Dear FreeSurfer Developers,
I have run recon-all....-qcache after reviewing the recon-all...-all outputs in freeview.....
I have been looking into: https://surfer.nmr.mgh.harvard.edu/fswiki/mris_preproc
Now it seems that I could have omitted the -qcache...and I am a bit lost with the examples showed in the link.
Any one could help me regarding the concatenation and how to created the FSGD file?
Taking into account I would like to run a cortical thickness analysis between three groups, how I should run the ANOVA?
Finally, should I have into account General Atrophy Measures such as: global average thickness for both hemispheres, only or in combination with estimated global intracranial volume as a nuissance regressors in the design? So = ANCOVA instead of ANOVA.
Does anyone have any thoughts on how to trouble-shoot those problems?
Kind regards, Rosalia