opmpolhemus

This package computes the three dimensional spatial location for the center of the sensor cell for all OPMs whose positions are measured by a polhemus device. This is a necessary step in solving the forward problem.

Test

test by running

python -m unittest test.test

from the root of this project folder, or run it as a module:

python -m opmpolhemus.sensors test/test_files/test01_raw.fif

Usage

Command line tool

To use this as a command line tool, first start a virtual environment with

python -m venv venv

and activate it with

source venv/bin/activate

Then, install the required packages with

pip install -r requirements.txt

python setup.py install

Now you can use this tool in the command line as:

python -m opmpolhemus.sensors $FILE_IN $FILE_OUT

where $FILE_IN is the input file in .fif or .txt format, and the $FILE_OUT is the full path to the output file where the array of sensor locations is written. For example:

python -m opmpolhemus.sensors test/test_files/test01_raw.fif out/test.txt

Library

Or, to use this as a library in your Python project, install with

python setup.py install

Then import as:

from opmpolhemus.sensors import sensors

The package does require: mne, numpy, scipy and matplotlib. The mne is required to accept fif files.

The function sensors accepts two required arguments: data, frame_style. The data should for now be a .txt file containing your measurements in matrix form (only opm measurements) or a .fif file containing the digitization. The frame_style should be either top or base (see below for more info on that).

Data

Both .fif files and .txt files are accepted as data. When input is a .txt, it is assumed the input is a matrix of the HPI measurements, but only the actual opm HPI measurements, so not including the fiducial points and the indicator points (typically 4 and 3 respectively). For a .fif file, nothing extra needs to be done as the parser will itself only select the actual HPI measurements.

Hardware

The OPM device is the QZFM Gen-2 produced by QuSpin. The dimensions that are listed here enter the code in constants.py.

For digitizing the points from which we compute the cell's locations, we use this device.

Currently, this cap is used. To digitize the location of the sensor, we tap specific points on or around the OPM. Currently, we accommodate two sets of specific points to tap, from which this program then computes the location of the sensor. Such a set of specific points will be called a frame, and the frames we allow for are dubbed: base and top, and are defined as follows:

frame: base

        <-------+  16.6 +------->

                 OxxxxxO
  ^     +---------xxxxx---------+
  |     |                       |
  +    O|                       |O
       xx                       xx
 12.4  xx         z=1.5         xx
       xx                       xx
  +    O|                       |O
  |     |                       |
  v     +---------xxxxx---------+
                 OxxxxxO

frame=base. Dimensions are in millimeters.

In this diagram, an x marks the location of the holder arms that are to encapsulate the OPM (see here). These arms extend outward in direction normal to the screen. The rectangle drawn by the - lines and the + on the corners is the base frame that sits close to the scalp and is the resting frame of the OPM. Finally, the eight O points are the reference points that we mark with the polhemus. With these measured points (N = 8 x # of OPMS in total for frame=top) as input in the form of an [N,3] array, the location of the sensor within the OPM is computed for every OPM. Because of the thickness of the base frame, the reference points O sit slightly higher (1.5mm) than the OPM bottom, as noted in the diagram.

frame: top

         <-------+  16.6 +------->

                   xxxxx
   ^     +---------xxxxx---------+
   |     |O                     O|
   +     |                       |
        xx                       xx
  12.4  xx         z=24.0        xx
        xx                       xx
   +     |                       |
   |     |O                     O|
   v     +---------xxxxx---------+
                   xxxxx

frame=top. Dimensions in millimeters.

For this frame style, we mark only the four top corners of the OPM, at the top face of the OPM at z=24mm. These are four points, obviously. As there is not real firm fixed base the polhemus style can rest on for this method, we advise to do this measurement twice, that is, to go clock-wise and perform a total of 8 measurements, tapping every corner twice. The program will recognize this and average over very nearby points (also for the case of accidental double-clicks).