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biac:courses:level3

Setting up a 3rd level analysis

For the purposes of your project, it is perfectly fine to present your results on a subject-by-subject basis. Therefore, you don't really need to do a 3rd-level (i.e., cross-subject level analysis). Nevertheless, some of you may want to try it (and have asked how to do it) and, frankly, it may bring out effects you weren't able to see at the subject level. The main thing to keep in mind is that your 3rd level analysis should be a fixed-effects analysis. I suspect you will all be able to justify this if you choose to do the 3rd level.

The quick and dirty "how to" in FEAT

The first thing to keep in mind about you third level analysis is that you will do one for every COPE (or contrast) you had at the lower level. So, if you had 6 contrasts at the first level, you should have 6 cope#.feat directories in your second level *.gfeat directory. If you want to see the group level effects for all of these COPEs, then you will do 6 third level analyses, and each one will use the cope image inside the stats directory of these cope#.feat directories (see below).

Once you open the FEAT GUI, the first thing you'll need to do is change the analysis type (in the upper left corner) to “Higher-level Analysis”, just as if you were doing a second level analysis.

Ignore the paths below. I edited a version I found for this description and I did not change the paths since they do not matter anyway.

Data tab

  1. Put a path in the “Output directory” e.g., /usr/local/sharity/var/mount/Goldman.Data/BIAC/Percept.02/Analysis/S-P.gfeat
    • this can be whatever you like, just make sure you can write to this directory
  2. for input type, change “Inputs are Lower level FEAT directories” to “Inputs are 3D cope images”
  3. enter number of subjects into “Number of inputs” – probably 2 for most of you
  4. now click “select cope images”
  5. in new window enter path to each subjects' cope image e.g.,

/usr/local/sharity/var/mount/Goldman.Data/BIAC/Percept.02/Data/FSL/32894/2ndLevel.gfeat/cope1.feat/stats/cope1.nii.gz

  • Note: If there is only one run of data for the subject, the path is:

/usr/local/sharity/var/mount/Goldman.Data/BIAC/Percept.02/Data/FSL/32845/run01.feat/stats/cope1.nii.gz

  • Also, if you wanted to run a 3rd level analysis looking only at data from a single run, your paths would look like this.
  • If these “one-run” solutions don't work, let me know. I've never ran across this situation and I'm not sure if it will work. If you only have one run for a particular condition, you may need to change the input type back to “Lower level FEAT directories”

Stats tab

  1. change the analysis type from “Mixed effects” to “Fixed effects”
  2. click “Full model setup”
  3. both columns for every input should have a “1” in it
  4. click “Done”
  5. If modeling with a covariate (which should always be de-meaned), enter “2” in “Number of EVs”
    • For EV2, enter demeaned scores for each subject in 3rd column.
    • But with two or three subjects, don't even bother with this. you should just have 1 EV


Now click “Go” and it should work. Repeat for your other COPES.

biac/courses/level3.txt · Last modified: 2014/08/04 16:03 (external edit)