The Neurophysiological Biomarker Toolbox (NBT)

Tutor guide to testing cleaning

Now that the students have cleaned their files, we want to see whether they made any common mistakes. To do this we compare their cleaned file to the same file that has been cleaned using automated methods (FASTER and ADJUST).

  1. For the test file that they clean during the tutorials you can find the automated info and analysis files in ../NBT/supportfunctions/CourseSpecific/HN13.S068.20130606.ECR_info.mat
  2. For the Course files you will need to download and unzip the Analysis files from blackboard. It would be useful if you carried these around on a memory stick.

The student should have three files on their computer. The analysis, the info, and the signal file.

To test their cleaning:

  1. run nbt_verify_cleaning; from the command line
  2. When prompted for the reference Signalinfo file, choose the appropriate automated info file (e.g. ../NBT/supportfunctions/CourseSpecific/HN13.S002.20130610.ECR_info.mat)
  3. When prompted for the Student Signalinfo file, choose the appropriate student info file (e.g. ..UserDirectory/HN13.S068.20130606.ECR_info.mat)

Once you have done this you will get some text information detailing how similar the files are, and a figure showing how similar the amplitude biomarkers are.

What to give feedback on:

  1. How much of the signal have they removed as artifact? (i.e. if they have cut away half of the signal then that is too much, and if none of the signal then they have likely missed some transient artifacts)
  2. How many channels have they set as bad? (If they have missed any, then they will show up clearly on the topoplots)
  3. Have they rereferenced the signal? (If this has not been done then you will see the topography centred around Cz)
  4. Have they performed ICA well? (This is harder to tell. The clearest things to see is if they have missed eye movements (seen by large delta in frontal regions), or removed too many signal containing alpha components (alpha reduced, and not as clear topography.)

Remember that it is possible that the students have cleaned the signal better than the automated methods, many students even manage this on their first go

If this has all been done well, then you should mark that file as cleaned on your checksheet (ask Klaus for this).

Common Errors and how to solve: (please update with problems you encounter)

  1. Problem: Students have called their saved info something other than CleanedSignal;
  2. Solution: Get them to reload and resave
tutorial/test_your_cleaning_tutors.txt · Last modified: 2017/06/08 11:15 by Mia Thomaidou
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