freesurfers,
i've been using my own scripts to compute tSNR for data i was running through FSL, but i'm now running the data through freesurfer and i wanted to better understand what the fsnr volumes spit out by selxavg3-sess are. i poked around the wiki and mailing archives and couldn't find answers to the following questions:
1. how is fsnr computed? tsnr is <mean_of_vox_time_course>/<std_of_vox_time_course> -- is fsnr the same thing with a different name? 2. what kind of preprocessing is done on the data before fsnr is computed? since freesurfer removes linear trends at the modeling stage, not the preprocessing stage, are linear trends removed from the data going into fsnr calculations? is anything else regressed out before fsnr is computed (e.g., other nuisance regressors)? 3. what's the difference between raw.fsnr.nii.gz, fsnr.nii.gz, and fsnr2.nii.gz? 4. is fsnr.dat the mean in the whole brain mask (i.e., gm and wm)?
separately, random other question: what are the h.dat, h.nii.gz, and h-offset.nii.gz file/volumes?
thanks in advance!
alex kell