Hi Freesurfer experts,
I was wondering about three things concerning the use of the mri_glmfit-sim command:
1) I tried running it with the --2spaces flag in order to Bonferroni correct over the two hemispheres but it tells me that the specific flag is not recognized. Is there another way to correct over the two hemispheres?
2) I set the cluster-based threshold to 0.999 in order to see all of the clusters and varied the voxel-based threshold in order to see the differences that it would make on the results. Specifically, i set it to be 1.3, 2.0, 2.3, and 3.0. Between the four different occurring cluster summaries, there was only one common cluster that appeared in all four summaries. As expected, the number of voxels of the specific cluster was decreasing as its voxel-wise threshold was increasing.
a) However, the reported cluster-wise threshold varied between 0.05 to 0.96 in those four cases. Does this sound reasonable? Shouldn't the cluster wise p values of the same cluster-between the four cases-be less dispersed?
b) If there is a cluster reported in only one of the four summaries (i.e. when the voxel-based threshold is 1.3) that say has a cluster-wise p value of 0.03, do I consider that significant or not, since it does not appear in any other summary with such a low cluster wise p value and since the only published p value is the cluster wise one?
Thank you in advance for your time, Panagiotis Fotiadis