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


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