Hi, Sondos-

I don't see any error here:

++ Number of ROIs in netw[0] = 9
++ No refset labeltable for naming things.
++ SEARCHING for vector files with prefix '/Users/dti-afni*':
FINDING: 'V1' 'V2' 'V3'
++ SEARCHING for scalar files with prefix '/Users/dti-afni*':
FINDING: not:'DT' 'FA' 'L1' not:'L2' not:'L3' 'MD' 'RD' not:'dwuncert'
++ Done with scalar search, found: 4 parameters
--> so will have 15 output data matrices.
++ Minor note: there is a tiny (magn < 0.1) vector in the 0-th direction set.
--> Will exclude that voxel from walkable mask-- recommend checking model fit.
++ Effective Monte iterations: 5000. Fraction threshold set: 0.00100
--> Ntrack voxel threshold: 5.

that looks fine. Though, I would use a higher fraction threshold, in general, like 0.1 (see "-alg_Thresh_Frac" in the help; and/or add "-alg_Thresh_Frac 0.1" to the command; i should probably update the default value).

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Does that mean it an't find DT, L2, L3 and dwuncert??

No, it doesn't; it just means it isn't using those for matrix output.

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Also, when I tried to run SUMA
I got the following error:
-- Error SUMA_LoadDsetOntoSO_eng (SUMA_Color.c:10630):
Could not find network_file "network6_ROI_TEST_000.niml.tract" on disk for dset /Users/network6_ROI_TEST_000.niml.dset

I would need to see the command you tried running. Note that "3dTrackID -mode PROB ..." does not output tract files.

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So I noticed that there was no outputted tract file from 3dTrackID either, and this could be because of the "missing scalars" (that are actually present in the folder)?

Nope, in probabilistic mode, tract files are not output. Please see this documentation, esp. from pg 22 onward about the different modes:
[afni.nimh.nih.gov]
as well as here for more about tracking and visualization tools for probabilistic tracking:
[afni.nimh.nih.gov]

--pt