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The data you will use are 5 runs of a blocked-design motor squeezing task. They are available at \\huxley\data\Class.01\Examples\FSL_sample. We've already done the first-level analyses for you. You are going to do the second-level analyses.

Remember that you can look at last week's laboratory (i.e., first-level analyses) for general information about running FSL (e.g., accessing the server).

2nd-Level FEAT Analyses

FEAT is used to compare one subject's data across all runs

  1. Once the first-level analyses have been done for all of the Block runs (odd runs), we will combine all the Block data across runs to improve our statistical power.
  2. Go to Huxley/data/Class.01/Examples/FSL_sample and click through the run# folders to look at the report.html files that were created when you ran first level.
  3. Log into Golgi and cd into Huxley/data/Class.01/Examples/FSL_sample and type fsl & to bring up the GUI
  4. Click FEAT

Data Tab

  1. In the Data tab at the top click where it should say First Level Analysis and select Higher Level Analysis
  2. The uppermost button within the Data tab should read Inputs are Lower Level FEAT directories
  3. The number of analyses for should be 5, for all of the odd numbered runs (1,3,5,7,9}.
  4. Click Select FEAT directories, you should already be in the FSL_sample directory and click into the run# folders. Once you click into all the run# directories in the Select input data GUI you are done and click ok. Do this for all the runs that you are combining, 1,3,5,7,9.
  5. Once you have loaded all of the FEAT directories that you need click ok
  6. Under select output directory type /mnt/huxley/data/Class.01/Students/your folder that you created when you did firstlevel/secondlevel this should create a folder in your first folder titled secondlevel.gfeat when we are all done.
  7. Use lower level copes should appear and 1 should be selected (yellow)

Stats Tab

  1. In the Stats tab, use Fixed Effects. Note that the standard used to be Mixed effects; Fixed is now recommended. (Mixed is still recommended for across-subjects analyses.)
  2. Click Full Model setup and you should have a column named EV1 and it should have all 1's in the column
  3. Click Done


  1. Click save and type /mnt/huxley/data/Class.01/Students/yourfolder/secondlevel in the selection box.
  2. Then exit FSL by closing its window.

Running FSL for 2nd-level Analyses

  1. In the terminal window, change to the directory that contains your .fsf file. For example: cd ../../Students/yourfolder
  2. Then, start FSL normally.
  3. Load your .fsf file.
  4. Click Go, a FEAT Watcher window should pop up and let it run through
  5. Examples of what your FEAT report should look like can be found in Students/Example FSL/FSL/Block or Event.gfeat
  6. Click the internet explorer icon that says report and compare it to yours
  7. You don't need to do a third-level analysis because there is only one subject.
biac/fsl/class_secondlevel.txt · Last modified: 2023/02/23 18:43 (external edit)