fsl.wrappers.fsl_mrs

This module provides wrapper functions for FSL-MRS command line tools.

fsl_mrs	Wrapper for the fsl_mrs command.
fsl_mrsi	Wrapper for the fsl_mrsi command.
fsl_mrs_preproc	Wrapper for the fsl_mrs_preproc command.
fsl_mrs_preproc_edit	Wrapper for the fsl_mrs_preproc_edit command.
svs_segment	Wrapper for the svs_segment command.
mrsi_segment	Wrapper for the mrsi_segment command.
fsl_dynmrs	Wrapper for the fsl_dynmrs command.
basis2spec	Wrapper for the basis2spec command.
fmrs_stats	Wrapper for the fmrs_stats command.

fsl.wrappers.fsl_mrs.fsl_mrs(data, basis, output, **kwargs)

Wrapper for the fsl_mrs command. The following arguments are currently supported: algo, ignore, keep, combine, ppmlim, h2o, baseline, baseline_order, metab_groups, lorentzian, free_shift, ind_scale, disable_MH_priors, mh_samples, t1, TE, TR, tissue_frac, t1_values, t2_values, internal_ref, wref_metabolite, ref_protons, ref_int_limits, h2o_scale, report, verbose, overwrite, conj_fid, no_conj_fid, conj_basis, no_conj_basis, no_rescale, export_baseline, export_no_baseline, export_separate, f/filename, config.

fsl.wrappers.fsl_mrs.fsl_mrsi(data, basis, output, **kwargs)

Wrapper for the fsl_mrsi command. The following arguments are currently supported: mask, algo, ignore, keep, combine, ppmlim, h2o, baseline, baseline_order, metab_groups, lorentzian, free_shift, ind_scale, disable_MH_priors, TE, TR, tissue_frac, internal_ref, wref_metabolite, ref_protons, ref_int_limits, h2o_scale, report, output_correlations, verbose, overwrite, single_proc, parallel, parallel_workers, parallel-batch-size-multiple, minimize-maxfun, slow-fit-log-threshold, slow-fit-log, slow-fit-worker-log-lines, conj_fid, no_conj_fid, conj_basis, no_conj_basis, no_rescale, config.

fsl.wrappers.fsl_mrs.fsl_mrs_preproc(data, reference, output, **kwargs)

Wrapper for the fsl_mrs_preproc command. The following arguments are currently supported: quant, ecc, noise, target, fmrs, noremoval, noaverage, noalign, align_limits, align_window, remove_water, hlsvd, truncate_fid, leftshift, t1, verbose, conjugate, overwrite, report, config.

fsl.wrappers.fsl_mrs.fsl_mrs_preproc_edit(data, reference, output, **kwargs)

Wrapper for the fsl_mrs_preproc_edit command. The following arguments are currently supported: quant, ecc, noise, noaverage, noalign, align_ppm_dynamic, align_window_dynamic, align_ppm_edit, dynamic_align, dynamic_align_edit, remove_water, hlsvd, truncate_fid, leftshift, t1, verbose, conjugate, overwrite, report, config.

fsl.wrappers.fsl_mrs.svs_segment(svs, **kwargs)

Wrapper for the svs_segment command. The following arguments are currently supported: t/t1, a/anat, o/output, f/filename, m/mask_only, no_normalisation.

fsl.wrappers.fsl_mrs.mrsi_segment(mrsi, **kwargs)

Wrapper for the mrsi_segment command. The following arguments are currently supported: t/t1, a/anat, o/output, f/filename, no_normalisation.

fsl.wrappers.fsl_mrs.fsl_dynmrs(data, basis, output, dyn_config, time_variables, **kwargs)

Wrapper for the fsl_dynmrs command. The following arguments are currently supported: ppmlim, baseline, baseline_order, metab_groups, lorentzian, free_shift, inversion_model, t1, report, verbose, overwrite, parallel, parallel_workers, no_rescale, save_fit, full_save, mean_mrsi, spatial_mask, spatial_index.

fsl.wrappers.fsl_mrs.basis2spec(basis, reference, output, **kwargs)

Wrapper for the basis2spec command. The following arguments are currently supported: linewidth, ignore.

fsl.wrappers.fsl_mrs.fmrs_stats(data, output, **kwargs)

Wrapper for the fmrs_stats command. The following arguments are currently supported: combine, fl_contrasts, mean_contrasts, reference_contrast, hl_design, hl_contrasts, hl_covariance, hl_contrast_names, hl_ftests, runmode, report, verbose, overwrite, config.