS data object.
get_dynsExtract a subset of dynamic scans.
get_even_dynsReturn even numbered dynamic scans starting from 1...
get_fh_dynsReturn the first half of a dynamic series.
get_fit_mapGet a data array from a fit result.
get_fit_tableCombine all fitting data points into a single dataframe.
get_fpReturn the first time-domain data point.
get_guassian_pulseGenerate a gaussian pulse shape.
get_metabExtract the metabolite component from an mrs_data object.
get_mol_namesReturn a character array of names that may be used with the...
get_mol_parasGet a 'mol_parameters' object for a named molecule.
get_mrsi2d_segCalculate the partial volume estimates for each voxel in a 2D...
get_mrsi_voiGenerate a MRSI VOI from an 'mrs_data' object.
get_mrsi_voxelGenerate a MRSI voxel from an 'mrs_data' object.
get_mrsi_voxel_xy_psfGenerate a MRSI voxel PSF from an 'mrs_data' object.
get_odd_dynsReturn odd numbered dynamic scans starting from 1 (1,3,5...).
get_refExtract the reference component from an mrs_data object.
get_seg_indGet the indices of data points lying between two values (end...
get_sh_dynsReturn the second half of a dynamic series.
get_sliceReturn a single slice from a larger MRSI dataset.
get_subsetExtract a subset of MRS data.
get_svs_voiGenerate a SVS acquisition volume from an 'mrs_data' object.
get_td_ampReturn an array of amplitudes derived from fitting the...
get_uncoupled_molGenerate a 'mol_parameters' object for a simple spin system...
get_voi_cogCalculate the centre of gravity for an image containing 0 and...
get_voi_segReturn the white matter, gray matter and CSF composition of a...
get_voi_seg_psfReturn the white matter, gray matter and CSF composition of a...
get_voxelReturn a single voxel from a larger mrs dataset.
gridplotArrange spectral plots in a grid.
gridplot.mrs_dataArrange spectral plots in a grid.
grid_shift_xyGrid shift MRSI data in the x/y dimension.
hsvdHSVD of an mrs_data object.
hsvd_filtHSVD based signal filter.
hsvd_vecHSVD of a complex vector.
hzReturn the frequency scale of an MRS dataset in Hz.
ift_shiftPerform an iffshift and ifft on a vector.
ift_shift_matPerform an ifft and ifftshift on a matrix with each column...
image.mrs_dataImage plot method for objects of class mrs_data.
img2kspace_xyTransform 2D MRSI data to k-space in the x-y direction.
Im.mrs_dataApply Im operator to an MRS dataset.
interleave_dynsInterleave the first and second half of a dynamic series.
int_specIntegrate a spectral region.
inv_even_dynsInvert even numbered dynamic scans starting from 1...
inv_odd_dynsInvert odd numbered dynamic scans starting from 1 (1,3,5...).
is_fdCheck if the chemical shift dimension of an MRS data object...
kspace2img_xyTransform 2D MRSI data from k-space to image space in the x-y...
l2_regPerform l2 regularisation artefact suppression.
lbApply line-broadening (apodisation) to MRS data or basis...
lw2alphaCovert a linewidth in Hz to an equivalent alpha value in the...
lw2betaCovert a linewidth in Hz to an equivalent beta value in the...
mask_dynsMask an MRS dataset in the dynamic dimension.
mask_xyMask an MRSI dataset in the x-y direction
mask_xy_matMask a 2D MRSI dataset in the x-y dimension.
mat2mrs_dataConvert a matrix (with spectral points in the column...
max_mrsApply the max operator to an MRS dataset.
max_mrs_interpApply the max operator to an interpolated MRS dataset.
mean_dyn_blocksCalculate the mean of adjacent dynamic scans.
mean_dyn_pairsCalculate the pairwise means across a dynamic data set.
mean_dynsCalculate the mean dynamic data.
mean.mrs_dataCalculate the mean spectrum from an mrs_data object.
median_dynsCalculate the median dynamic data.
Mod.mrs_dataApply Mod operator to an MRS dataset.
mrs_data2basisConvert an mrs_data object to basis object - where basis...
mrs_data2matConvert mrs_data object to a matrix, with spectral points in...
mrs_data2vecConvert mrs_data object to a vector.
mvfftshiftPerform a fftshift on a matrix, with each column replaced by...
mvifftshiftPerform an ifftshift on a matrix, with each column replaced...
n2coordPrint fit coordinates from a single index.
NcoilsReturn the total number of coil elements in an MRS dataset.
NdynsReturn the total number of dynamic scans in an MRS dataset.
nifti_flip_lrFlip the x data dimension order of a nifti image. This...
norm_mrsNormalise mrs_data to a spectral region.
NptsReturn the number of data points in an MRS dataset.
NspecReturn the total number of spectra in an MRS dataset.
NxReturn the total number of x locations in an MRS dataset.
NyReturn the total number of y locations in an MRS dataset.
