One small thing to add as well - you should not use 12 DOF for the
main structural image (this controls the registration of the functional
to the structural image) since it is within-subject and so 6 DOF is
All the best,
On 10 Aug 2009, at 10:34, Mark Woolrich wrote:
> If you have not done so already, you will really benefit from going
> through the Feat practicals (http://www.fmrib.ox.ac.uk/fslcourse)
> You want to establish if your data is alright, if the pre-processing
> went alright, and if your EVs/model is set up alright.
> The EV you are using is a boxcar with period of 32 secs is quite
> crude - you may need to consider more subtle modelling using 3
> column format EVs (see the Feat prac)
> Also you can look at Melodic results to see if there is any
> plausible activation, what timings that activation might have, and
> if there are any nasty artefacts in the data.
> The best way to qualitatively assess the straightforward voxelwise
> GLM stats is to go into the stats directory inside the feat
> directory, and take a look at the zstat files in Fslview.
> To look for negative activations you need an extra contrast that is
> [-1] ; presumably the one you have at the moment is just .
> Cheers, Mark.
> Dr Mark Woolrich
> EPSRC Advanced Research Fellow University Research Lecturer
> Oxford University Centre for Functional MRI of the Brain (FMRIB),
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.
> Tel: (+44)1865-222782 Homepage: http://www.fmrib.ox.ac.uk/~woolrich
> On 10 Aug 2009, at 03:12, Eric Zalusky wrote:
>> 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
>> paradigms - each of which are scanned during two separate
>> sequences. The
>> first sequence alternates between thinking and passive activities.
>> 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
>> 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
>> 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
>> 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
>> 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-
>> 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