[Freesurfer] subcortical analysis in native space

Hi Freesurfer experts,

I would like to do a resting state analysis not in mni305, but in subject's native subcortical space. Here is the command I wrote:

mkanalysis-sess -analysis seed.native -native -fwhm 0 -notask -taskreg seed.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -nuisreg mcprextreg 2 -polyfit 5 -nskip 4 -fsd rest -TR 2.34 -per-run -lpf .08 -hpf .01

The output is a whole brain map with noisy dots everywhere but no clusters (not even autocorrelation within seed location). Am I specifying everything correctly? I know my seed.dat is not the issue because I tested it using mkanalysis-sess -surface $subjectname and the output is as expected.

Thanks, Jiahe

-- Jiahe Zhang Ph.D. Candidate Department of Psychology Northeastern University 617-373-2649