Reconstruction File

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The data is stored

• for BIDS version, under: derivatives/leaddbs/patientID/reconstructions/sub-patientID_desc-reconstruction.mat

• for classic version under the ea_reconstruction.mat file inside the patient directory.

There is a single variable reco.

reco.native stores reconstruction in native postoperative space, reco.scrf is after subcortical refine (brainshift correction - if it was applied) and reco.mni stores the reconstruction in the mni space.

reco.native.coords stores the coordinates for electrode contacts. For instance, reco.native.coords_mm{2}(3,:) is the left ({2}) third lowest ((3,:)) contact coordinates in x, y, z in native postoperative space.

The indexing of the contacts usually follow the same order as defined by lead manufacture, starting from the bottom. For segmented contacts, different manufacturers may have different order definition. For example, at level 2 of the directed electrode from Boston Scientific(Fig. 1), the order is 2 -> 3 -> 4 (counter-clock wise seen from top). But for Abbott, it’s 1A -> 1B -> 1C (clock wise seen from top)(Fig.2)

Figure 1: order of directed electrodes from Boston scientific.

Fig 2: Abbott directional lead organization.