Hi!
I ran into a funny problem when calculating contrasts in Freesurfer 4.5.0.
Namely, the center of my cluster of significant voxels has a p-value
of -0.0, resulting in a funny whole where you would otherwise expect
to find the most significant voxel(s).
It seems that the p-value is too small. Is
Hi Doug,
I deleted all old analyses manually, switched to 5.1, redid
mkanalysis-sess, mkcontrast-sess, and selxavg3-sess, and still have
zeros in the most significant voxels.
If there was a bug fix in the meantime, could you please let me know
where to obtain it?
The version numbers are the follow
Oh, I did not realize this was an fsfast issue, I thought you were using
mri_glmfit. In that case, I'm not sure what could be causing the problem
since the p-values are being computed by matlab. How many runs do you
have? Is is a contrast that has a huge amount of power(eg, something vs
fixati
Hi Doug, hi Caspar,
which matlab version are you using? We had some issues in the past that some
matlab 2007 and 2009 statistics toolbox versions returned p values of 0, which
obviously will not work as overlay, since those typically assume a volume of:
-log10(p_value)
and on matlab 2007b (maci
Hi Doug and Sebastian,
thanks for your input. I think I can confirm that it is the problem
that Sebastian described. FS 5.1 uses betainc, which returns 0, even
in Matlab R2011b.
The workaround that Sebastian suggested works, with a slight modification.
In line 888 in fast_selxavg3.m currently reads
sorry, -log10(1) gives 0 of course.
caspar
2012/11/30 Caspar M. Schwiedrzik :
> Hi Doug and Sebastian,
> thanks for your input. I think I can confirm that it is the problem
> that Sebastian described. FS 5.1 uses betainc, which returns 0, even
> in Matlab R2011b.
> The workaround that Sebastian su
Hi Caspar,
On Nov 30, 2012, at 08:25 , Caspar M. Schwiedrzik wrote:
> Hi Doug and Sebastian,
> thanks for your input. I think I can confirm that it is the problem
> that Sebastian described. FS 5.1 uses betainc, which returns 0, even
> in Matlab R2011b.
> The workaround that Sebastian suggested
That should work. I just made a slightly different modification to the
code, which will be in 5.2
pmat = FTest(dof1, dof2, Fmat);
ind = find(rvarmat == 0); pmat(ind) = 1; % in case all time points
are same value
ind = find(pmat == 0);pmat(ind) = eps(0); % for REALLY sig voxels
Hi Caspar, I think I fixed this in later versions. If you upgrade, you
can run the stats from 5.1 with recons from 4.5 (just don't mix recons
from different versions).
doug
On 11/26/2012 01:15 PM, Caspar M. Schwiedrzik wrote:
> Hi!
> I ran into a funny problem when calculating contrasts in Frees
On 11/26/2012 02:12 PM, Caspar M. Schwiedrzik wrote:
> Hi Doug,
> I'll do that.
> Two quick follow-up questions regarding 5.1:
> - it seems that I cannot specify taumax anymore in mkanalysis-sess. Is
> there another argument that would allow me to set the autocorrelation?
What do you mean by "set
Hi Doug,
thanks for the input. What I meant is that in version 5.1,
mkanalysis-sess does not seem to recognize the -taumax flag to set the
maximum delay for the autocorrelation function.
Caspar
2012/11/26 Douglas N Greve :
>
>
> On 11/26/2012 02:12 PM, Caspar M. Schwiedrzik wrote:
>>
>> Hi Doug,
No, it does not. With version 5 I went to a simple AR1 model instead.
doug
On 11/26/12 10:34 PM, Caspar M. Schwiedrzik wrote:
> Hi Doug,
> thanks for the input. What I meant is that in version 5.1,
> mkanalysis-sess does not seem to recognize the -taumax flag to set the
> maximum delay for the a
Hi Doug,
I am afraid the p values are still too small in Free Surfer
Linux-centos4_x86_64-stable-pub-v5.1.0-full.
I redid
mkanalysis-sess
mkcontrast-sess
selxavg3-sess
in 5.1., it looks verz similar as in 4.5., including a whole of 0.0 in
the center of the cluster.
Any further advice?
Thanks,
Caspa
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