The following is just a very quick primer on what to do to test out the LEAD-toolbox if you work with postoperative CT-scans. If you work with MR-images, check out a similar MR-primer here. There is a more detailed manual and some walkthrough videos available on this website, too.

  • To get started with a first patient you need to put the following into a folder:
    • anat.nii / anat_t1.nii / anat_pd.nii – A nifti-file of the preoperative MRI
      • anat.nii assumes T2 modality. If you have T1 only, please name it anat_t1.nii instead. For multimodal normalizations, you can add anat.nii, anat_t1.nii, anat_pd.nii and/or dti.nii+dti.bval+dti.bvec (will use FA). As a quick start and just to test out things, just use anat.nii for now (no matter which MR modality it is).
    • rpostop_ct.nii – A nifti-file of the postop CT that has been coregistered to the anat.nii (e.g. use 3D Slicer to do so). There is also limited support of coregistration within the toolbox itself. In case you want to try this, please name the raw postoperative CT file postop_ct.nii and run one of the coregistration methods to generate rpostop_ct.nii.
  • Then you can start LEAD-DBS by typing “lead dbs” in the MATLAB-prompt, check only the “Normalize” option and press “Run”, which will perform the selected normalization routine (there are several options in the toolbox, relying on SPM12 which needs to reside in your MATLAB-path).
  • By checking (only) the “Check Normalization” option in the “Normalize” panel and pressing “Run”, you can check the normalization results.
  • You can then reconstruct the lead trajectory by checking (only) the “Reconstruct” checkbox and pressing “Run”.
  • If all went well, you can review the lead and manually re-position the contacts by checking (only) the “Review Reconstruction” Box and pressing “Run”. Commands for repositioning the Contacts can be found inside the figure. Use arrow keys to move things around and press shift to increase the step size. Press plus and minus to increase the spacing between the contacts.
  • Finally, you can visualize your reconstruction either in 2D or 3D by checking (only) the “Write out 2D” or “Render 3D” option and pressing run. Select an atlas that suits your need. Installing different atlases is easy, for more info about that please consult the manual.
  • You can also simulate monopolar stimulations and get statistics / do fibertracking from the volume of activated tissue. All this happens from within the 3D viewer. Check out the manual and / or some walkthrough videos.