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).                                                                                   |
+---------------------------------------+----------------------------------------------------------------------------------------------------------+