Files in spant

MR Spectroscopy Analysis Tools

NEWS.md R/mol_parameters.R R/fitting.R R/mrs_write_nifti.R R/fmrs.R R/fit_display.R R/pnnls.R R/precomp.R R/mrs_data_display.R R/varpro_3_para.R R/interactive_plotting.R R/data.R R/varpro_basic.R R/mrs_read_paravis.R R/rats.R R/mrs_read_pfile.R R/mrs_read_rda.R R/benchmark.R R/spant.R R/mrs_read_dicom.R R/mrs_read_list_data.R R/mrs_read_ima.R R/image_reg.R R/mrs_data_proc.R R/lofdc.R R/svs_batch_fit.R R/mrs_read_spar_sdat.R R/mrs_read_varian.R R/mrs_read_nifti.R R/varpro.R R/pulse_sequences.R R/pulse_shapes.R R/mrs_read_lcm_raw.R R/mrs_data_io.R R/tdsr.R R/mrs_read_twix.R R/dicom_reader.R R/qm_simulation.R R/amp_scaling.R R/relaxation_fitting.R R/mrs_read_jmrui_txt.R R/utils.R R/abfit.R R/basis_set.R R/gsl_functions.R inst/doc/spant-preprocessing.Rmd inst/doc/spant-basis-simulation.R inst/doc/spant-metabolite-simulation.Rmd inst/doc/spant-basis-simulation.Rmd inst/doc/abfit-baseline-opts.R inst/doc/spant-intro.R inst/doc/spant-intro.Rmd inst/doc/abfit-baseline-opts.Rmd inst/doc/spant-preprocessing.R inst/doc/spant-metabolite-simulation.R inst/reports/mpress_gaba.Rmd inst/rmd/dataset_summary_svs_qa.Rmd inst/rmd/single_scan_svs_qa.Rmd inst/rmd/spec_glm_results.Rmd tests/testthat.R tests/testthat/test_fitting.R tests/testthat/test_preproc.R tests/testthat/test_qm_sim.R tests/testthat/test_nifti.R vignettes/spant-preprocessing.Rmd vignettes/spant-metabolite-simulation.Rmd vignettes/spant-basis-simulation.Rmd vignettes/spant-intro.Rmd vignettes/abfit-baseline-opts.Rmd man/fd2td.Rd man/read_pulse_bruker.Rd man/scale_amp_molal.Rd man/auto_phase.Rd man/get_uncoupled_mol.Rd man/ortho3.Rd man/fit_t1_ti_array.Rd man/get_1h_brain_basis_paras_v3.Rd man/beta2lw.Rd man/sim_basis_1h_brain.Rd man/get_1h_brain_basis_paras_v1.Rd man/seq_pulse_acquire.Rd man/bc_poly.Rd man/plot.mrs_data.Rd man/sim_resonances.Rd man/mask_xy.Rd man/add_noise.Rd man/recon_imag_vec.Rd man/reslice_to_mrs.Rd man/write_mrs_nifti.Rd man/fp_scale.Rd man/print.fit_result.Rd man/read_mrs_tqn.Rd man/read_siemens_txt_hdr.Rd man/resample_basis.Rd man/def_nuc.Rd man/mean.list.Rd man/glm_spec_fmrs_fl.Rd man/bc_gauss.Rd man/preproc_svs.Rd man/mrs_data2bids.Rd man/calc_coil_noise_cor.Rd man/fd_conv_filt.Rd man/mvfftshift.Rd man/gen_F.Rd man/Conj.mrs_data.Rd man/comb_coils_mrsi_gls.Rd man/comb_coils.Rd man/Npts.Rd man/read_lcm_coord.Rd man/sim_basis.Rd man/Arg.mrs_data.Rd man/re_weighting.Rd man/reexports.Rd man/Re.mrs_data.Rd man/decimate_mrs_fd.Rd man/def_N.Rd man/sort_basis.Rd man/get_mol_paras.Rd man/dicom_reader.Rd man/get_metab.Rd man/get_basis_subset.Rd man/get_slice.Rd man/gen_impulse_reg.Rd man/hsvd_vec.Rd man/mean.mrs_data.Rd man/te.Rd man/ft_dyns.Rd man/basis2mrs_data.Rd man/get_guassian_pulse.Rd man/inv_even_dyns.Rd man/resample_voi.Rd man/sim_zero.Rd man/mean_dyns.Rd man/read_pulse_ascii.Rd man/scale_mrs_amp.Rd man/calc_design_efficiency.Rd man/recon_twix_2d_mrsi.Rd man/seq_steam_ideal.Rd man/tdsr.Rd