Hi Freesurfers,

I am using preproc-sess in Freesurfer/Fsfast 5 with per-run motion
correction (these subjects have a lot of between-run motion), and I want to
analyze the volumes in each subject's individual space (I'd prefer native
functional space, but I am happy to do it in each subject's anatomical
space).  Do preproc-sess, mkanalysis-sess, or selxavg3-sess have any
built-in flags that would automatically align the functional volumes using
the 6 rigid parameters generated from bbregister?  Or do they have a
built-in way to align and to upsample the functional volumes to the
subject's anatomical space (not the surface)?  I am happy to upsample each
run's functional volume to anatomical space with an mri_vol2vol call, and
then to estimate my glm with selxavg3-sess on these volumes.  But I figure
there may be some flags that do this automatically.  I've looked through
the documentation and I haven't found these flags.  Is this possible to do
automatically?

Thanks, guys!


Alex

Kanwisher Lab Manager
McGovern Institute for Brain Research
MIT
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