Yes, c_thresh is a t-value.
You don't need to specify a cluster size threshold -- this is what
randomise is computing, ie, the probability of gettting a cluster of
certain size or larger (this is the cluster-wise pvalue). Thus, by
choosing a cluster-wise pvalue threshold, you are effectively choosing a
cluster size threshold (but the pvalue is more meaningful:).
A few more hints from my experience:
I think randomise will try to compute a mask from the data if you don't
pass one on the command-line. Is this right? If so, it's likely that it
will not compute mask that make sense.
Tom Nichols recommends using 10,000 iterations to test at p <= .05
The "neighborhood" of a voxel (ie, it's connected components) are the 26
voxels around it (touching edges and corners are connected, not just
touching faces).
Hope this helps!
doug
bas Jasperse wrote:
>Dear FSL-list,
>
>Recently we started using randomise to perform voxelwise statistics on
>SIENA displacement maps and are currently performing correlations and group
>comparisons.
>
>We also want to use cluster thresholding for our analysis, but are a bit
>puzzled by the option provided.
>
>The manual tells us that the only thing we can specify is <c_thresh>.
>We assume that this means setting the supra-threshold based on the
>T-stat image. Is this correct?
>
>There is no option provided for cluster size in voxels or mm, so we were
>wondering
>if and how randomise sets the cluster size. Could you provide some insight
>in this matter?
>
>
>We've tried searching the Jiscmail archives, but could not find an answer
>to these issues.
>
>Thanks in advance for your help,
>
>kind regards,
>
>Bas Jasperse
>Vu medical centre, Amsterdam
>
>
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
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Phone Number: 617-724-2358
Fax: 617-726-7422
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