Hi Anderson,
Thank you very much for the reply.
First, I want to clarify that in the file * _clustere_tstat_fwep.mgz, the values of the vertices are the same within each cluster, when I wrote the question I had looked at a wrong file. Sorry for the inconvenience.
Related to the other question, yes, I want to apply a -C 3.1 (which corresponds to p = 0.001) to the t-maps. But when applying that threshold, the file * _clustere_tstat_fwep.mgz contains p>0.05 values. Should I threshold the values in this file to keep only the significant results?
Finally, I would like to know out of curiosity if the way to build the design contrast file by hand is the same as freesurfer or if the logic to build the contrasts is different.
Thank you in advance.
Marina
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Hi Marina,
Please see below:
On Mon, 14 Dec 2020 at 13:00, Marina Fernandez Alvarez <[log in to unmask]> wrote:
Hi experts,
We have used PALM to apply permutation testing and correct FWER at the level of cluster.
In the command line we have included –C 3.1 option to enable cluster inference. If this value corresponds to the cluster-p, how can I specify the vertex-p? I would like to apply a vertex-p of 0.001.
Not sure what you mean. The -C 3.1 means that a threshold of 3.1 is applied to the t-maps, and the vertices that survive are then labelled as clusters if they are neighbours. The 3.1 corresponds to the t-stat that has a p=0.001 for a very large sample. Maybe it's already what you need?
Finally, I would like to know why the p values of each vertex are different within the same cluster in the *_clustere_tstat_fwep.mgz output file. Shouldn't the values of the same cluster be the same?
Yes, they should be the same inside the same cluster. I'm surprised they aren't in your case and I too wonder what may be going on... any more details?
Thanks!
All the best,
Anderson
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