man/calc_spec_snr.Rd man/glm_spec_fmrs_group.Rd man/ppm.Rd man/scale_amp_ratio.Rd man/glm_spec_group_linhyp.Rd man/find_bids_mrs.Rd man/fs.Rd man/plot_slice_map.Rd man/apply_axes.Rd man/comb_fit_tables.Rd man/acquire.Rd man/stackplot.fit_result.Rd man/zf_xy.Rd man/calc_basis_crlbs.Rd man/hsvd.Rd man/apodise_xy.Rd man/hsvd_filt.Rd man/fp_phase.Rd man/mean_dyn_pairs.Rd man/mask_xy_corners.Rd man/fit_t1_tr_array.Rd man/set_def_acq_paras.Rd man/max_mrs_interp.Rd man/mask_dyns.Rd man/set_precomp_verbose.Rd man/abfit_opts_v1_9_0.Rd man/diff_mrs.Rd man/ssp.Rd man/get_1h_brain_basis_names.Rd man/get_head_dyns.Rd man/sim_brain_1h.Rd man/get_mrsi_voxel_xy_psf.Rd man/fit_t2_te_array.Rd man/read_ima_dyn_dir.Rd man/ecc.Rd man/gausswin_2d.Rd man/sim_basis_1h_brain_press.Rd man/is_fd.Rd man/def_ref.Rd man/append_coils.Rd man/l2_reg.Rd man/sub_first_dyn.Rd man/qn_states.Rd man/gen_I.Rd man/hz.Rd man/back_extrap_ar.Rd man/coherence_filter.Rd man/get_acq_paras.Rd man/plot_slice_fit.Rd man/shift.Rd man/calc_sd_poly.Rd man/crop_td_pts.Rd man/get_voi_seg_psf.Rd man/write_pulse_ascii.Rd man/gen_conv_reg.Rd man/gen_F_xy.Rd man/lb.Rd man/seq_steam_ideal_cof.Rd man/tr.Rd man/set_Ntrans.Rd man/vec2mrs_data.Rd man/mrs_data2vec.Rd man/mask_fit_res.Rd man/scale_basis_amp.Rd man/svs_1h_brain_analysis.Rd man/gen_group_reg.Rd man/bin_spec.Rd man/plot_slice_fit_inter.Rd man/calc_peak_info_vec.Rd man/get_fit_map.Rd man/rep_mrs.Rd man/plot_voi_overlay_seg.Rd man/ift_shift_mat.Rd man/get_voi_cog.Rd man/lofdc.Rd man/get_voxel.Rd man/mvifftshift.Rd man/get_spin_num.Rd man/set_td_pts.Rd man/plot_bc.Rd man/gridplot.Rd man/scale_basis_from_singlet.Rd man/mrs_data2mat.Rd man/gen_poly_reg.Rd man/abfit_opts.Rd man/print.mrs_data.Rd man/align.Rd man/crop_td_pts_pot.Rd man/downsample_mrs_td.Rd man/varpro_3_para_opts.Rd man/calc_basis_corr_mat.Rd man/get_seg_ind.Rd man/conv_mrs.Rd man/mrs_data2spec_mat.Rd man/dyn_acq_times.Rd man/nifti_flip_lr.Rd man/get_mrsi_voxel.Rd man/sd.mrs_data.Rd man/rats.Rd man/matexp.Rd man/get_tqn_cmd.Rd man/write_basis.Rd man/scale_amp_ratio_value.Rd man/ift_shift.Rd man/set_ref.Rd man/td_conv_filt.Rd man/def_ft.Rd man/median_dyns.Rd man/sim_basis_tqn.Rd man/calc_coil_noise_sd.Rd man/gridplot.mrs_data.Rd man/set_tqn_cmd.Rd man/spant_abfit_benchmark.Rd man/zero_higher_orders.Rd man/plot_spec_sd.Rd man/mod_td.Rd man/crop_xy.Rd man/interleave_dyns.Rd man/gen_baseline_reg.Rd man/set_mask_xy_mat.Rd man/get_lcm_cmd.Rd man/reson_table2mrs_data.Rd man/crop_basis.Rd man/array2mrs_data.Rd man/plot_slice_map_inter.Rd man/downsample_mrs_fd.Rd man/inv_odd_dyns.Rd man/sum_mrs_list.Rd man/mrs_data2basis.Rd man/get_fp.Rd man/smooth_dyns.Rd man/rm_dyns.Rd man/phase.Rd man/one_page_pdf.Rd man/zero_fade_spec.Rd man/scale_spec.Rd man/find_mrs_files.Rd man/get_odd_dyns.Rd man/seq_press_ideal.Rd man/elliptical_mask.Rd man/bc_als.Rd man/Nspec.Rd man/ortho3_inter.Rd man/spant-package.Rd man/Ncoils.Rd man/comb_coils_svs_gls.Rd man/get_mrsi_voi.Rd man/bbase.Rd