Hi,
What randomise call are you using?
If you want the t-test outputs then you need to get rid of the --fonly option.
This should allow you to get 4 t-statistic outputs, although I cannot figure out how you got 4 f-statistic outputs.
Anyway, try again and see if this helps.
If not, let us know your exact randomise command line call.
All the best,
Mark
From: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> on behalf of Paul Macey <[log in to unmask]<mailto:[log in to unmask]>>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>>
Date: Friday, 6 November 2015 23:02
To: "[log in to unmask]<mailto:[log in to unmask]>" <[log in to unmask]<mailto:[log in to unmask]>>
Subject: Re: [FSL] Fwd: [FSL] FIRST beta values
I'd value feedback on this question of obtaining FIRST beta values, even if the answer is they can only be calculated outside of FSL.
Thanks!
Paul
On Thu, 22 Oct 2015 15:08:23 +0200, Rosalia Dacosta Aguayo <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Dear FSL experts,
I am very interested in knowing the answer to this question.
I would highly appreciate your help in this issue.
Kind regards,
Rosalia.
---------- Forwarded message ----------
From: Paul Macey <[log in to unmask]<mailto:[log in to unmask]>>
Date: 2015-10-20 18:00 GMT+02:00
Subject: [FSL] FIRST beta values
To: [log in to unmask]<mailto:[log in to unmask]>
I'm running a 4-variable analysis in FIRST (one group, three covariates),
and I have significant results with the F-test. I now want to see the
direction and size of the effects; in a typical model I would look at the
betas/model coefficients, but these are not available with the vertex
analysis. I see in the documentation (
http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIRST/UserGuide#randomise) the
recommended approach is to do a t-test, or look at the actual values with
the FSL timeseries tool (or by extracting the data).
The problem with the t-test is that I only get one result ("....tstat1")
even though I have 4 contrasts (see design.con below), and I get 4 F stats.
I'm not sure which contrast tstat1 refers to, and furthermore I'm not sure
how to translate the t statistic for this 4-variable model to an effect
size. For a t statistic from a 2-sample t test multiplying by std/sqrt(N)
would work - is it the same with a 4 variable model?
Similarly, the issue with extracting the individual values is that I while
I could look for group differences, I cannot account for the 3 other
variables in the model without running another analysis on the extract
values, which is possible but no ideal.
So my questions are:
- is it possible to obtain the betas?
if no,
- how can I obtain the t statistic maps for my 4 contrasts?
- is there a way to translate the t statistic in this 4-variable model to a
non-standardized effect size?
Any guidance appreciated!
-------------------
design.con
/ContrastName1 group mean
/ContrastName2 TIVvol mean
/ContrastName3 age mean
/ContrastName4 sex mean
/NumWaves 4
/NumContrasts 4
/PPheights 1.552420e+00 1.719039e+00 9.529518e+01
1.722726e+00
/RequiredEffect 0.673 0.673 0.560 0.417
/Matrix
1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00
0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00
0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00
