> 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

This page might be outdated. We continuously work on updating our documentation, thank you for your patience.

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><img src="https://652347722-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FaEKrtfptpsNlKGfPk7Bs%2Fuploads%2Fv0hdQn4dXkKYzgIMZ9Cv%2FBoston%20Scientific%20Vercise%20Directed.png?alt=media&amp;token=18d5c526-7d8b-4942-88c3-a62c37e0f7b1" alt=""><figcaption><p>Figure 1: order of directed electrodes from Boston scientific.</p></figcaption></figure>

![](https://652347722-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FaEKrtfptpsNlKGfPk7Bs%2Fuploads%2Fl2I7XEP6FJ1GR3A2WueW%2FSt.Jude%20Directed.png?alt=media\&token=b87b9420-5602-4c1a-a0cb-9c45f8bb032b)Fig 2: Abbott directional lead organization.