Downloads

Complete atlas

The MesoConnect Atlas is distributed as one package, MesoConnect_Atlas.zip (3.4 MB). The canonical copy and the individual files are in the atlas authors' GitHub repository; the copy served here is identical (SHA-256 checksum file).

The package contains the 28 atlas maps (seven pathways, two hemispheres, two map types), mesoconnect_subject_counts.csv, the FSL MNI152 1 mm brain template (Montreal Neurological Institute, MNI) used as the spatial reference, a README and the licence notice:

MesoConnect_Atlas/
  README.md   LICENSE   mesoconnect_subject_counts.csv
  templates/MNI152_T1_1mm_brain.nii.gz
  inferior_vta_nac/   superior_vta_nac/   vta_amygdala/   vta_anterior_hpc/
  vta_posterior_hpc/  hpc_nac_vp/         vp_vta/

Each pathway folder holds four files named {hemisphere}_{pathway}_mni152_1mm_{map_type}.nii.gz, for example vta_posterior_hpc/left_vta_posterior_hpc_mni152_1mm_thr50.nii.gz. Table 1 gives the two map types. All maps are on the FSL MNI152 1 mm grid (182 × 218 × 182 voxels, 1 mm isotropic) as compressed NIfTI-1.

Table 1

Map Types in the Atlas Package

File suffix	Contents	Use
_overlap_prop.nii.gz	Probabilistic map. Each voxel holds the proportion of contributing participants whose binarized tract included it (0 to 1).	Visualization, custom thresholds, probability-weighted extraction
_thr50.nii.gz	Binary map. A voxel is 1 when the tract was present in at least half of the contributing participants.	Corridor construction (this tutorial), whole-tract extraction

Note. mesoconnect_subject_counts.csv gives the number of contributing participants for every pathway and hemisphere, the denominator of the corresponding overlap-proportion map. Binary maps are warped with nearest-neighbour interpolation. A map at another threshold is made from the overlap-proportion map and kept outside the package folders, for example fslmaths left_vta_posterior_hpc_mni152_1mm_overlap_prop.nii.gz -thr 0.25 -bin derived/left_vta_posterior_hpc_thr25.nii.gz.

The package's terms are scoped by material: the Human Connectome Project (HCP)-derived maps and participant counts fall under the WU-Minn HCP Consortium Open Access Data Use Terms, the documentation under CC BY 4.0, and the MNI152 template under the FSL licence; the LICENSE file in the package gives the full notice.

Seed and target regions

The atlas package does not redistribute the third-party regions used as seeds and targets during atlas construction (Harvard–Oxford hippocampus, amygdala and nucleus accumbens; the ventral tegmental area (VTA) of Trutti et al., 2021; the ventral pallidum of Pauli et al., 2018). The atlas authors' region-of-interest resources page gives the download locations, thresholds and citations. The four regions used for the VTA → hippocampus example on this site are provided here (Table 2), thresholded and binarized on the same MNI 1 mm grid.

Table 2

Seed and Target Regions Distributed With This Site

File	Hemisphere	Contents
left_VTA_0.25_bin.nii.gz	Left	VTA seed (Trutti et al., 2021; 25% threshold)
right_VTA_0.25_bin.nii.gz	Right	VTA seed (Trutti et al., 2021; 25% threshold)
HPC_L_0.5_bin.nii.gz	Left	Hippocampus target (Harvard–Oxford; 50% threshold)
HPC_R_0.5_bin.nii.gz	Right	Hippocampus target (Harvard–Oxford; 50% threshold)

Setting up the files for the scripts

The scripts expect the unzipped package as ATLAS_DIR, with the seed and target regions in a roi_maps folder inside it. The following commands produce that layout for the VTA → hippocampus example.

curl -sSLO "https://diffusiontensorimaging-repos.github.io/MesoConnect-Tutorial/downloads/MesoConnect_Atlas.zip"
unzip -q MesoConnect_Atlas.zip
mkdir -p MesoConnect_Atlas/roi_maps
base="https://diffusiontensorimaging-repos.github.io/MesoConnect-Tutorial/atlas"
for f in left_VTA_0.25_bin right_VTA_0.25_bin HPC_L_0.5_bin HPC_R_0.5_bin; do
  curl -sSL "$base/$f.nii.gz" -o "MesoConnect_Atlas/roi_maps/$f.nii.gz"
done

In 00_config.sh, ATLAS_DIR then points at MesoConnect_Atlas, and the atlas map of a tract is named by its package path, for example $ATLAS_DIR/vta_posterior_hpc/left_vta_posterior_hpc_mni152_1mm_thr50.nii.gz.

Source atlases

• Trutti et al. (2021): probabilistic VTA in MNI space; threshold at 25% for a seed region.
• Pauli et al. (2018): subcortical atlas including the ventral pallidum, VTA and substantia nigra.
• Harvard–Oxford subcortical atlas (Frazier et al., 2005; Makris et al., 2006), distributed with FSL: hippocampus, amygdala, accumbens, caudate, putamen, thalamus.
• Murty et al. (2014): functional–anatomical substantia nigra/VTA masks, a comparison resource for the dopaminergic midbrain.
• MNI152 templates (FSL, $FSLDIR/data/standard): the 1 mm brain image and brain mask used for registration.