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
Richard Parker Postgraduate Research Student
Maurice Wohl Clinical Neuroscience Institute King's College London
Telephone: 07943515208 Email: Richard.r.parker@kcl.ac.uk