I was trying to visualize the leads and also find VAT .I did all the steps you told i.e running ea_reslice_nii and then doing normalization using ANTs but the normalization does not work properly and shows this error in a pop up window ”antsApplyTransform.exe has stopped working”.
I was only able to visualize the leads in 3D using the non linear segment method but that too was not correct as the leads were horizontally placed instead of being vertical.
The mri images I used were already in .nii format but we only had a sagittal view for postoperative image and no transversal view.Could this be a problem?
I also have mri images in DICOM format but when I converted them into .nii using the toolbox they were also sagittal view so those also did not work as when I reached the reconstruction step it said mask out of bounds.
So, these are the problems I am facing.Your help will be really appreciated.