Module 1

Purpose: Label electrodes in CT scans using VoxTool, a graphical user interface application.

Description

In this module, electrode locations will be manually identified on a subject’s CT scan. Make sure your input patient data is organized according to the pseudo-BIDS structure outlined in Data Setup.

  • Inputs:

    • post-implant CT: ct/sub-XXXX_ses-YYYY_acq-3D_space-T01ct_ct.nii.gz

    • electrode labels

  • Output:

    • Electrode coordinates in CT space: ieeg/sub-XXXX_ses-YYYY_space-T01ct_ desc-vox_electrodes.txt

Setup & Run

If using the ieeg-recon App, select the VoxTool option at the bottom of the GUI. If running from the command line: In a terminal window, type the following to install voxtool

$ pip install voxtool

Run voxtool:

$ voxtool

Label Electrodes

Click on the image below for a voxTool video tutorial

Single contact selected

VoxTool GUI

  1. Click on Load Scan in the bottom left corner to load a subject’s CT file (anat/…acq-3D_space-T01ct_ct.nii.gz). If necessary, change the CT Threshold in the box at the top of the window, then press the Update button.

    Note

    If continuing a previous localization: load the existing coordinates from a JSON coordinate file using the Load Coordinates button.

  2. Press Define leads to set the names, shapes, types (e.g. Depth, Grid, Strip), and microcontacts for each implanted lead. Shapes are rows x columns. Press confirm on the dialog when complete.

  3. To label electrode contacts: select a lead in the Label dropdown menu in the upper left corner. Ensure that the contact number and X,Y position are consistent (e.g. for an 8x8 grid array, contact 9 corresponds to X=2, Y=1) .

  4. Click on the contact location in the CT. When it is highlighted, press Submit to mark its location. The electrode contact number and X, Y positions may automatically increment.

  5. Click on the next contact on the lead, then press Submit to mark its location

    • Alternatively, press the Seeding button to turn on seeding. VoxTool will attempt to extrapolate the locations of the remaing contacts as you select them, incrementing the contact number. Be sure to double-check that the results make sense, as occasionally two contacts will be given the same location

    • Alternatively, add the ends of a strip or depth or the corners of the grid with the Submit button, then press the Interpolate button. VoxTool will attempt to fill in the lead. It may not be completely successful. Pressing Interpolate again may interpolate additional contacts.

      Note

      The list of contact names is sorted by lead name, and within each lead by contact number. The Interpolate button does not always assign contact numbers in the expected order, so be sure to double-check that the numbers it has assigned are the ones that you want after using it.

  6. Press Add Micro-Contacts to add micro-contacts to any macro/micro leads.

  7. Press the Save as button to save the list of localized contacts. If the checkbox labelled Include Bipolar Pairs is checked, locations will also be saved for the midpoint of each pair of neighboring contacts.

    Save the electrode labels as a text file in the following location: BIDS/sub-<subjectID>/ses-<sessionName>/ieeg/ sub-<subjectID>_ses-<sessionName>_space-T01ct_desc-vox_electrodes.txt

Keyboard Shortcuts

Button

Key Sequence

Load Scan

Ctrl-O

Define Leads

Ctrl-D

Save As

Ctrl-S

Submit (contact panel)

S

Submit (lead definition window)

S

Delete (contact panel)

Delete

Delete (lead definition window)

Delete

Confirm (lead definition window)

Enter

Example

In this example, we label electrodes for subject RID0031 in the post-implant CT scan collected during their first clinical session.

  • Load CT scan from BIDS/sub-RID0031/ses-clinical01/ct/sub-RID0031_ses-clinical01_acq-3D_space-T01ct_ct.nii.gz

  • Define Leads:

    Define leads dialogue

    Define Leads Pop-Up Dialog

  • Label each electrode:

    • Choose contact in dropdown (LA1), click on the corresponding contact (pink highlight):

      Single contact selected

    • Choose final contact in electrode (LA10), set X:10, Y:1, click on contact in CT (blue highlight):

      Single contact selected

    • Click interpolate to label all contacts in the electrode:

      Single contact selected

  • Repeat above procedure until all electrodes are labeled.

  • Save to:

    BIDS/
    sub-RID0031/
    ses-clinical01/
    ieeg/
    sub-RID0031_ses-clinical01_space-T01ct_desc-vox_electrodes.txt
    SaveAs screen