SEPIA Output Files

Output files of Total field reconvery and phase unwrapping

Data	Description
<Prefix>_fieldmap.nii.gz	Unwrapped total frequency shift map in Hz.
<Prefix>_weights.nii.gz	SNR-weighted image derived from standard deviation of noise in phase data.
<Prefix>_noisesd.nii.gz	Estimated standard deviation of noise in the phase data.
<Prefix>_part-phase_rad.nii.gz	Wrapped phase data in radian (only if the input data contains voxel exceeds the range of [-pi,pi]).
<Prefix>_part-phase_unwrapped.nii.gz	Unwrapped phase data in radian (if selected).
<Prefix>_part-phase_reverse.nii.gz	inverted phase data, = -(phase)
<Prefix>_part-phase_bipolarcorr.nii.gz	phase data corrected for bipolar readout gradient
<Prefix>_bipolar_phase.nii.gz	Estimated phase offset induced by bipolar gradient readout.
<Prefix>_mask_brain.nii.gz	Brain mask derived from brain extraction of FSL (if selected).
<Prefix>_mask_localfield.nii.gz	Signal mask for background field removal step (if voxel exclusion is selected with ‘Brain mask’ option).
<Prefix>_relativeresidual.nii.gz	Relative residual derived using mono-exponential model with a single frequency shift (if voxel exclusion is selected).
<Prefix>_relativeresidualweights.nii.gz	Weighting maps [0,1] derived from thresholding relative-residual map using user-defined value.
<Prefix>_mask_reliable.nii.gz	Derived from thresholding relative-residual map using user-defined value.

Output files of Background field removal

Data	Description
<Prefix>_localfield.nii.gz	Local (tissue) field map in Hz.
<Prefix>_mask_QSM.nii.gz	Signal mask for QSM step.

Output files of QSM dipole inversion

Data	Description
<Prefix>_Chimap.nii.gz	Magnetic susceptibility map in ppm.
<Prefix>_mask_referenceregion.nii.gz	Reference region used in QSM normalisation (if selected).

Other output files

Data	Description
sepia_config.m	Automatic generated script by the GUI of SEPIA containing all user specified parameters.
run_sepia.log	Event log file of the Matlab’s command window output.
run_sepia.error	Error message of SEPIA (if any).

Output files of SWI/SMWI

Data	Description
<Prefix>_swi-phase.nii.gz	High-pass filtered phase data.
<Prefix>_swi-positive.nii.gz	Positive susceptibility-weighted images (if selected).
<Prefix>_swi-mIP-positive.nii.gz	Positive susceptibility-weighted images with minimum intensity projection over user-defined field of view (if selected).
<Prefix>_swi-negative.nii.gz	Negative susceptibility-weighted images (if selected).
<Prefix>_swi-mIP-negative.nii.gz	Negative susceptibility-weighted images with minimum intensity projection over user-defined field of view (if selected).
<Prefix>_smwi-paramagnetic.nii.gz	Paramagnetic susceptibility map-weighted images (if selected).
<Prefix>_smwi-mIP-paramagnetic.nii.gz	Paramagnetic susceptibility map-weighted images with minimum intensity projection over user-defined field of view (if selected).
<Prefix>_smwi-diamagnetic.nii.gz	iamagnetic susceptibility map-weighted images (if selected).
<Prefix>_smwi-mIP-diamagnetic.nii.gz	Diamagnetic susceptibility map-weighted images with minimum intensity projection over user-defined field of view (if selected).