I am new to FSL and functional analysis and would like to see if Iím setting
up my analysis correctly in FEAT.  Briefly the experiment uses two different
paradigms - each of which are scanned during two separate sequences.  The
first sequence alternates between thinking and passive activities.  The
passive activity last 16 seconds and requires the subject to view 2 rows of
asterisks for 3 seconds, followed by a 7 second pause.  Then the word yes or
no appears and the subject clicks the correct hand clicker.  Next there is a
6 second pause then a thinking activity occurs. The subject is then given a
row of letters to memorize for 3 seconds.  This is followed by a 7 second
pause and then a single letter appears and the subject must click yes/no if
the letter was in the previous row of letters.  Then there is a 6 second
pause before a new set appears.

The second paradigm uses the same timing but a different task - this is a
separate scan.

When I use FEAT this is how I set up the analysis.

select analyze data
TR =2
High pass = 100
Volume = filled in automatically

slice timing correction = interleaved
nothing else changed

Full Model Set Up:
Number of original EVs = 1
Basic Shape = square
Skip = 0
Off = 16
On = 16
Phase = 0
Stop after = -1
Convolution = Gamma
Phase = 0
Stddev = 3
Mean lag = 6
Yes to temporal derivative
Yes to Apply temporal filtering
Contrasts = 1
F-tests = 0

I change nothing.  I use cluster thresholding, z=2.3 p=0.05

I do not use the initial structural image
For the main structural image I use a high res T1 after BET at 12 DOF.
The standard space is the default  MNI152 T1 2mm 12 DOF.

Then I hit go and after the analysis is done, I go under Utils in FEAT and
upsample+overlay using the FEAT directory that was created and I upsample to
standard with the background image as the main structural.

I do this the same for both paradigms that we scanned.

When I go into FSL Viewer I am getting some weird activation.  I tried to 
attach some pictures of what Iím seeing, but the files were too big, even
when I zipped them.  So I'll try to describe what I see in the viewer

After I open my background image and add the activation, the
contrast/brightness is already set and there is significant activation
outside of the brain.  I can manually adjust this, but I can never seem to
get the image the same as my rendered thresh image.

My questions are:
Am I setting up the analysis correctly in FEAT?

Under the model set up, would I create more EVs, contrasts, or F-test?

How do I correctly change the contrast and brightness to give me images that
are the same to the rendered thresh images?

Is there a way to see negative activation?  I am able to see this on the
Siemens scanner.  I would like to be able to measure both the positive and
negative activation.

Eric Zalusky