I am wondering if your tractographic output is in the same location in space as the TT_N27 data set?

The standard space's origin is:

$ 3dinfo -o3 ~/.afni/data/suma_TT_N27/brain.nii 
-127.000000	139.000000	144.000000

and the cube of space it occupies, from the full 3dinfo output of the same set, is:

R-to-L extent:  -127.000 [R] -to-   128.000 [L] -step-     1.000 mm [256 voxels]
A-to-P extent:  -111.000 [A] -to-   144.000 [P] -step-     1.000 mm [256 voxels]
I-to-S extent:  -116.000  -to-   139.000 [S] -step-     1.000 mm [256 voxels]

What are the similar outputs for the data set you tracked? (You can't run 3dinfo on the *.ply, but instead on the *.nii or *.BRIK data set that you input to 3dIsoSurface.)

I believe that AFNI and FSL pay attention to different things when overlaying in viewer windows-- AFNI uses the (x,y,z) coordinate values in units of 'mm', so that the data set's origin and voxel size matter (rationale being that data sets with different voxel sizes can be overlaid easily; possibly of differing spatial orientation, as well). In FSL, I'm not sure that this is the case, meaning that just because something appears to overlay there is not a guarantee it will overlay in AFNI.

--pt