This is the kind of thing that happens with clusterwise corrections. It is hard to predict what happens. When you raise the threshold, you lose some of the activation in your real map (ie, clusters become smaller). But in the Null map, clusters also become smaller. So, at the lower threshold, the frequency of a cluster of a size in your real data may be high (so you have a high clusterwise p-value). When you raise the threshold, the real data has a new (smaller) cluster size, but in the Null map, the frequency of that clustersize may be low (and so a lower (ie, more sig) clusterwise p-value). It's confusing, I know.
On 9/29/2023 3:35 PM, Guthrie, Andrew J. wrote:
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Hi all,
I took the freesurfer course in the recent past, and I am now beginning to run some glm thickness analyses!
Currently I am doing a thickness analysis looking at the difference between two groups while controlling for age, and two continuous measures of depression and anxiety. The general commands I run are as follows:
mris_preproc --fsgd [fsgd filename] --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --o lh.[filename].thickness.10.mgh
mris_preproc --fsgd [fsgd filename] --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi rh --o rh.[filename].thickness.10.mgh
mri_glmfit --y lh.[filename].thickness.10.mgh --fsgd [fsgd filename] doss --C contrast.mtx --surf fsaverage lh --glmdir lh_[filename]_fwhm10.glmdir
mri_glmfit --y rh.[filename].thickness.10.mgh --fsgd [fsgd filename] doss --C contrast.mtx --surf fsaverage rh --glmdir rh_[filename]_fwhm10.glmdir
mri_glmfit-sim --glmdir lh_[filename]_fwhm10.glmdir --cwpvalthresh .05 --cache 2.0 abs --2spaces
mri_glmfit-sim --glmdir rh_[filename]_fwhm10.glmdir --cwpvalthresh .05 --cache 2.0 abs --2spaces
I noticed that in some analyses there would be no significant clusters when the threshold is set at 2.0 (p<0.01) but if you were to run the same analyses with a threshold at 2.3 (p<0.005) there would be a significant cluster, in the lingual for example. If I go one step further and set the threshold to 3.0 there is also a significant cluster – however the cluster is now in the isthmuscingulate.
Am I doing something incorrectly or is this possible? And if so, could you help me understand what is going on here.
Best,
Andrew
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