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