| 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... |
| acquire | Simulate pulse sequence acquisition. |
| add_noise | Add noise to an mrs_data object. |
| align | Align spectra to a reference frequency using a convolution... |
| 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... |
| append_dyns | Append MRS data across the dynamic dimension, assumes they... |
| apply_axes | Apply a function over specified array axes. |
| apply_mrs | Apply a function across given dimensions of a MRS data... |
| apply_pulse | Simulate an RF pulse on a single spin. |
| Arg.mrs_data | Apply Arg operator to an MRS dataset. |
| array2mrs_data | Convert a 7 dimensional array in into a mrs_data object. The... |
| auto_phase | Perform zeroth-order phase correction based on the... |
| back_extrap_ar | Back extrapolate time-domain data points using an... |
| basis2mrs_data | Convert a basis object to an mrs_data object - where basis... |
| bbase | Generate a spline basis, slightly adapted from : "Splines,... |
| bc_als | Baseline correction using the ALS method. |
| bc_constant | Remove a constant baseline offset based on a reference... |
| bc_gauss | Apply and subtract a Gaussian smoother in the spectral... |
| 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... |
| beta2lw | Covert a beta value in the time-domain to an equivalent... |
| bin_spec | Bin equally spaced spectral regions. |
| 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_ed_from_lambda | Calculate the effective dimensions of a spline smoother from... |
| calc_peak_info_vec | Calculate the FWHM of a peak from a vector of intensity... |
| calc_sd_poly | Perform a polynomial fit, subtract and return the standard... |
| calc_spec_diff | Calculate the sum of squares differences between two mrs_data... |
| 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... |
| coherence_filter | Zero all coherence orders other than the one supplied as an... |
| collapse_to_dyns | Collapse MRS data by concatenating spectra along the dynamic... |
| comb_coils | Combine coil data based on the first data point of a... |
| comb_fit_list_fit_tables | Combine all fitting data points from a list of fits into a... |
| 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. |
| Conj.mrs_data | Apply Conj operator to an MRS dataset. |
| 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... |
| crop_xy | Crop an MRSI dataset in the x-y direction |
| crossprod_3d | Compute the vector cross product between vectors x and y.... |
| decimate_mrs_fd | Decimate an MRS signal to half the original sampling... |
| decimate_mrs_td | Decimate an MRS signal by filtering in the time domain before... |
| deconv_mrs | Deconvolve two MRS data objects. |
| def_acq_paras | Return (and optionally modify using the input arguments) a... |
| 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... |
| 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... |
| downsample_mrs_fd | Downsample an MRS signal by a factor of 2 using an FFT... |
| downsample_mrs_td | Downsample an MRS signal by a factor of 2 by removing every... |
| ecc | Eddy current correction. |
| elliptical_mask | Create an elliptical mask stored as a matrix of logical... |
| est_noise_sd | Estimate the standard deviation of the noise from a segment... |
| 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_mrs_files | Find valid MRS data files recursively from a directory path. |
| fit_amps | Extract the fit amplitudes from an object of class... |
| fit_diags | Calculate diagnostic information for object of class... |
| fit_mrs | Perform a fit based analysis of MRS data. |
| fit_res2csv | Write fit results table to a csv file. |
| fit_t1_ti_array | Fit a T1 recovery curve, from multiple TIs, to a set of... |
| fit_t1_tr_array | Fit a T1 recovery curve, from multiple TRs, to a set of... |
| fit_t2_te_array | Fit a T2 relaxation curve, from multiple TEs, to a set of... |
| 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... |
| 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... |
| gausswin_2d | Create a two dimensional Gaussian window function stored as a... |
| 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. |
| get_1h_brain_basis_paras | Return a list of 'mol_parameter' objects suitable for 1H... |
| get_1h_brain_basis_paras_v1 | Return a list of 'mol_parameter' objects suitable for 1H... |
| get_1h_brain_basis_paras_v2 | Return a list of 'mol_parameter' objects suitable for 1H... |
| get_1h_brain_basis_paras_v3 | Return a list of 'mol_parameter' objects suitable for 1H... |
| get_2d_psf | Get the point spread function (PSF) for a 2D phase encoded... |
