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Nicolas Ignatescu edited this page Jul 12, 2017 · 8 revisions

How to use EIT to acquire images with EIT

Prerequisites :

First of all you will need the following repositories cloned to your computer from github (this will take a while). If you haven’t set up github yet you can follow the tutorial here.

The ScouseTom repository

git clone https://github.com/EIT-team/ScouseTom

The Load_data repository

git clone https://github.com/EIT-team/Load_data

The Reconstruction repository

git clone https://github.com/EIT-team/Reconstruction

The Neonate2016 repository

git clone https://github.com/EIT-team/Neonate2016

Make sure these folders are in a drive partition where the user has read/write permissions.

Make sure the folders and subfolders where the matlab functions are located are added to path otherwise the functions will not work

Install Biosemi software

To install the Biosemi software just go to this link download the actiview version compatible with your screen resolution and download the respective Labview runtime engine.

Install the Labview runtime engine first and then install Actiview.

Install Paraview software

To install Paraview software just go to this link choose your OS, click download and then install the program.

Step 1

Components:

  • Current Source
  • Biosemi + Biosemi DC battery
  • ScouseTom
  • Switch network
  • USB Link
  • PC
  • Tank Set up the components following this schematic:

Step 2

Matlab Set-up

  1. Run [ Ard ] = ScouseTom_Init( ArdComPortStr ).

Change the ArdComPortStr with the comport the Arduino is connected to.

For example:

[ Ard ] = ScouseTom_Init( ‘COM4’ )

You can find the com port in the device manager

Further info about how to find the COM port will be added later

  1. Run

    [ Ard,ExpSetup,OKFLAG ] = ScouseTom_SendSettings( Ard,ExpSetup)

Step 3

Data acquisition

Biosemi

  • Select A32 channels
  • Deselect checkboxes and filters
  • Start new file, name it and select a folder to save it, remember the folder because you will need it later

Matlab

  • Run

    [ Ard,ExpSetup ] = ScouseTom_Start( Ard,ExpSetup)

(note that you don’t need the NoPrompt argument found in the scrip file, thus you can delete it)

  • A prompt will appear select the yes option
  • Select the file you created with Biosemi
  • Another prompt will appear, don’t press anything go back to biosemi and click the Pause button witch will start the recording
  • Now go back to matlab, press ok to start the injection
  • After the injection finishes press stop to stop the recording and then you can start the data acquisition process again.

Step 4 Data Processing Matlab

  • Run [ BVstruc ] = ScouseTom_LoadBV( ); • Replace the varargin argument with empty brackets
  • Select one of the data files you recorded, you will have the same procedure with all of the data files you have recorded
  • The function will create a data file that will look like this Filename-BV.mat, we will use this files in the reconstruction phase
  • Make a new folder here Neonate2016\SerialInj\Recon ex Yourname_Recon
  • Find the recon_Hadi_Sim.m file in the Neonate2016 repository …Neonate2016\SerialInj\Recon\Hadi , rename the file and copy it to the folder you have just created.
  • Open the scrip file
  • On line 32 replace the string with the location of the baseline file
  • On line 33 replace the string with the location of the perturbation file
  • On line 136 replace the string with the name of the perturbation file
  • This scrip will create a .vtk file wich we will use in the Paraview program in order to visualise the data. Paraview
  • On the top left press the open button and select the .vtk file you have just created and click apply
  • In order to visualise the data better, multiply the value in the min box and insert it in to the max box • Optional:
  • You can adjust the opacity with this slider
  • You can change DATA to SOLIDCOLOR
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