Patrick,
See below.
On Fri, Aug 17, 2012 at 9:55 AM, Patrick Ross
<[log in to unmask]> wrote:
> Hi,
>
>
>
> I’m using the peak_nii toolbox and can’t work out how to change the default
> corrected threshold of p<0.05?
Set mapparameters.threshc to a new number. This will compute the
corrected values for the new corrected p-value. It should be noted
that this does not change the thresholding of the data, but rather
allows the minimum cluster or minimum peak value to be determined. The
thresholding is actually based on the uncorrected value. To threshold
with the corrected threshold, you would need to rerun peak_nii with
the appropriate thresh or cluster values. For example, say you came up
with 100 voxels at p<0.001 to reach cluster FWE. Then you could rerun
peak_nii with 0.001 for the thresh and 100 as the cluster.
I can change the T statistic threshold ok,
> but is there a way to say run the program at an uncorrected p<0.001
> threshold?
Yes. mapparameters.thresh=0.001 (in this case you also need to specify
the degrees of freedom for the program to compute the t-statistic in
the actual image.
The manual says that the mapparameters.thresh input can be the
> T/F statistic, a p-value, or any other number, but entering 0.001 in here
> makes no difference to the default p<0.05 corrected threshold?
As stated above, and to be inserted into the new manual, the corrected
threshold only calculates the corrected values. Because of the
numerous ways to apply correction (cluster FWE, cluster FDR, voxel
FWE, voxel FDR, peak FDR/topological FDR), I have not implemented
automatic thresholding. What the program does is compute the p-value
or cluster size needed to reach the threshc for each of these methods.
Hope this helps. Let me know if you have any more questions.
>
>
>
> Any help gratefully received!
>
> Thanks,
>
> Paddy
>
>
>
> ----------------------------------------------------------
>
> Paddy Ross
>
> PhD Student
>
> Institute of Neuroscience and Psychology
>
> University of Glasgow
>
>
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