> For the complete documentation index, see [llms.txt](https://netstim.gitbook.io/leaddbs/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://netstim.gitbook.io/leaddbs/lead-dbs/step5-optional-reconstruction-of-electrode-trajectories/reconstruction-file.md).
# Reconstruction File
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.coord`s 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.
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