The Neurophysiological Biomarker Toolbox (NBT)


Table of Contents

Define Groups

Version: 2015

Approximate time of completing this tutorial: 15 minutes.

In the NBT, a group is a set of files, e.g., the recordings from one or more conditions. To be able to do group comparisons, we first need to select the recordings, the biomarkers and the channels/regions that we want to compare.

In this experiment there were two conditions, and so we want to be able to compare between them. It would also be useful to be able to compare all the recordings and their biomarkers to look for condition-invariant results (e.g., the full continuum of EEG and ARSQ biomarkers across multiple conditions).

Therefore, we define 3 groups ALL, ECR1, and HOR. First, however, we need to let NBT know where your analysis files are. Thus, change your current directory to the folder where you unzipped your demoset files to (hopefully, you just called the folder “demoSet”).

To define the groups, we need to open the statistics GUI:

  1. type NBT to open the nbt GUI
  2. select statistics GUI from Biomarker statistics|Statistics GUI

You should now see a GUI which looks like this.

Define Groups

  1. Select Define new Group(s) and enter 3 in the pop-up box.
  2. You will be prompted to select the parameter by which you want to define your groups: select Condition.
  3. We now want to define the 3 groups. The selection box allows you to filter the conditions you want to put into the group. For the first group we want the first eyes closed rest session, and so we select ECR1 under the condition menu, and call the group ECR1. For the second group we want the condition after they watched the horror movie, and so we select HOR from the condition menu and call the group HOR. For the final group we want all the recordings so we select both conditions and call the group ALL.

Select Biomarkers

As we want to be able to compare all of the biomarkers between the groups, select all in the panel Select Biomarker(s).

Select Channels and Regions

  1. Click on Select Channels and Regions.
  2. A window will pop up asking you to choose an info file that contains the channel information: select any info file in your folder and click on Open. Now you get the pop up window Select Channels and Regions . We want to be able to compare all of the channels and so select ALL under the channel list
  3. We also need to define which channels are used to make up the regions. It is possible for you to be able to define your own regions; however, for this task we will use the predefined ones.
  4. Select Load Regions
  5. The file browser should open up in the folder statistics GUI and will contain one file which you should select, default_regions129.mat
  6. Now click Submit Channels and/or Regions

You have now completed the loading of groups' biomarkers and channels and you are ready to start doing analysis. Go back to Analyzing neural correlates of cognition during rest and follow the rest of the tutorials.

tutorial/definegroups.txt · Last modified: 2015/06/08 23:01 by Klaus Linkenkaer-Hansen
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