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spant

Star Watch Copy Code

MR Spectroscopy Analysis Tools

View on CRAN: Click here

Download and install spant package within the R console
Install from CRAN:

 install.packages("spant")

Install from Github:

 library("remotes")

                        install_github("cran/spant")

Install by package version:

 library("remotes")

                        install_version("spant", "2.23.0")

Attach the package and use:

 library("spant")

Maintained by
Martin Wilson
[Scholar Profile | Author Map]

All associated links for this package

First Published: 2017-04-26

Latest Update: 2023-07-19

Description:

Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data. The package includes methods for spectral fitting: Wilson (2021) <doi:10.1002/mrm.28385> and spectral alignment: Wilson (2018) <doi:10.1002/mrm.27605>.

How to cite:

Martin Wilson (2017). spant: MR Spectroscopy Analysis Tools. R package version 2.23.0, https://cran.r-project.org/web/packages/spant. Accessed 07 Nov. 2024.

Previous versions and publish date:

0.1.0 (2017-04-26 19:20), 0.2.0 (2017-05-25 01:09), 0.3.0 (2017-06-20 10:39), 0.4.0 (2017-08-09 12:39), 0.5.0 (2017-10-10 15:22), 0.6.0 (2017-10-25 14:36), 0.7.0 (2018-01-31 12:08), 0.9.0 (2018-03-07 16:41), 0.10.0 (2018-06-25 18:05), 0.11.0 (2018-07-20 14:50), 0.12.0 (2018-11-05 17:10), 0.13.0 (2019-04-25 17:10), 0.14.0 (2019-05-28 17:30), 0.15.0 (2019-09-19 17:40), 0.16.0 (2019-10-30 12:20), 0.18.0 (2019-11-11 11:20), 0.19.0 (2019-12-06 17:30), 1.0.0 (2020-02-17 10:10), 1.1.0 (2020-03-01 13:50), 1.2.0 (2020-03-11 18:20), 1.2.1 (2020-03-15 23:00), 1.3.0 (2020-04-03 16:10), 1.4.0 (2020-04-20 22:40), 1.5.0 (2020-05-11 11:10), 1.6.0 (2020-06-05 17:40), 1.7.0 (2020-07-10 01:00), 1.8.0 (2020-11-18 08:50), 1.9.0 (2020-12-15 16:20), 1.10.0 (2021-01-06 03:40), 1.11.0 (2021-03-28 04:20), 1.12.0 (2021-05-05 11:20), 1.13.0 (2021-06-09 12:10), 1.14.0 (2021-07-23 11:20), 1.15.0 (2021-10-22 12:50), 1.16.0 (2021-11-18 12:00), 1.17.0 (2022-01-07 10:40), 1.18.0 (2022-02-08 15:00), 1.19.0 (2022-02-14 17:10), 1.20.0 (2022-03-30 15:10), 1.21.0 (2022-05-03 15:10), 1.22.0 (2022-05-27 14:40), 2.0.0 (2022-06-22 11:40), 2.1.0 (2022-07-21 15:10), 2.2.0 (2022-09-08 13:50), 2.3.0 (2022-10-12 11:50), 2.4.0 (2022-11-07 17:20), 2.5.0 (2022-12-06 18:00), 2.6.0 (2023-01-06 14:00), 2.7.0 (2023-01-28 10:40), 2.9.0 (2023-03-03 14:20), 2.10.0 (2023-03-20 14:20), 2.11.0 (2023-04-22 15:30), 2.12.0 (2023-05-22 14:00), 2.13.0 (2023-06-26 17:30), 2.14.0 (2023-07-19 16:00), 2.15.0 (2023-09-14 22:20), 2.16.0 (2023-10-23 17:50), 2.17.0 (2023-11-28 17:10), 2.18.0 (2024-02-23 15:00), 2.19.0 (2024-03-22 18:30), 2.20.0 (2024-05-01 16:52), 2.21.0 (2024-05-30 09:00), 2.22.0 (2024-07-11 14:00)

