Checking QSM result

Sometimes the values of QSM might be inverted (i.e. the positive susceptibility source appears in dark colour and negative susceptibility source appears in bright colour). This may be caused by how the phase data being read. To check if this is the case you could look into the QSM map. The deep gray matter structure should be appeared as bright (positive value) If it appears in the opposite way then you might check the 'Invert phase' option in the GUI to reserve the phase direction.