Tract families and regions of interest

The atlas contains seven bilateral pathways (Table 1). Each is processed with the same nine-step workflow; only the seed, target and atlas file change. The exclusion masks used during atlas construction are already reflected in each atlas map. They are listed here so that users can anticipate where a reconstruction may leak when the corridor is dilated too far. Throughout, the ventral tegmental area is abbreviated VTA, the nucleus accumbens NAc, the ventral pallidum VP, and a region of interest ROI.

Table 1

Pathways in the MesoConnect Atlas

Pathway	Grouping	File stem (left / right)	Seed	Target	Notes
VTA → posterior hippocampus	Motivated memory	left_vta_posterior_hpc, right_vta_posterior_hpc	VTA	posterior hippocampus	The example dataset's primary tract. A ventral secondary bundle occurs in some participants (see Step 6).
VTA → anterior hippocampus	Motivated memory	left_vta_anterior_hpc, right_vta_anterior_hpc	VTA	anterior hippocampus	Shares its course with the posterior pathway for roughly the first 60 to 80 of 100 nodes.
VTA → amygdala	Motivated salience and learning	left_vta_amygdala, right_vta_amygdala	VTA	amygdala	Fornix and hippocampus exclusions.
Inferior VTA → NAc	Motivated salience and learning	left_inferior_vta_nac, right_inferior_vta_nac	VTA	NAc	Inferior and superior divisions are separated by different anterior-commissure exclusions.
Superior VTA → NAc	Motivated salience and learning	left_superior_vta_nac, right_superior_vta_nac	VTA	NAc	As above.
Hippocampus → NAc → VP	Regulation of motivated behaviour	left_hpc_nac_vp, right_hpc_nac_vp	hippocampus	VP, with the NAc as a required waypoint	Frequently reconstructs as two bundles; see Step 6.
VP → VTA	Regulation of motivated behaviour	left_vp_vta, right_vp_vta	VP	VTA

Note. File stems are those of the atlas package (<stem>_mni152_1mm_thr50.nii.gz and <stem>_mni152_1mm_overlap_prop.nii.gz). The atlas-generation settings of each pathway are on the construction page; the number of contributing participants is listed there as well.

Regions of interest

Seeds and targets are derived from published atlases, thresholded and binarized in Montreal Neurological Institute (MNI) 1 mm space (Table 2). The atlas package does not redistribute them; the downloads page gives their sources and provides the VTA and hippocampus regions used in the example dataset.

Table 2

Sources and Preparation of the Regions of Interest

Region	Source	Preparation
VTA	7 T probabilistic VTA atlas (Trutti et al., 2021), 25% threshold	Used unmodified; the VTA is subtracted from the red-nucleus, lateral-hypothalamus and mammillary-body exclusion masks.
Hippocampus	Harvard–Oxford subcortical atlas (Frazier et al., 2005; Makris et al., 2006), 50% threshold	Anterior and posterior divisions for the two VTA → hippocampus pathways.
Amygdala	Harvard–Oxford subcortical atlas	Hippocampus subtracted; divided by hemisphere masks.
Nucleus accumbens	Harvard–Oxford subcortical atlas	Ventral pallidum subtracted.
Ventral pallidum	Subcortical atlas (Pauli et al., 2018)	Divided by hemisphere masks.
SN/VTA (alternative)	Functional–anatomical SN/VTA masks (Murty et al., 2014)	Comparison resource for the dopaminergic midbrain; not the VTA region used for the atlas.

Note. SN = substantia nigra.

Exclusion masks used during atlas construction

The corridor workflow does not require these masks. They are listed so that users know what the atlas already excludes and can reintroduce any of them as an additional -exclude argument if a reconstruction enters a specific structure.

• Thalamus; cortical gray matter with cerebellum (single mask); inferior brainstem.
• Dorsal striatum: caudate and putamen, with accumbens and ventral pallidum subtracted.
• Lateral hypothalamus and mammillary bodies, with the VTA subtracted.
• Red nucleus, with the VTA subtracted.
• Fornix body, with hippocampus and amygdala subtracted (VTA → hippocampus and VTA → amygdala).
• Ipsilateral off-target regions of the circuit, per pathway (for example the ventral pallidum and striatum for VTA → hippocampus, the hippocampus for VTA → NAc).
• Contralateral hemisphere and contralateral target, enforcing ipsilateral tracking.
• Two anterior-commissure exclusion masks, one per division, defining the superior and inferior VTA → NAc pathways.

The ROI preparation script (prepare_rois.sh) and the tractography commands with these masks are in the atlas repository's analysis-code folder.