Command line options

Option	Description
-dicomcheck	Import DICOM series
-coreg_checkbox	Run coregistration
-coregctmethod	CT to MRI coregistration method
-coregmrpopup	MRI to MRI coregistration method
-normalize_checkbox	Run normalization
-normmethod	Normalization method 1: SPM SHOOT 2: SPM Segment 3: SPM Dartel 4: three step affine 5: MaGeT Brain like segmentation 6: MaGet Brain like normalization 7: FSL FNIRT 8: Re-Apply 9: ANTs (default)
-scrf	Run Brain Shift Correction
-scrfmask	Brain Shift Correction method
-extractsurface	Run extract surface
-surcafemethod	Extract surface method
-doreconstruction_checkbox	Run pre-Recontruct algorithm
-reconmethod	pre-Recontruct method
-manualheight_checkbox	Manual localization of DBS electrodes
-render_checkbox	Open 3D viewer