You can run preproc-sess like this (don't include -mni305 or -surf)

preproc-sess -per-session -fsd bold -fwhm 5 -s session

Then mkanalysis:

mkanalysis-sess -a mains -native -fwhm 5 -fsd bold ...

This will analyze things in the native fmri space. You can then convert 
the results to the anatomical space with

mri_vol2vol --reg register.dof6.lta --mov sig.nii.gz --fstarg --o 

On 2/7/18 11:32 AM, Tuominen, Lauri Johannes wrote:
> Dear Freesurfers!
> I would like have my fMRI runs in the native T1 volume space and do the first 
> level analyses there. I can only find -self flag for surface based analyses 
> in preproc-sess. What would be there recommended way to do the analyses in 
> the T1 volume space? This is 7T data and I’d like to use the individual 
> segmentations as ROIs.
> Thank you so much!
> Lauri Tuominen
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