GESeries.MRSISeries

GESeries.MRSISeries(DATA_FOLDER, SERIES_ID, load_processed_data=False)

A raw MRSI series: spectroscopic imaging spectra, fitting, and voxel maps.

Attributes¶

Name	Description
`RAW_exp`
`SNR_map`	The per-voxel SNR, computed from the FIDs via pyAMARES.fidSNR.
`avg_fid`	Average fid across voxels with SNR above threshold.
`default_SNR_mask`	The default SNR mask, computed with get_SNR_mask’s default threshold.
`dims`
`fids`	The FIDs, derived from the spectra via FFT.
`fids_flat`	The FIDs with the voxel dimensions stacked into a single voxel dim.
`fitted_metabolite_maps`
`goodness_of_fit_maps`
`npts`
`ppm`
`spec`
`spec_flat`	The spectra with the voxel dimensions stacked into a single voxel dim.
`voxel_size`	The in-plane voxel size (mm), derived from the field of view and matrix.

Name	Description
create_MRSI_affine	Return an affine matrix rescaled to the MRSI voxel size and offset.
create_MRSI_nii	Return the RAW magnitude image as a NiiBase, with the MRSI affine.
create_map_nii	Wrap a per-voxel map array as a NiiBase, with the MRSI affine.
fit_all_voxels	Fit all voxels above the SNR threshold with AMARES and store the maps.
fit_single_voxel	Fit the FID at voxel (x, y, slice) with AMARES.
get_SNR_mask	Return a boolean mask of voxels with SNR at or above threshold.
get_voxel_spectrum	Return the spectrum at voxel (x, y, slice).
load_processed_data	Load the most recent processed-data HDF5 file for this series.
save_processed_data	Save fitted maps, FIDs, and identifying attributes to an HDF5 file.
visualize_fitted_metabolite_map	Display the fitted metabolite map for metabolite_name.
visualize_fitted_values	Not yet implemented.
visualize_goodness_of_fit_map	Display the goodness-of-fit map for metric_name.

GESeries.MRSISeries.create_MRSI_affine()

Return an affine matrix rescaled to the MRSI voxel size and offset.

GESeries.MRSISeries.create_MRSI_nii()

Return the RAW magnitude image as a NiiBase, with the MRSI affine.

GESeries.MRSISeries.create_map_nii(map_data)

Wrap a per-voxel map array as a NiiBase, with the MRSI affine.

GESeries.MRSISeries.fit_all_voxels(
    init_params,
    batch_fitting_params=None,
    bad_fit_chisqr_threshold=-1.0,
    testing_mode=False,
)

Fit all voxels above the SNR threshold with AMARES and store the maps.

Name	Type	Description	Default
init_params	dict	Initial fit parameters, merged with series-derived MHz/sw/deadtime.	required
batch_fitting_params	dict	Forwarded to `fitting.AMARES.fit_multiple_fids`.	`None`
bad_fit_chisqr_threshold	float	Chi-squared threshold above which a fit is flagged as bad. Defaults to -1.0 (disabled).	`-1.0`
testing_mode	bool	If True, limit fitting to the first 100 voxels above the SNR threshold.	`False`

Name	Type	Description
	numpy.ndarray	Flattened voxel indices of fits flagged as bad.

GESeries.MRSISeries.fit_single_voxel(x, y, slice, init_params, fit_params=None)

Fit the FID at voxel (x, y, slice) with AMARES.

GESeries.MRSISeries.get_SNR_mask(threshold=1.5)

Return a boolean mask of voxels with SNR at or above threshold.

GESeries.MRSISeries.get_voxel_spectrum(x, y, slice)

Return the spectrum at voxel (x, y, slice).

GESeries.MRSISeries.load_processed_data(output_folder=None, force_load=False)

Load the most recent processed-data HDF5 file for this series.

Name	Type	Description	Default
output_folder	Path	Directory to search in. Defaults to `OUTPUT_FOLDER / "processing_data"`.	`None`
force_load	bool	If True, load the data even if SERIES_ID, exam_number, or acquisition time do not match this series.	`False`

Name	Type	Description
	bool	True if data was loaded successfully, False otherwise.

GESeries.MRSISeries.save_processed_data(output_folder=None)

Save fitted maps, FIDs, and identifying attributes to an HDF5 file.

Name	Type	Description	Default
output_folder	Path	Directory to save into. Defaults to `OUTPUT_FOLDER / "processing_data"`.	`None`

Name	Type	Description
	Path	Path to the saved (or, if a file already exists, the existing) HDF5 file.

Name	Type	Description
	OSError	If the saved file fails the post-save integrity check.

GESeries.MRSISeries.visualize_fitted_metabolite_map(metabolite_name, **kwargs)

Display the fitted metabolite map for metabolite_name.

GESeries.MRSISeries.visualize_fitted_values()

Not yet implemented.

GESeries.MRSISeries.visualize_goodness_of_fit_map(metric_name, **kwargs)

Display the goodness-of-fit map for metric_name.