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April 16, 2021 10:50AM
Hi-

When you provide a mask, you provide both:
1) a grid, with voxel dimensions, and
2) a certain number of voxels (and shape of region)
within which to calculate noise-like simulations. When a mask is *not* provided, I don't see how the program would even know what size matrix or voxel sizes it should be useful in the simulations.

In your case of using a mask, the output tables notes that the grid (matrix size) and voxel size are:
# Grid: 91x109x91 2.00x2.00x2.00 mm^3 (172610 voxels in mask)
... as well as how many of the total voxels (91*109*91 = 902629) are in the mask. That makes sense.

However, in the case of *not* using a mask, note that the (apparently internal) dset being used for testing has a different grid (matrix size) and voxel size:
# Grid: 64x64x32 3.50x3.50x3.50 mm^3 (131072 voxels)

Soooo, trying to compare output tables is an apples-to-oranges comparison. The total number of voxels being compared in each case is different (just by chance here, not too different). But note that the major difference is that the voxel sizes are totally different between runs: 2x2x2 voxels have a volume of 8 mm**3. The 3.5 mm iso voxels have a volume of ~43 mm**3. So, the same ACF params (from which the effective smoothness size is calculated) covers the noise fields in each volume preettty differently.

You cannot check the differences of running 3dClustSim with or without a mask in this way. If you wanted to, you could make a "mask" that covers your whole volume (i.e., something that is 1s across the whole grid specified by the input volume; check in the GUI to verify):
3dcalc -a ${mask}  -expr '1' -prefix mask_of_whole_fov.nii
... and run 3dClustSim with *that*, and compare results to your sub-FOV mask.
(Note that in the present case with such small 2mm iso voxels as you have, and a pretty large FOV, this will be pretty computationally intensive.)

I am actually surprised that 3dClustSim runs at all without any mask given, because then it has to guess at a grid. I will have to look more deeply into the code to see how it picks the grid and voxel size in such a case (the terminal text suggest it depends on ACF params), but I would not run 3dClustSim without providing a "-mask .." to specify this kind of information, regardless of whether that mask really is a brain mask or a whole FOV "mask".

--pt



Edited 1 time(s). Last edit at 04/16/2021 11:12AM by ptaylor.
Subject Author Posted

inflated 3dclustsim values with no mask?

jef March 24, 2021 10:47AM

Re: inflated 3dclustsim values with no mask?

RWCox March 24, 2021 05:26PM

Re: inflated 3dclustsim values with no mask?

ptaylor March 24, 2021 06:09PM

Re: inflated 3dclustsim values with no mask?

jef April 16, 2021 10:15AM

Re: inflated 3dclustsim values with no mask?

ptaylor April 16, 2021 10:50AM

Re: inflated 3dclustsim values with no mask?

jef April 16, 2021 02:47PM

Re: inflated 3dclustsim values with no mask?

jef April 28, 2021 05:12PM

Re: inflated 3dclustsim values with no mask?

ptaylor April 28, 2021 05:56PM



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