Hi Jeremy,
When you are running flame1, zflame1lowerfstatX is an irrelevance, it
only gets used (along with zflame1upperfstatX) when flame1+2 is being
used (to determine which voxels are near threshold following flame1,
and for which we therefore want to run flame2). We recommend though
that people just stick to using flame1.
However, that still leaves the question as to why the zfstatX output
is different to your ftoz call.
Not immediately clear what is going on here. One problem is that I
could not see the attached images with enough resolution to make out
exactly what was going on - so please could you resend those. Plus,
are you just running flame1?
Cheers, Mark.
On 7 Apr 2010, at 16:54, Reynolds, Jeremy wrote:
> Hello all,
>
> I am having some difficulty understanding the relationship between
> the fstatX and zfstatX (and zflame1lowerfstatX) files produced by
> flameo (running flame1), and I was wondering if someone could help
> me out.
>
> After looking at the source of flameo and gsmanager.cc, I can see
> that zfstatX is the same as zflame1lowerfstatX, which is consistent
> with my results. What confuses me, though, is that these 2 files are
> not the same as if I performed:
>
> ftoz -zout zfstatX_f2zredo fstatX fdof1_fX fdof2_fX
>
> despite the fact that my look at the source code seemed to indicate
> that the z statistic should be created with very similar internal
> calls across ftoz and flameo (in Gsmanager::f_ols_contrast within
> flameo). Because the z-converted files are not the same, I'm not
> sure which file I should trust to use for inference. The fstat file
> (and the zfstat file produced by an explicit call to ftoz) looks
> like what I would expect, in that the image histogram looks
> continuous, and the spatial distribution of those statistics across
> the brain looks exactly like I would expect. The zfstat file
> produced directly by flameo looks like a thresholded image in which
> the absolute value of all voxels is greater than approximately 5.75.
> I have attached a picture of the three image histograms, with the
> fstat image on the left, the zfstat image produced by flameo in the
> middle, and the zfstat file produced by a call at the command line
> to ftoz.
>
> To help with interpretation, here is some more information regarding
> my design. In the first-level analysis, I am attempting to use FIR
> basis functions to estimate a timecourse in response to various
> stimulus conditions. I am using a set of 10 delta functions that
> span the 20 s following stimulus onset. I am then using a second-
> level model on the copes reflecting each of the delta functions,
> such that I have 10 copes for each of the 18 subjects (180 input
> files total). In the second-level model, I am using an intercept (1
> regressor) and dummy coded factors for subject (17 regressors, each
> corresponding to the presence of a different subject) and timepoint
> (9 regressors, each corresponding to the presence of a different
> time point). The f statistic of interest is the main effect of
> timepoint, which should have a first degree of freedom of 9, and a
> second degree of freedom of 153 (the fdof1_fX and fdof2_fX files do
> reflect this).
>
> Any help would be much appreciated. Thanks in advance.
>
>
> -Jeremy
>
> Jeremy Reynolds, Ph.D.
> Assistant Professor
> Department of Psychology,
> University of Denver
> 2155 S. Race St
> Denver, CO 80208
> Phone: 303.871.4622
> Fax: 303.871.4747
> [log in to unmask]
>
> <Screen shot 2010-04-06 at 10.36.31 AM.png>
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