| 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... |
| 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_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 | 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... |
| 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... |
| get_sh_dyns | Return the second half of a dynamic series. |
| get_slice | Return a single slice from a larger MRSI dataset. |
| 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... |
| 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... |
| get_voi_cog | Calculate the centre of gravity for an image containing 0 and... |
| get_voi_seg | Return the white matter, gray matter and CSF composition of a... |
| get_voi_seg_psf | Return the white matter, gray matter and CSF composition of a... |
| get_voxel | Return a single voxel from a larger mrs dataset. |
| gridplot | Arrange spectral plots in a grid. |
| gridplot.mrs_data | Arrange spectral plots in a grid. |
| grid_shift_xy | Grid shift MRSI data in the x/y dimension. |
| 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... |
| 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. |
| Im.mrs_data | Apply Im operator to an MRS dataset. |
| Imzap | Complex rounding function taken from complexplus package to... |
| 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... |
| 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... |
| is_fd | Check if the chemical shift dimension of an MRS data object... |
| kspace2img_xy | Transform 2D MRSI data from k-space to image space in the x-y... |
| l2_reg | Perform l2 regularisation artefact suppression. |
| lb | Apply line-broadening (apodisation) to MRS data or basis... |
| lofdc | Correct linear frequency drift. |
| lw2alpha | Covert a linewidth in Hz to an equivalent alpha value in the... |
| lw2beta | Covert a linewidth in Hz to an equivalent beta value in the... |
| make_basis_from_raw | Make a basis-set object from a directory containing LCModel... |
| 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... |
| mask_xy_mat | Mask a 2D MRSI dataset in the x-y dimension. |
| mat2mrs_data | Convert a matrix (with spectral points in the column... |
| matexp | Matrix exponential function taken from complexplus package to... |
| 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. |
| mean.list | Calculate the mean spectrum from an mrs_data object. |
| mean.mrs_data | Calculate the mean spectrum from an mrs_data object. |
| 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.mrs_data | Apply Mod operator to an MRS dataset. |
| mod_td | Apply the Modulus operator to the time-domain MRS signal. |
| mrs_data2basis | Convert an mrs_data object to basis object - where basis... |
| mrs_data2mat | Convert mrs_data object to a matrix, with spectral points in... |
| mrs_data2vec | Convert mrs_data object to a vector. |
| mvfftshift | Perform a fftshift on a matrix, with each column replaced by... |
| mvifftshift | Perform an ifftshift on a matrix, with each column replaced... |
| n2coord | Print fit coordinates from a single index. |
| Ncoils | Return the total number of coil elements in an MRS dataset. |
| Ndyns | Return the total number of dynamic scans in an MRS dataset. |
| nifti_flip_lr | Flip the x data dimension order of a nifti image. This... |
| 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... |
| 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. |
| 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... |
| peak_info | Search for the highest peak in a spectral region and return... |
| pg_extrap_xy | Papoulis-Gerchberg (PG) algorithm method for k-space... |
| phase | Apply phasing parameters to MRS data. |
| plot_bc | Convenience function to plot a baseline estimate with the... |
| 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_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... |
| 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... |
| 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_ima_coil_dir | Read a directory containing Siemens MRS IMA files and combine... |
| read_ima_dyn_dir | Read a directory containing Siemens MRS IMA files and combine... |
| read_lcm_coord | Read an LCModel formatted coord file containing fit... |
| read_mrs | Read MRS data from a file. |
| read_mrs_tqn | Read MRS data using the TARQUIN software package. |
| read_pulse_bruker | Read a Bruker formatted pulse file |
| read_pulse_pta | Read a .pta formatted pulse file compatible with Siemens... |
| read_siemens_txt_hdr | Read the text format header found in Siemens IMA and TWIX... |
