Hello FreeSurfer Developers,
I have run a glm on the left hemisphere to compare cortical thickness between 2 groups. After, I did a cluster-wise correction with permutation testing using this command
mri_glmfit-sim --glmdir lh.sv2a_group.glmdir.10 --perm 1000 2 abs
It completes without error, but I have a question about the log file and --surf argument. My concern if about this part of the log file where it shows "--surf fsaverage lh white" (see section from log file and complete log file attached). White is the default I based on the help file for mri_glmfit. Should I be running with --surf fsaverage lh pial?
Does this imply that the glm is performed on the white matter surface. I am then visualizing on the inflated pial surface so does this cause a problem? ------------------------------------------------------------ -------------------------------------------------- 1/1 Fri Mar 2 03:23:25 EST 2018 mri_glmfit --C lh.sv2a_group.glmdir.10/tmp.mri_glmfit-sim-13158/sv2a_thickness_group.mtx --sim perm 1000 2 lh.sv2a_group.glmdir.10/csd/perm.th20.abs.j001 --sim-sign abs --fwhm 0 --fsgd lh.sv2a_group.glmdir.10/y.fsgd dods --y lh.sv2a.group.thickness.10.mgh --mask lh.sv2a_group.glmdir.10/mask.mgh --surf fsaverage lh white simbase lh.sv2a_group.glmdir.10/csd/perm.th20.abs.j001 FWHM = 0.000000 gdfRead(): reading lh.sv2a_group.glmdir.10/y.fsgd INFO: gd2mtx_method is dods Reading source surface /home1/am2359/fs6_data/fpeb_ app_fs/fsaverage/surf/lh.white ---------------------------------------------------
Thank you, Adam