Subject-Specific Probability Maps of Scalp, Skull and Cerebrospinal Fluid for Cranial Bones Segmentation in Neonatal Cerebral MRIs

• Published in: Ingénierie et recherche biomédicale Vol. 45; no. 4; p. 100844
• Main Authors: Hokmabadi, Elham, Abrishami Moghaddam, Hamid, Mohtasebi, Mehrana, Kazemloo, Amirreza, Gity, Masume, Wallois, Fabrice
• Format: Journal Article
• Language: English
• Published: Elsevier Masson SAS 01.08.2024; Elsevier Masson
• Subjects: Cognitive science; Computed tomography image; Internal Medicine; Magnetic resonance image; Neonatal brain atlas; Neuroscience; Skull segmentation; Skull stripping; Subject-specific template; Skull segmentation; Neonatal brain atlas; Skull stripping; Subject-specific template; Computed tomography image; Magnetic resonance image
• ISSN: 1959-0318
• DOI: 10.1016/j.irbm.2024.100844

Segmentation of cranial bones in magnetic resonance images (MRIs) is a challenging and indispensable task to study neonatal brain development and injury. This paper presents a new approach for creating subject-specific probability maps of the scalp, skull and cerebrospinal fluid (CSF) from retrospective bimodal (MR and CT) images acquired from neonates in the gestational age range of 39 to 42 weeks. These maps are subsequently employed for the segmentation of cranial bones in cerebral MRIs from neonates in the same age range. Retrospective MR and CT of neonates with normal head in the gestational age range of 39-42 weeks were preprocessed, segmented semi-automatically and employed as atlas data. For an input MR image acquired from a subject under study, a preprocessing stage and three main processing blocks were performed: First, subject-specific head and intracranial templates and CSF probability map were created using retrospective MR atlas data. Second, the CT atlas data were coregistered to MR templates and the resulted deformation matrices were fed to the next block to create subject-specific scalp and skull probability maps. Finally, some novel performance measures were presented to evaluate the performance of subject-specific CSF, scalp and skull probability maps for skull and intracranial segmentation in neonatal MRIs. The subject-specific probability maps were employed for brain tissue extraction and compared with two public methods such as Brain Extraction Tool (BET) and Brain Surface Extractor (BSE). They were also applied for cranial bone extraction. Then, the similarity in shape between the frontal and occipital sutures (which had been reconstructed from segmented cranial bones) and the ground truth landmarks was evaluated. For this purpose, modified versions of the Dice similarity coefficient (DSC) were used. Finally, a retrospective bimodal (MR-CT) data acquired from a neonate within a short time interval was used for evaluation. After co-alignment of the two images, the DSC and modified Hausdorff distance (MHD) were used to compare the similarity of cranial bones in the MR and CT images. Significant improvements were achieved compared to conventional methods which rely solely on MR image intensities. These advancements hold promise for enhancing neurodevelopmental studies in neonates. The algorithm for creating subject-specific atlases is publicly accessible through a graphical user interface at medvispy.ee.kntu.ac.ir. •Recent neuroscience studies require accurate extraction of skull from neonatal MRIs.•Probability maps of neonatal scalp, skull and CSF are indispensable for this purpose.•Subject-specific probability maps are created using retrospective CT and MR data.•They are employed for skull segmentation in MRIs of 39-42 weeks GA neonates.•The segmentation accuracy was superior than the well-known conventional methods.