| 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... |
| recon_imag_vec | Reconstruct complex time-domain data from the real part of... |
| recon_twix_2d_mrsi | Reconstruct 2D MRSI data from a twix file loaded with... |
| rectangular_mask | Create a rectangular mask stored as a matrix of logical... |
| reexports | Objects exported from other packages |
| Re.mrs_data | Apply Re operator to an MRS dataset. |
| 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... |
| 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... |
| re_weighting | Apply a weighting to the FID to enhance spectral resolution. |
| rm_dyns | Remove a subset of dynamic scans. |
| scale_amp_molal | Apply water reference scaling to a fitting results object to... |
| scale_amp_molal_pvc | Apply water reference scaling to a fitting results object to... |
| scale_amp_molar | Apply water reference scaling to a fitting results object to... |
| scale_amp_molar2molal_pvc | Convert default LCM/TARQUIN concentration scaling to molal... |
| 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... |
| 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... |
| 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 | Calculate the standard deviation spectrum from an mrs_data... |
| sd.mrs_data | Calculate the standard deviation spectrum from an mrs_data... |
| seconds | Return a time scale vector to match the FID of an MRS data... |
| seq_cpmg_ideal | CPMG style sequence with ideal pulses. |
| seq_mega_press_ideal | MEGA-PRESS sequence with ideal localisation pulses and... |
| 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... |
| seq_steam_ideal_young | STEAM sequence with ideal pulses using the z-rotation... |
| 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... |
| set_mask_xy_mat | Set the masked voxels in a 2D MRSI dataset to given spectrum. |
| set_Ntrans | Set the number of transients for an mrs_data object. |
| 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... |
| 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_basis | Simulate a basis set object. |
| sim_basis_1h_brain | Simulate a basis-set suitable for 1H brain MRS analysis... |
| sim_basis_1h_brain_press | Simulate a basis-set suitable for 1H brain MRS analysis... |
| sim_basis_mm_lip_lcm | Simulate a macromolecular and lipid basis-set suitable for 1H... |
| sim_basis_tqn | Simulate a basis file using TARQUIN. |
| sim_brain_1h | Simulate MRS data with a similar appearance to normal brain... |
| sim_mol | Simulate a 'mol_parameter' object. |
| sim_noise | Simulate an mrs_data object containing simulated Gaussian... |
| sim_resonances | Simulate a MRS data object containing a set of simulated... |
| sim_th_excit_profile | Simulate an ideal pulse excitation profile by smoothing a... |
| sim_zero | Simulate an mrs_data object containing complex zero valued... |
| smooth_dyns | Smooth data across the dynamic dimension with a Gaussian... |
| sort_basis | Sort the basis-set elements alphabetically. |
| spant_abfit_benchmark | Simulate and fit some spectra with ABfit for benchmarking... |
| spant_mpress_drift | Example MEGA-PRESS data with significant B0 drift. |
| spant-package | spant: spectroscopy analysis tools. |
| spant_simulation_benchmark | Simulate a typical metabolite basis set for benchmarking.... |
| spec_decomp | Decompose an mrs_data object into white and gray matter... |
| 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... |
| 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'... |
| stackplot.mrs_data | Stackplot plotting method for objects of class mrs_data. |
| sub_first_dyn | Subtract the first dynamic spectrum from a dynamic series. |
| sub_mean_dyns | Subtract the mean dynamic spectrum from a dynamic series. |
| 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. |
| svs_1h_brain_analysis | Standard SVS 1H brain analysis pipeline. |
| svs_1h_brain_batch_analysis | Batch interface to the standard SVS 1H brain analysis... |
| td2fd | Transform time-domain data to the frequency-domain. |
| td_conv_filt | Time-domain convolution based filter. |
| tdsr | Time-domain spectral registration. |
| tr | Return the repetition time of an MRS dataset. |
| varpro_3_para_opts | Return a list of options for VARPRO based fitting with 3 free... |
| 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_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. |
| zero_fade_spec | Fade a spectrum to zero by frequency domain multiplication... |
| 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... |
| zf | Zero-fill MRS data in the time domain. |
| zf_xy | Zero-fill MRSI data in the k-space x-y direction. |
