Hello freesurfers,
I have one quick question and appreciate it very much if you could please respond.
I have been running some resting state fmri analysis acquired on 7T scanner. In order to do the analysis on the surface, I’ve been using "-surface self lh” for left hemisphere analysis in mkanalysis-sess. My question is if there is an equivalent command to use for subcortical analysis. I have been using -mni305 1 for subcortical analysis. but I’m not sure if this the right flag to use when doing the analysis on the subject’s own space and not on fsaverage?
here are the commnds I’ve been using. running the analysis with mni305 1, gives me maps like the one attached. I can’t see any blob, but I see dots of activation, which makes me think there’s something wrong.
mkanalysis-sess -a stat_native.lh -runlistfile goodruns -fsd bold3 -surface self lh -fwhm 0 -event-related -TR 3 -nc 24 -polyfit 2 -nuisreg mcprextreg 6 -tpef TPEF.txt -spmhrf 0 -refeventdur 3 -per-run -nskip 0 -p stat.par -force
mkanalysis-sess -a stat_native.mni -runlistfile goodruns -fsd bold3 -mni305 1 -fwhm 0 -event-related -TR 3 -nc 24 -polyfit 2 -nuisreg mcprextreg 6 -tpef TPEF.txt -spmhrf 0 -refeventdur 3 -per-run -nskip 0 -p stat.par -force
Thanks, Mona