Parameters
Table 1 consolidates the parameters used in atlas construction at 7 T and in the example dataset at 3 T.
Table 1
Consolidated Parameters
| Step | Parameter | Atlas construction (7 T) | Example dataset (3 T) | Notes |
|---|---|---|---|---|
| Atlas | threshold | 50% | 50% | 25% when a warped core is short or discontinuous |
| Registration | tool | antsRegistrationSyNQuick.sh | same | Skull-stripped participant image against MNI152_T1_1mm_brain |
| Warping | interpolation | nearest-neighbour | same | Linear for probabilistic maps, then threshold |
| Corridor | dilation | 1–2 voxels | 2 | 4 when registration is uncertain |
| Tractography | algorithm | iFOD2 (default) | same | |
| Tractography | -cutoff | 0.03 to 0.08 by pathway; 0.06 for VTA → hippocampus (Atlas construction) | 0.01 | 0.01 is the value in routine use with the corridor mask and the default in 00_config.sh; confirm by pilot (Step 4). MRtrix3 default 0.05 |
| Tractography | -select | 2500 | 2500 | |
| Tractography | -seeds | 25,000,000 | 25,000,000 | |
| Tractography | -minlength, -maxlength | 35, 65 mm | 35, 65 mm | Per tract family |
| Tractography | -seed_unidirectional, -stop | on | on | |
| Tractography | ACT, backtrack, angle, step size | off / default | off / default | ACT did not reconstruct with these masks |
| Cleaning | n_points, clean_rounds | 100, 5 | same | |
| Cleaning | distance_threshold, length_threshold | 3, 2 | same | Mahalanobis SD; length SD |
| Cleaning | QuickBundles threshold | 5 mm | not used | For two-bundle tracts |
| Quality control | flags | voxels < 50 or > 5,000; maximum density < 5 | ||
| Profiling | nodes | 100 | 100 | End nodes 0–4 and 95–99 may be trimmed |
| Profiling | weighting | Gaussian (Mahalanobis) | same | |
| NODDI | intrinsic parallel diffusivity, white / gray matter | 1.7 / 1.1 × 10⁻³ mm²/s | same | Refit for gray-matter regions |
| NODDI | maps | modulated NDI and ODI; FWF | same | |
| Inference, whole tract | model | mixed model with subregion term; likelihood-ratio test for interaction | one value per participant per tract | |
| Inference, quartiles | segments and correction | nodes 0–24, 25–49, 50–74, 75–99; FDR or maximum-statistic permutation | seed-end versus target-end contrast for uniformity | |
| Inference, nodes | permutations | 5,000 | 5,000 | Freedman–Lane |
| Inference, nodes | cluster criterion | extent ≥ 95th percentile of null maximum | same | α = .05 per node |
| Inference, nodes | covariates | ICV, length, count, motion, age | Count is collinear with NDI; decide in advance |
Note. VTA = ventral tegmental area; ACT = anatomically constrained tractography; NODDI = neurite orientation dispersion and density imaging; NDI = neurite density index; ODI = orientation dispersion index; FWF = free-water fraction; FDR = false discovery rate; ICV = intracranial volume.