man/read_tqn_fit.Rd man/ft_shift_mat.Rd man/mean_vec_blocks.Rd man/is.def.Rd man/lw2beta.Rd man/comb_metab_ref.Rd man/Ny.Rd man/stackplot.mrs_data.Rd man/read_basis.Rd man/read_mrs.Rd man/read_ima_coil_dir.Rd man/spant_sim_fmrs_dataset.Rd man/sim_noise.Rd man/read_pulse_pta.Rd man/rep_array_dim.Rd man/Im.mrs_data.Rd man/seconds.Rd man/ft_shift.Rd man/get_subset.Rd man/sum_coils.Rd man/get_mrs_affine.Rd man/scale_amp_molal_pvc.Rd man/glm_spec.Rd man/mat2mrs_data.Rd man/get_ref.Rd man/write_mrs.Rd man/recon_imag.Rd man/comb_fit_list_result_tables.Rd man/mean_dyn_blocks.Rd man/svs_1h_brain_analysis_dev.Rd man/fit_mrs.Rd man/sum_mrs.Rd man/fit_diags.Rd man/max_mrs.Rd man/shift_basis.Rd man/basis2dyn_mrs_data.Rd man/spm_pve2categorical.Rd man/check_lcm.Rd man/set_lcm_cmd.Rd man/scale_amp_molar.Rd man/fit_amps.Rd man/Imzap.Rd man/sim_basis_mm_lip_lcm.Rd man/seq_slaser_ideal.Rd man/mean_mrs_list.Rd man/get_1h_brain_basis_paras_v2.Rd man/check_tqn.Rd man/fp_phase_correct.Rd man/scale_amp_molar2molal_pvc.Rd man/get_mol_names.Rd man/plot_voi_overlay.Rd man/get_2d_psf.Rd man/make_basis_from_raw.Rd man/mask_xy_ellipse.Rd man/sub_mean_dyns.Rd man/zf.Rd man/set_tr.Rd man/set_lw.Rd man/gen_trap_reg.Rd man/get_voi_seg.Rd man/apply_mrs.Rd man/get_td_amp.Rd man/sub_median_dyns.Rd man/seq_mega_press_ideal.Rd man/set_precomp_mode.Rd man/def_fs.Rd man/seq_steam_ideal_young.Rd man/mask_xy_mat.Rd man/kspace2img_xy.Rd man/get_sh_dyns.Rd man/Mod.mrs_data.Rd man/fit_res2csv.Rd man/Ntrans.Rd man/svs_1h_brain_batch_analysis.Rd man/get_dyns.Rd man/apply_pulse.Rd man/crop_spec.Rd man/preproc_svs_dataset.Rd man/circ_mask.Rd man/spant_mpress_drift.Rd man/write_basis_tqn.Rd man/add_noise_spec_snr.Rd man/bc_constant.Rd man/phase_ref_1h_brain.Rd man/sd.Rd man/bc_spline.Rd man/lw2alpha.Rd man/append_basis.Rd man/calc_ed_from_lambda.Rd man/crossprod_3d.Rd man/img2kspace_xy.Rd man/plot.fit_result.Rd man/spec_decomp.Rd man/spin_sys.Rd man/seq_cpmg_ideal.Rd man/precomp.Rd man/n2coord.Rd man/t_test_spec.Rd man/sim_mol.Rd man/varpro_opts.Rd man/deconv_mrs.Rd man/stackplot.Rd man/Nx.Rd man/zero_td_pts_end.Rd man/varpro_basic_opts.Rd man/collapse_to_dyns.Rd man/calc_spec_diff.Rd man/def_acq_paras.Rd man/get_mrsi2d_seg.Rd man/append_dyns.Rd man/seq_spin_echo_ideal.Rd man/image.mrs_data.Rd man/sum_dyns.Rd man/spant_simulation_benchmark.Rd man/rep_dyn.Rd man/pg_extrap_xy.Rd man/est_noise_sd.Rd man/get_svs_voi.Rd man/Ndyns.Rd man/Nz.Rd man/get_1h_brain_basis_paras.Rd man/resample_img.Rd man/scale_amp_water_ratio.Rd man/get_fh_dyns.Rd man/append_regs.Rd man/get_1h_braino_basis_names.Rd man/grid_shift_xy.Rd man/comb_fit_list_fit_tables.Rd man/fd_gauss_smo.Rd man/td2fd.Rd man/peak_info.Rd man/get_1h_spectre_basis_names.Rd man/gen_bold_reg.Rd man/rectangular_mask.Rd man/get_tail_dyns.Rd man/crop_td_pts_end.Rd man/read_tqn_result.Rd man/get_even_dyns.Rd man/int_spec.Rd man/decimate_mrs_td.Rd man/spec_op.Rd man/plot_reg.Rd man/sim_th_excit_profile.Rd man/seq_press_2d_shaped.Rd