Other packages that cited spant R package

View spant citation profile

Other R packages that spant depends, imports, suggests or enhances

View spant dependency map

Complete documentation for spant

View documentation PDF

Functions, R codes and Examples using the spant R package

Some associated functions: Arg.mrs_data . Conj.mrs_data . Im.mrs_data . Imzap . Mod.mrs_data . Ncoils . Ndyns . Npts . Nspec . Ntrans . Nx . Ny . Nz . Re.mrs_data . abfit_opts . abfit_opts_v1_9_0 . acquire . add_noise . align . apodise_xy . append_basis . append_coils . append_dyns . apply_axes . apply_mrs . apply_pulse . array2mrs_data . auto_phase . back_extrap_ar . basis2mrs_data . bbase . bc_als . bc_constant . bc_gauss . bc_poly . bc_spline . beta2lw . bin_spec . calc_coil_noise_cor . calc_coil_noise_sd . calc_ed_from_lambda . calc_peak_info_vec . calc_sd_poly . calc_spec_diff . calc_spec_snr . check_lcm . check_tqn . circ_mask . coherence_filter . collapse_to_dyns . comb_coils . comb_fit_list_fit_tables . comb_fit_list_result_tables . comb_fit_tables . comb_metab_ref . conv_mrs . crop_basis . crop_spec . crop_td_pts . crop_td_pts_end . crop_td_pts_pot . crop_xy . crossprod_3d . decimate_mrs_fd . decimate_mrs_td . deconv_mrs . def_N . def_acq_paras . def_fs . def_ft . def_nuc . def_ref . dicom_reader . diff_mrs . downsample_mrs_fd . downsample_mrs_td . ecc . elliptical_mask . est_noise_sd . fd2td . fd_conv_filt . fd_gauss_smo . find_mrs_files . fit_amps . fit_diags . fit_mrs . fit_res2csv . fit_t1_ti_array . fit_t1_tr_array . fit_t2_te_array . fp_phase . fp_phase_correct . fp_scale . fs . ft_dyns . ft_shift . ft_shift_mat . gausswin_2d . gen_F . gen_F_xy . gen_I . get_1h_brain_basis_names . get_1h_brain_basis_paras . get_1h_brain_basis_paras_v1 . get_1h_brain_basis_paras_v2 . get_1h_brain_basis_paras_v3 . get_1h_braino_basis_names . get_1h_spectre_basis_names . get_2d_psf . get_acq_paras . get_basis_subset . get_dyns . get_even_dyns . get_fh_dyns . get_fit_map . get_fp . get_guassian_pulse . get_head_dyns . get_lcm_cmd . get_metab . get_mol_names . get_mol_paras . get_mrs_affine . get_mrsi2d_seg . get_mrsi_voi . get_mrsi_voxel . get_mrsi_voxel_xy_psf . get_odd_dyns . get_ref . get_seg_ind . get_sh_dyns . get_slice . get_spin_num . get_subset . get_svs_voi . get_tail_dyns . get_td_amp . get_tqn_cmd . get_uncoupled_mol . get_voi_cog . get_voi_seg . get_voi_seg_psf . get_voxel . grid_shift_xy . gridplot.mrs_data . gridplot . hsvd . hsvd_filt . hsvd_vec . hz . ift_shift . ift_shift_mat . image.mrs_data . img2kspace_xy . int_spec . interleave_dyns . inv_even_dyns . inv_odd_dyns . is.def . is_fd . kspace2img_xy . l2_reg . lb . lofdc . lw2alpha . lw2beta . make_basis_from_raw . mask_dyns . mask_fit_res . mask_xy . mask_xy_corners . mask_xy_ellipse . mask_xy_mat . mat2mrs_data . matexp . max_mrs . max_mrs_interp . mean.list . mean.mrs_data . mean_dyn_blocks . mean_dyn_pairs . mean_dyns . mean_mrs_list . mean_vec_blocks . median_dyns . mod_td . mrs_data2basis . mrs_data2mat . mrs_data2vec . mvfftshift . mvifftshift . n2coord . nifti_flip_lr . one_page_pdf . ortho3 . ortho3_inter . peak_info . pg_extrap_xy . phase . plot.fit_result . plot.mrs_data . plot_bc . plot_slice_fit . plot_slice_fit_inter . plot_slice_map . plot_slice_map_inter . plot_spec_sd . plot_voi_overlay . plot_voi_overlay_seg . ppm . precomp . print.fit_result . print.mrs_data . qn_states . rats . re_weighting . read_basis . read_ima_coil_dir . read_ima_dyn_dir . read_lcm_coord . read_mrs . read_mrs_tqn . read_pulse_ascii . read_pulse_bruker . read_pulse_pta . read_siemens_txt_hdr . read_tqn_fit . read_tqn_result . recon_imag . recon_imag_vec . recon_twix_2d_mrsi . rectangular_mask . reexports . rep_array_dim . rep_dyn . rep_mrs . resample_basis . resample_img . resample_voi . reslice_to_mrs . reson_table2mrs_data . rm_dyns . scale_amp_molal . scale_amp_molal_pvc . scale_amp_molar . scale_amp_molar2molal_pvc . scale_amp_ratio . scale_amp_ratio_value . scale_amp_water_ratio . scale_basis_amp . scale_basis_from_singlet . scale_mrs_amp . scale_spec . sd.mrs_data . sd . seconds . seq_cpmg_ideal . seq_mega_press_ideal . seq_press_2d_shaped . seq_press_ideal . seq_pulse_acquire . seq_slaser_ideal . seq_spin_echo_ideal . seq_steam_ideal . seq_steam_ideal_cof . seq_steam_ideal_young . set_Ntrans . set_def_acq_paras . set_lcm_cmd . set_lw . set_mask_xy_mat . set_precomp_mode . set_precomp_verbose . set_ref . set_td_pts . set_tqn_cmd . set_tr . shift . shift_basis . sim_basis . sim_basis_1h_brain . sim_basis_1h_brain_press . sim_basis_mm_lip_lcm . sim_basis_tqn . sim_brain_1h . sim_mol . sim_noise . sim_resonances . sim_th_excit_profile . sim_zero . smooth_dyns . sort_basis . spant-package . spant_abfit_benchmark . spant_mpress_drift . spant_simulation_benchmark . spec_decomp . spec_op . spin_sys . spm_pve2categorical . ssp . stackplot.fit_result . stackplot.mrs_data . stackplot . sub_first_dyn . sub_mean_dyns . sub_median_dyns . sum_coils . sum_dyns . sum_mrs . sum_mrs_list . svs_1h_brain_analysis . svs_1h_brain_analysis_dev . svs_1h_brain_batch_analysis . td2fd . td_conv_filt . tdsr . te . tr . varpro_3_para_opts . varpro_basic_opts . varpro_opts . vec2mrs_data . write_basis . write_basis_tqn . write_mrs . write_mrs_nifti . write_pulse_ascii . zero_fade_spec . zero_higher_orders . zero_td_pts_end . zf . zf_xy .
Some associated R codes: abfit.R . amp_scaling.R . basis_set.R . benchmark.R . data.R . dicom_reader.R . fit_display.R . fitting.R . gsl_functions.R . image_reg.R . interactive_plotting.R . lofdc.R . mol_parameters.R . mrs_data_display.R . mrs_data_io.R . mrs_data_proc.R . mrs_read_dicom.R . mrs_read_ima.R . mrs_read_jmrui_txt.R . mrs_read_lcm_raw.R . mrs_read_list_data.R . mrs_read_nifti.R . mrs_read_paravis.R . mrs_read_pfile.R . mrs_read_rda.R . mrs_read_spar_sdat.R . mrs_read_twix.R . mrs_read_varian.R . mrs_write_nifti.R . pnnls.R . precomp.R . pulse_sequences.R . pulse_shapes.R . qm_simulation.R . rats.R . relaxation_fitting.R . spant.R . svs_batch_fit.R . tdsr.R . utils.R . varpro.R . varpro_3_para.R . varpro_basic.R . Full spant package functions and examples

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