The Ganglionic Eminence (GE) is a transitory fetal brain structure evaluated via MRI during pregnancy. Anomalies within the GE may result in failure cell proliferation or migration, leading to significant postnatal effects.

We define GE label maps from 19 to 36 gestational weeks (GW), extending the spatio-temporal dHCP atlas (defined between 21-36 GW).

Six fetuses at 19 and 20 GW were scanned using a 3T MRI at IRCCS Fondazione Ca’ Granda Ospedale Maggiore Policlinico. Fetal brain images were reconstructed from T2w-TSE sequences at 0.5mm isotropic resolution using NeSVoR. The ANTs software was used to construct the T2w brain reference image at 19 and 20 GW. The GE was initially segmented coarsely on the T2w reference atlas image for 19–36 GW using ITK-SNAP and subsequently refined manually by three senior neuroradiologists. An ensemble approach was adopted to fuse their maps and derive the final GE segmentation.

Neuroradiologists achieved strong agreement in GE segmentation (Dice coefficient score: 0.91±0.06,  volume similarity: 0.15±0.11, F1-score: 0.92±0.02), with a slight decline in the third trimester due to cell migration and reduced contrast. GE volume reached its maximum at 21 GW, then decreased significantly in the late second trimester, stabilizing in the third. Overall, GE volume ranged from 40 to 500 mm³.

The proposed spatio-temporal atlas supports clinical GE evaluation and represents a repository of knowledge for innovative atlas-based deep learning models.