There are actually three ways! The 3rd is fslregister-sess. I prefer spmregister-sess or fslregister-sess. These compute a registration directly between the functional and the brain.mgz anatomical. autoreg-sess performs a multi-step registration. First it looks for a same-session anatomical which is then registered with the brain.mgz, it then uses information about the slice prescriptions between the same-session anat and the functional to compute a registration between them. It then concatenates these two to give the registration between brain.mgz and the functional. The problem with this is that the subject can move or the scanner can drift making this registration innacurate.

doug

Tsung-Ren Huang wrote:

Dear Freesurfers,

There seems to be two ways for functional/structural registration. One is spmregister-sess, and the other is autoreg-sess.

What are the differences between these two scripts? Which one do you prefer to use and why?

Thanks! Tren _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Dear FS-FAST experts,

I'm following the FS-FAST workflow on this webpage: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastAnlysisBySteps

I preprocess my functional data by preproc-sess with "-fwhm 5" and specify "-funcstem fmcsm5" for mkanalysis-sess.new.

My question is then if I need to also specify "-funcstem fmcsm5" for spmregister-sess to make the final SPMs properly aligned to the anatomical data? Or, will the default value "-funcstem f" be sufficient, as suggested by the webpage?

Thanks! Tren