Hi Freesurfers,

I am interested in running a functional connectivity analysis outside of the Freesurfer environment, using freesurfer-derived ROIs

I've run recon-all, and I have run preproc-sess to carry out initial fmri preprocessing steps (motion correction, warping to the anatomical, etc)

Next, I need to produce a .nii version of the T1-coregistered (and slice time corrected) fMRI timecourse, which I don't believe is created by preproc-sess.

I've tried applying the register.dof6.dat to the motion corrected functional timeseries with mri_vol2vol, but the output is upsampled to the space of the T1 (and also is rotated 90 degrees, a phenomenon already discussed in several previous posts, I believe). I'm trying to produce a co-registered (but not upsampled) timeseries.

Final point: another forum post details a process whereby T1-ROIs can be warped to the space of the native, non-coregistered fMRI data. This isn't appropriate for my analysis unfortunately, as I am running a multi-modal analysis, whereby everything needs to be in alignment with the T1.

Any help would be greatly appreciated!

Best wishes,

Richard