We will try the "randomize" function but if I was to use the approach with 3dMVM -resid:
This gives me a _resid output file with 1800 values per voxel (we have 1800 subjects).

1) Should I loop through this sub-brik with 3dFWHMx, where the loop index is used to give 3dFWHMx one sub-brick at a time or can I just give it the full 4D-volume?

2) Should I use any of these option?

-demed      = If the input dataset has more than one sub-brick
                (e.g., has a time axis), then subtract the median
                of each voxel's time series before processing FWHM.
                This will tend to remove intrinsic spatial structure
                and leave behind the noise.
                [Default = don't do this]
  -unif       = If the input dataset has more than one sub-brick,
                then normalize each voxel's time series to have
                the same MAD before processing FWHM.  Implies -demed.
                [Default = don't do this]
  -detrend [q]= Instead of demed (0th order detrending), detrend to

>>>>>
  -geom      }= If the input dataset has more than one sub-brick,
    *OR*     }= compute the final estimate as the geometric mean
>>>>>
  -combine    = combine the final measurements along each axis into
                one result

3) Should I for structural data still use -ACF or is classical -fwhm sufficient?

I tried this:

3dFWHMx -input resid+tlrc. -ShowMeClassicFWHM

Got this:

++ start ACF calculations out to radius = 8.19 mm
 + ACF done (0.00 CPU s thus far)
 2.73652  2.60893  2.85135     2.73047
 0.773993  1.5801  7.99712    4.18496
++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to 3dFWHMx.1D
++ 1dplot: AFNI version=AFNI_21.0.12 (Feb 25 2021) [64-bit]
++ Authored by: RWC et al.
 + and 1dplot-ed to file 3dFWHMx.1D.png

Are those values for all 1800 subjects?:
2.73652 2.60893 2.85135 2.73047



Edited 2 time(s). Last edit at 09/17/2021 07:21AM by Robin.