This should work

mkanalysis-sess -analysis fmcsm5_functionals_Stable5 -TR 2 -paradigm paradigm -event-related -native -fwhm 5 -mcextreg -nconditions 9 -fir 4 24

I would also run the preprocessing from scratch.

doug

Adam Nitenson wrote:

Hi Freesurfers,

I'm trying to update our analysis for Stable 5, and I'm having some

trouble trying to recreate our current Stable 4 version (espcially since I have not yet made a gui-less analysis). The command I used was:

mkanalysis-sess -analysis fmcsm5_functionals_Stable5 -TR 2 -paradigm paradigm -event-related -funcstem fmcsm5 -motioncor -inorm -polyfit 2 -mcextreg -nconditions 9 -timewindow 24 -prestim 4 -TER 2 -autostimdur

However, it's not accepting the -motioncor flag, and I'm not sure what the correct replacement is.

For reference, I'm trying to replicate the analysis as close to the original, which has the following analysis.info file:

analysis fmcsm5_functionals TR 2.000000 fsd bold funcstem fmcsm5 inorm 100.000000 runlistfile tpexclude parname paradigm designtype event-related nconditions 9 Condition 1 Condition01 Condition 2 Condition02 Condition 3 Condition03 Condition 4 Condition04 Condition 5 Condition05 Condition 6 Condition06 Condition 7 Condition07 Condition 8 Condition08 Condition 9 Condition09

and analysis.cfg text

-extreg mcextreg -nextreg 3 -delay 0.000000 -TER 2.000000 -polyfit 2 -gammafit 2.250000 1.250000 -gammaexp 2.000000 -timewindow 24.000000 -prestim 4.000000 -autostimdur

Thank you,

Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer