SEPIA Output Files

Output files of Total field reconvery and phase unwrapping

Data	Description
<Prefix>_total-field.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>_noise-sd.nii.gz	Estimated standard deviation of noise in the phase data.
<Prefix>_phase.nii.gz	Wrapped phase data in radian (only if the input data contains voxel exceeds the range of [-pi,pi]).
<Prefix>_unwrapped-phase.nii.gz	Unwrapped phase data in radian (if selected).
<Prefix>_mask.nii.gz	Brain mask derived from brain extraction of FSL (if selected).
<Prefix>_mask-local_field.nii.gz	Signal mask for background field removal step (if voxel exclusion is selected with ‘Brain mask’ option).
<Prefix>_relative-residual.nii.gz	Relative residual derived using mono-exponential model with a single frequency shift (if voxel exclusion is selected).
<Prefix>_mask-reliable.nii.gz	Derived from thresholding relative-residual map using user-defined value.

Output files of Background field removal

Data	Description
<Prefix>_local-field.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>_QSM.nii.gz	Magnetic susceptibility map in ppm.
<Prefix>_mask_reference_region.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).