This should be fine. When you're doing the second level to combine across
runs for a given subject, select "inputs are lower level FEAT directories"
so that it will grab all of your copes from the 1st level. If you do this,
your second level analysis will have outputs pertaining to cope1.feat
through cope4.feat. Then, once you do the group analysis at the 3rd level,
you can select "inputs are 3D cope images" -- for this, you would select the
cope images from the 2nd level of each subject (e.g.,
subject1.gfeat/cope1.feat/stats/cope1.nii.gz).
David
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Melissa Farmer
Sent: Sunday, July 26, 2009 12:50 PM
To: [log in to unmask]
Subject: [FSL] can't find the lower level copes I need
My question has to do with feeding lower level copes to higher level
analyses. I have
checked through the archives and thought I found my answer, but I can't see
how my
existing cope files allow me to do what I want to do.
At first level, each subject has multiple files that are fed into a second
level:
Grp EV1 EV2
"A" "B"
Input 1 1 1 0
Input 2 1 1 0
Input 3 2 0 1
and 4 contrasts are formed:
EV1 EV2
A 1 0
-A -1 0
A-B 1 -1
B-A -1 1
I want to feed the mean A contrast and the A-B contrasts up to separate
higher level
analyses. My assumption was that each of these contrasts should form a
cope.feat file,
so if I want to group multiple subjects on the first contrast (mean of A), I
select
cope1.feat files for the input at higher levels (and cope3.feat for the A-B
contrast).
However, the above design only has 2 copes in its output (within each cope
in the stats
subfolder, I do see cope1.nii.gz, cope2.nii.gz, etc), so it doesn't seem
like I can feed each
of the 4 contrasts up to higher levels. Previous archive posts indicate that
feat files (not
.nii.gz files) are to be fed into 2nd and higher levels.
Can you please offer some direction as to what I'm missing here?
Thanks,
Melissa
