
Open-source tools enable accurate 3D reconstruction and segmentation of brain photographs, offering a cost-effective alternative to ex vivo MRI for neuropathological-neuroimaging correlations.


coremsg

We present open-source tools for 3D analysis of photographs of dissected slices of human brains, which are routinely acquired in brain banks but seldom used for quantitative analysis. Our tools can: (i) 3D reconstruct a volume from the photographs and, optionally, a surface scan; and (ii) produce a high-resolution 3D segmentation into 11 brain regions per hemisphere (22 in total), independently of the slice thickness. Our tools can be used as a substitute for ex vivo magnetic resonance imaging (MRI), which requires access to an MRI scanner, ex vivo scanning expertise, and considerable financial resources. We tested our tools on synthetic and real data from two NIH Alzheimer’s Disease Research Centers. The results show that our methodology yields accurate 3D reconstructions, segmentations, and volumetric measurements that are highly correlated to those from MRI. Our method also detects expected differences between post mortem confirmed Alzheimer’s disease cases and controls. The tools are available in our widespread neuroimaging suite “FreeSurfer” (<https://surfer.nmr.mgh.harvard.edu/fswiki/PhotoTools>).

### Competing Interest Statement

Bruce Fischl has a financial interest in CorticoMetrics, a company developing brain MRI measurement technology. His interests are reviewed and managed by Massachusetts General Hospital.

Machine learning of dissection photographs and surface scanning for quantitative 3D neuropathology

3d-analysis-of-dissection-photographs-with-surface-scanning-and-machine-learning-for-quantitative-neuropathology


3D Analysis of Dissection Photographs with Surface Scanning and Machine Learning for Quantitative Neuropathology
