Hello all,
Apologies in advance if this is a duplicate question, but I could not find a similar question.
This is for a manuscript in which we report the results of an fMRI experiment. We wish to conform to the requests of a reviewer from the journal to whic the manuscript has been submitted.
Our experiment involved a single group of participants (N = 22), with only one scanning session ("run") per participant. During the run, the participants were presented with 80 stimuli. These stimuli were subdivided into 20 in each of the four conditions. The conditions were in a two-by-two design, two levels for each factor. This was of course coded into the first-level analysis that had four main EVs (not counting the ones not of interest):
EV1: A1B1; EV2: A1B2; EV3: A2B1; EV4: A2B2
The submitted draft included the results from the following six contrasts:
A1 - A2: [1 1 -1 -1]
A2 - A1: [-1 -1 1 1]
B1 - B2: [1 -1 1 -1]
B2 - B1: [-1 1 -1 1]
AXB: [1 -1 -1 1]
BXA: [-1 1 1 -1]
However, one of the reviewers asked for f-tests looking for:
Main effect of A
Main effect of B
Interaction between A and B
Which gives rise to the current question-- I do not know how to obtain these statistics. I tried two things. First, I ran f-tests in the first-level analysis:
F1: [1 0 0 0 0 0]
F2: [0 0 1 0 0 0]
F3: [0 0 0 0 1 0]
The corresponding f stats images were thereby generated, but these simply did not show up in a second-level analysis which took the feat directories as the input.
Then, I tried inputting fstatX.nii.gz images as the "cope image" inputs in three separate second-levels. This generated an error message:
$FSLDIR/bin/fsl_sub -T 60 -l logs -N feat2_pre $FSLDIR/bin/feat $OUTPUTDIR/design.fsf -D $OUTPUTDIR/fstat1.gfeat -gfeatprep
syntax error in expression "1 + fstat1": variable references require preceding $
while executing
"if { [ catch {
for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
switch -- [ lindex $argv $argindex ] {
-I {
incr argin..."
(file "$FSLDIR/bin/feat" line 119)
*** note: $FSLDIR and $OUTPUTDIR are my edits replacing the actual path names in the error message.
Which made me think: hmm, something is not right. I also consulted the FSL wiki, but as far as I understand, these only concern multiple runs within each subjects.
In summary, I want to know how to obtain group-level f-test statistics on a single group, single run, two-by-two factorial design. Additionally, I need to run TFCE on these statsitics, so I want to know how the GLM should be set.
Thank you for reading this long message.
Best,
Han-Gyol Yi