Hi Lars,
sorry for the late response, I've been gone for two weeks.
Qs 1and 2: Did you look at mri_glmfit --help? It describes what all these things are. You can also look at https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis.
Q3: If you are loading a surface-based overlay, then you do not need a registration matrix. If you are loading a volume, then you need a registration (but it might be such that the reg can be computed from the header, which is what "compute identity matrix" does).
doug
Lars M. Rimol wrote:
Hi, I have three questions:
- Where can I find information on what the different output files of
mri_glmfit represent, i.e. ar1.mgh eres.mgh rstd.mgh rvar.mgh
These can all be plotted (Load Overlay) since they are .mgh files but they seem to rarely show any blobs (except with extremely liberal thresholding). Can they be used for QA of the analyses? What to look for?
- What does gamma.mgh represent? I assume the sig.mgh is some kind of
p-value distribution, is that correct?
- What is the difference between the "Calculate identity matrix" and
"No registration needed" options when loading Overlay? Do I need any registration if I do the statistical analysis e.g. in Matlab (after having done mris_preproc and mris_surf2surf) and export the results back to FS as mgh files? Or can I just choose No registration needed, given that registration did take place in the mris_preproc and mris_surf2surf steps previous to Matlab analysis?
-- yours, LMR
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer