Hi Freesurfer experts, I am running a group analysis of functional data on a custom template/average subject for which I do not have a talairach.xfm file, an orig.mgz nor aparc data (it is a primate dataset). I ran into some error messages when trying to use mri_glmfit-sim.
1) I get an error message that the flag --no-cortex is not recognized. I am using --no-cortex in mri_glmfit because I do not have a cortex label file for my template subject. This error does not crash the program, but may be worth a minor bug fix in future releases.
2) For the primate data, I did not make an average volume yet, but only an average surface. Hence, I do not have an orig.mgz file for the average subject. All analyses I currently run are surface based. Can I just copy any orig.mgz into the mri folder without negatively affecting mri_glmfit-sim?
3) I do not have a Talairach.xfm file for the average subject either. Can I copy an identity matrix into mri/transforms without negatively affecting mri_glmfit-sim? Again, all analyses are surface-based.
4) I removed the --annot flag where mri_glmfit-sim where mri_surfclusters is being called. Is that expected to result in any problems?
5) Anything else I should observer?
Thanks, Caspar