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 fixation)? Does it happen in other subjects? One path to debugging is to run selxavg3-sess with -run-wise. This will create an analysis for each run separately. You can then see whether one run in particular is causing the problem. doug
On 11/27/2012 08:34 PM, Caspar M. Schwiedrzik wrote:
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, Caspar
2012/11/26 Douglas Greve greve@nmr.mgh.harvard.edu:
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 autocorrelation function. Caspar
2012/11/26 Douglas N Greve greve@nmr.mgh.harvard.edu:
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 the autocorrelation"? You can turn it off with -no-whiten.
- in a block design, would refeventduration be the block length or the
length of the individual events within a block?
The block length. This will not change the p-values, only percent signal change values (often not even looked at). doug
Thanks, Caspar
2012/11/26 Douglas N Grevegreve@nmr.mgh.harvard.edu:
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 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 there a workaround > available? > Thank you very much, > Caspar > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
>
Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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