Robust cortical thickness measurement with LOGISMOS-B

Synthetic Atrophy for Longitudinal Cortical Surface Analyses

In the fields of longitudinal cortical segmentation and surface-based cortical thickness (CT) measurement, difficulty in assessing accuracy remains a substantial limitation due to the inability of experimental validation against ground truth. Although methods have been developed to create synthetic datasets for these purposes, none provide a robust mechanism for measuring exact thickness changes with surface-based approaches. This work presents a registration-based technique for inducing synthetic cortical atrophy to create a longitudinal ground truth dataset specifically designed to address this gap in surface-based accuracy validation techniques. Across the entire brain, our method can induce up to between 0.8 and 2.5 mm of localized cortical atrophy in a given gyrus depending on the region's original thickness. By calculating the image deformation to induce this atrophy at 400% of the original resolution in each direction, we can induce a sub-voxel resolution amount of atrophy while minimizing partial volume effects. We also show that cortical segmentations of synthetically atrophied images exhibit similar segmentation error to those obtained from images of naturally atrophied brains. Importantly, our method relies exclusively on publicly available software and datasets.

Synthetic atrophy for longitudinal surface-based cortical thickness measurement

Difficulty in validating accuracy remains a substantial setback in the field of surface-based cortical thickness (CT) measurement due to the lack of experimental validation against ground truth. Although methods have been developed to create synthetic datasets for this purpose, none provide a robust mechanism for measuring exact thickness changes with surface-based approaches. This work presents a registration-based technique for inducing synthetic cortical atrophy to create a longitudinal, ground truth dataset specifically designed for accuracy validation of surface-based CT measurements. Across the entire brain, we show our method can induce up to between 0.6 and 2.6 mm of localized cortical atrophy in a given gyrus depending on the region's original thickness. By calculating the image deformation to induce this atrophy at 400% of the original resolution in each direction, we can induce a sub-voxel resolution amount of atrophy while minimizing partial volume effects. We also show that our method can be extended beyond application to CT measurements for the accuracy validation of longitudinal cortical segmentation and surface reconstruction pipelines when measuring accuracy against cortical landmarks. Importantly, our method relies exclusively on publicly available software and datasets.

Machine learning in a graph framework for subcortical segmentation

Automated and reliable segmentation of subcortical structures from human brain magnetic resonance images is of great importance for volumetric and shape analyses in quantitative neuroimaging studies. However, poor boundary contrast and variable shape of these structures make the automated segmentation a tough task. We propose a 3D graph-based machine learning method, called LOGISMOS-RF, to segment the caudate and the putamen from brain MRI scans in a robust and accurate way. An atlas-based tissue classification and bias-field correction method is applied to the images to generate an initial segmentation for each structure. Then a 3D graph framework is utilized to construct a geometric graph for each initial segmentation. A locally trained random forest classifier is used to assign a cost to each graph node. The max-flow algorithm is applied to solve the segmentation problem. Evaluation was performed on a dataset of T1-weighted MRI's of 62 subjects, with 42 images used for training and 20 images for testing. For comparison, FreeSurfer and FSL approaches were also evaluated using the same dataset. Dice overlap coefficients and surface-to-surfaces distances between the automated segmentation and expert manual segmentations indicate the results of our method are statistically significantly more accurate than the other two methods, for both the caudate (Dice: 0.89 ± 0.03) and the putamen (0.89 ± 0.03).

LOGISMOS-B for Primates: Primate Cortical Surface Reconstruction and Thickness Measurement

Cortical thickness and surface area are important morphological measures with implications for many psychiatric and neurological conditions. Automated segmentation and reconstruction of the cortical surface from 3D MRI scans is challenging due to the variable anatomy of the cortex and its highly complex geometry. While many methods exist for this task in the context of the human brain, these methods are typically not readily applicable to the primate brain. We propose an innovative approach based on our recently proposed human cortical reconstruction algorithm, LOGISMOS-B, and the Laplace-based thickness measurement method. Quantitative evaluation of our approach was performed based on a dataset of T1- and T2-weighted MRI scans from 12-month-old macaques where labeling by our anatomical experts was used as independent standard. In this dataset, LOGISMOS-B has an average signed surface error of 0.01 ± 0.03mm and an unsigned surface error of 0.42 ± 0.03mm over the whole brain. Excluding the rather problematic temporal pole region further improves unsigned surface distance to 0.34 ± 0.03mm. This high level of accuracy reached by our algorithm even in this challenging developmental dataset illustrates its robustness and its potential for primate brain studies.