biac:fsl:class_secondlevel
Table of Contents
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
- 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.
- 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.
- Log into Golgi and cd into Huxley/data/Class.01/Examples/FSL_sample and type fsl & to bring up the GUI
- Click FEAT
Data Tab
- In the Data tab at the top click where it should say First Level Analysis and select Higher Level Analysis
- The uppermost button within the Data tab should read Inputs are Lower Level FEAT directories
- The number of analyses for should be 5, for all of the odd numbered runs (1,3,5,7,9}.
- 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.
- Once you have loaded all of the FEAT directories that you need click ok
- 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.
- Use lower level copes should appear and 1 should be selected (yellow)
Stats Tab
- 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.)
- Click Full Model setup and you should have a column named EV1 and it should have all 1's in the column
- Click Done
Saving
- Click save and type /mnt/huxley/data/Class.01/Students/yourfolder/secondlevel in the selection box.
- Then exit FSL by closing its window.
Running FSL for 2nd-level Analyses
- In the terminal window, change to the directory that contains your .fsf file. For example: cd ../../Students/yourfolder
- Then, start FSL normally.
- Load your .fsf file.
- Click Go, a FEAT Watcher window should pop up and let it run through
- Examples of what your FEAT report should look like can be found in Students/Example FSL/FSL/Block or Event.gfeat
- Click the internet explorer icon that says report and compare it to yours
- You don't need to do a third-level analysis because there is only one subject.
biac/fsl/class_secondlevel.txt · Last modified: 2024/06/21 15:44 by 127.0.0.1