Hi freesurfer people,
I'm trying to understand preprocessing a little better, especially registration of functional data to anatomical space. I am currently running everything in the volume, doing motion correction per-run and then pooling all the runs in the session together for the first level analysis.
As far as I can tell, running preproc-sess with -per-run takes the raw functional data (f.nii.gz), pulls out the middle timepoint and calls it template.nii.gz, bbregisters func to anat and creates a register.dof6.lta file in each of the functional run folders, transforms the aparc+aseg from the subject's mri folder and binarizes it into a brainmask (brain.nii.gz), and runs mc-afni using f.nii.gz as the input vol and template.nii.gz as the template vol to create the motion corrected volume (fmcpr.nii.gz). Is this correct?
Then when I run selxavg3-sess it somehow mri_converts an intermediary motion corrected volume from the mc-afni command above (eg <run#>/tmp.mc-afni2.20097/outvol.nii.gz) into an fmc.nii.gz file in each run folder. Are these fmc.nii.gz's supposed to be coregistered between runs? (i.e. if the subject moved a bunch between two of the runs, would those two volumes be aligned at all?). How do these files work?
At the end I have an analysis directory with my betas, sigmaps, etc. What functional volume is everything registered to? Is the transform between this functional volume and anatomical space the register.dof6.lta file located in the session directory?
Thanks for bearing with me! -David