29 weeks gestational age

Fetal Brain Atlas

The CRL has developed a mathematical framework for the generation of an unbiased, deformable spatiotemporal atlas of the fetal brain from magnetic resonance imaging (MRI) of normal fetuses scanned prenatally. Our atlas serves to capture the inter-subject anatomic variability of the fetal brain over the fetal brain growth period (Gholipour et al., 2014) and is currently available between 21 weeks gestational age to 37 weeks. The atlas has been constructed following an unbiased minimum distance template estimation approach which utilizes symmetric diffeomorphic deformation and the cross-correlation (CC) similarity metric integrated with kernel regression in age.

The main characteristic of our atlas construction method, as compared to other schemes such as those that have employed affine registration, Demons registration, or free-form deformation (FFD), is its sharpness, which indicates superior inter-subject registration performance achieved through symmetric diffeomorphic deformable registration. The atlas can thus be effectively used in spatial normalization (inter-subject image registration), fetal brain localization and matching, and atlas-based segmentation.

For these purposes, the atlas comes with brain tissue and structure labels including cortical gray matter, white matter, subcortical gray matter structures, CSF, lateral ventricles, brainstem, and cereblleum labels, and more. In addition, gestational age weeks 21-33 include labels for developing white matter layers, including the subplate, intermediate zone, and ventricular zone. A new release of the atlas including a 38 weeks gestational age template and divided cortex parcels is scheduled for the summer of 2017. Please check back for updates.


Potential applications of the deformable spatiotemporal atlas of the fetal brain are the development of faster, more accurate, automated methods of MRI structural analysis, and disease biomarker identification in utero. Assessing the volume and overall morphology of the fetal ventricles, identifying and segmenting the transitory fetal subplate zone, and developing a method of automatic fetal MRI brain localization are some of the ongoing research projects.

Download the CRL fetal brain atlas

Updated 03/03/2017

A report of our atlas construction method was published in 2014[2] which corresponds with the previous version of the atlas. The paper reporting the updated atlas[1] has been accepted in 2017 and is forthcoming in Scientific Reports. Please check back for updates and a link.


1. A Gholipour, CK Rollins, C Velasco-Annis, A Ouaalam, A Akhondi-Asl, O Afacan, C Ortinau, S Clancy, C Limperopoulos, E Yang, JA Estroff, and SK Warfield. A normative spatiotemporal MRI atlas of the fetal brain for automatic segmentation and analysis of early brain growth, Scientific Reports, Nature Publishers, forthcoming, 2017.

2. A Gholipour, C Limperopoulos, S Clancy, C Clouchoux, A Akhondi-Asl, J A Estroff, and S K Warfield. Construction of a Deformable Spatiotemporal MRI Atlas of the Fetal Brain: Evaluation of Similarity Metrics and Deformation Models. MICCAI 2014. [PDF]