voxtool 0.0.1

VoxTool: A tool for labeling intracranial electrodes on CT images

VoxTool 2.0

Setup

• Clone the repository from GitHub
• Create a Conda environment from the definition file

  conda env install -f conda_env.yml
  

  This creates an environment named vt in which to run voxTool.

Running

• Activate the conda environment:

  source activate vt
  

• Launch the program:

  python launch_pyloc.py
  

Usage

0. Load a CT file, adjusting the threshold as necessary. To adjust the threshold, change the number in the bar at the top of the window marked CT Threshold, then press the Update button next to it.
1. 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, and microcontacts for each implanted lead. Shapes are rows x columns.
3. Select the lead you wish to localize in the dropdown menu labeled Label in the upper left corner
4. Click on the CT to highlight the next contact on that 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.
5. Press Add Micro-Contacts to add micro-contacts to any macro/micro leads.
6. 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.

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

Other Notes

• 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.