NzReturn the total number of z locations in an MRS dataset.
ortho3Display an orthographic projection plot of a nifti object.
ortho3_intDisplay an interactive orthographic projection plot of a...
peak_infoSearch for the highest peak in a spectral region and return...
pg_extrap_xyPapoulis-Gerchberg (PG) algorithm method for k-space...
phaseApply phasing parameters to MRS data.
plot_bcConvenience function to plot a baseline estimate with the...
plot.fit_resultPlot the fitting results of an object of class 'fit_result'.
plot.mrs_dataPlotting method for objects of class mrs_data.
plot_slice_fitPlot a 2D slice from an MRSI fit result object.
plot_slice_fit_interPlot a 2D slice from an MRSI fit result object.
plot_slice_mapPlot a slice from a 7 dimensional array.
plot_slice_map_interPlot an interactive slice map from a data array where voxels...
plot_voi_overlayPlot a volume as an image overlay.
plot_voi_overlay_segPlot a volume as an overlay on a segmented brain volume.
ppmReturn the ppm scale of an MRS dataset or fit result.
precompSave function results to file and load on subsequent calls to...
print.fit_resultPrint a summary of an object of class 'fit_result'.
print.mrs_dataPrint a summary of mrs_data parameters.
qn_statesGet the quantum coherence matrix for a spin system.
ratsRobust Alignment to a Target Spectrum (RATS).
read_basisRead a basis file in LCModel .basis format.
read_ima_coil_dirRead a directory containing Siemens MRS IMA files and combine...
read_ima_dyn_dirRead a directory containing Siemens MRS IMA files and combine...
read_lcm_coordRead an LCModel formatted coord file containing fit...
read_mrsRead MRS data from a file.
read_mrs_dptRead MRS data stored in dangerplot (dpt) v3 format.
read_mrs_tqnRead MRS data using the TARQUIN software package.
read_siemens_txt_hdrRead the text format header found in Siemens IMA and TWIW...
read_tqn_fitReader for csv fit results generated by TARQUIN.
read_tqn_resultReader for csv results generated by TARQUIN.
reexportsObjects exported from other packages
Re.mrs_dataApply Re operator to an MRS dataset.
rep_array_dimRepeat an array over a given dimension.
rep_dynReplicate a scan in the dynamic dimension.
rep_mrsReplicate a scan over a given dimension.
resample_imgResample an image to match a target image space.
resample_voiResample a VOI to match a target image space using...
reslice_to_mrsReslice a nifti object to match the orientation of mrs data.
reson_table2mrs_dataGenerate mrs_data from a table of single Lorentzian...
re_weightingApply a weighting to the FID to enhance spectral resolution.
rm_dynsRemove a subset of dynamic scans.
scale_amp_molal_pvcApply partial volume correction to a fitting result object.
scale_amp_molarApply water reference scaling to a fitting results object to...
scale_amp_ratioScale fitted amplitudes to a ratio of signal amplitude.
scale_amp_water_ratioScale metabolite amplitudes as a ratio to the unsuppressed...
sdCalculate the standard deviation spectrum from an mrs_data...
sd.mrs_dataCalculate the standard deviation spectrum from an mrs_data...
secondsReturn a time scale vector to match the FID of an MRS data...
seq_cpmg_idealCPMG style sequence with ideal pulses.
seq_mega_press_idealMEGA-PRESS sequence with ideal localisation pulses and...
seq_press_idealPRESS sequence with ideal pulses.
seq_pulse_acquireSimple pulse and acquire sequence with ideal pulses.
seq_pulse_acquire_31pSimple pulse and acquire sequence with ideal pulses.
seq_slaser_idealsLASER sequence with ideal pulses.
seq_spin_echo_idealSpin echo sequence with ideal pulses.
seq_spin_echo_ideal_31pSpin echo sequence with ideal pulses.
seq_steam_idealSTEAM sequence with ideal pulses.
set_def_acq_parasSet the default acquisition parameters.
set_lcm_cmdSet the command to run the LCModel command-line program.
set_lwApply line-broadening to an mrs_data object to achieve a...
set_precomp_modeSet the precompute mode.
set_precomp_verboseSet the verbosity of the precompute function.
set_refSet the ppm reference value (eg ppm value at 0Hz).
set_td_ptsSet the number of time-domain data points, truncating or...
set_tqn_cmdSet the command to run the TARQUIN command-line program.
shiftApply a frequency shift to MRS data.
sim_basisSimulate a basis set object.
sim_basis_1h_brainSimulate a basis-set suitable for 1H brain MRS analysis...
sim_basis_1h_brain_pressSimulate a basis-set suitable for 1H brain MRS analysis...
sim_basis_tqnSimulate a basis file using TARQUIN.
sim_brain_1hSimulate MRS data with a similar appearance to normal brain...
sim_molSimulate a 'mol_parameter' object.
sim_noiseSimulate a time-domain mrs_data object containing simulated...
sim_resonancesSimulate a MRS data object containing a set of simulated...
spant_mpress_driftExample MEGA-PRESS data with significant B0 drift.
spant-packagespant: spectroscopy analysis tools.
spin_sysCreate a spin system object for pulse sequence simulation.
spm_pve2categoricalConvert SPM style segmentation files to a single categorical...
sspSignal space projection method for lipid suppression.
stackplotProduce a plot with multiple traces.
stackplot.fit_resultPlot the fitting results of an object of class 'fit_result'...
stackplot.mrs_dataStackplot plotting method for objects of class mrs_data.
sum_coilsCalculate the sum across receiver coil elements.
sum_dynsCalculate the sum of data dynamics.
td2fdTransform time-domain data to the frequency-domain.
td_conv_filtTime-domain convolution based filter.
tdsrTime-domain spectral registration.
varpro_3_para_optsReturn a list of options for VARPRO based fitting with 3 free...
varpro_optsReturn a list of options for VARPRO based fitting.
vec2mrs_dataConvert a vector into a mrs_data object.
write_basisWrite a basis object to an LCModel .basis formatted file.
write_basis_tqnGenerate a basis file using TARQUIN.
write_mrsWrite MRS data object to file.
write_mrs_niftiWrite MRS data object to file in NIFTI format.
zero_nzocZero all non-zero-order coherences.
zfZero-fill MRS data in the time domain.
zf_xyZero-fill MRSI data in the k-space x-y direction.
spant documentation built on Nov. 18, 2020, 9:07 a.m.