Sanches, L. G. | bioRxiv Science

bioRxiv2025

Comparison of T1- and T2-weighted MRI contrasts of ex vivo ex situ brains fixed with solutions used in gross anatomy laboratories

Post-mortem magnetic resonance imaging (MRI) offers high resolution and histological correlation, so protocols have been developed by brain banks using hemispheres fixed by immersion in Neutral-buffered formalin (NBF), but they provide limited tissue samples. Conversely, anatomy laboratories could supply complete brains perfused either with a salt-saturated (SSS) or an alcohol-formaldehyde (AFS) solution. These fixation methods alter the brains molecular properties, potentially affecting MRI quality and structural characteristics. T1- and T2-weighted (T1w, T2w) contrasts change with NBF fixation, but the effects of SSS or AFS remain unknown. We compared T1w and T2w intensities of different regions of interest (ROIs), including subcortical white matter (WM), cortical and deep gray matter (GM), in brains fixed with NBF, SSS and AFS. We scanned 20 ex situ hemispheres (NBF-immersed=7; SSS-perfused=7; AFS-perfused=6) in a 3T MRI scanner using T1w (0.7mm3) and T2w (0.64mm3) sequences overnight. Mean intensities of 29 ROIs in T1w and T2w MRIs and GM-WM ratios were calculated and compared in brains fixed with the three solutions. We found that T1w images were more affected by the fixation process, inverting the contrast of in vivo T1w and reducing the GM-WM contrast in AFS-fixed brains. T2w images resembled in vivo scans and maintained a sharp contrast in brains fixed with the three solutions, although the GM-WM intensity ratios were lowered in SSS-fixed brains. In conclusion, brains fixed with SSS and AFS from anatomy laboratories could be used for MRI studies, especially with the T2w sequence that seems more appropriate for structural analyses in different ROIs.

neuroscience↗

bioRxiv2025

Ex vivo human brain volumetry: validation of magnetic resonance imaging measurements

BackgroundNeurodegenerative diseases are associated with brain atrophy. The volume of in vivo human brains is determined with various magnetic resonance imaging (MRI) measurement tools of which the validity has not been assessed against a gold standard. Here, we propose to validate the MRI brain volumes by scanning ex vivo-in situ specimens (i.e., anatomical heads), which allows the extraction of the brain after the scan to compare its volume with the gold standard water displacement method (WDM). MethodsWe acquired 3T MRI T2-weighted, T1-weighted, and MP2RAGE images of seven anatomical heads fixed with an alcohol-formaldehyde solution routinely used in anatomy laboratories and segmented the gray and white matter of the brain using two methods: 1) a manual intensity-based threshold segmentation using Display (MINC-ToolKit, McConnell BIC), and 2) an automatic Deep-Learning-based segmentation tool (SynthSeg). The brains were then extracted, and their volumes were measured with the WDM after the removal of their meninges and a midsagittal cut (to allow water penetration into the ventricles). Volumes from all methods were compared to the ground truth (WDM volumes) using a repeated-measures ANOVA. ResultsMean brain volumes, in cubic centimeters, were 1111.14{+/-}121.78 for WDM, 1020.29{+/-}70.01 for manual T2-weighted, 1056.29{+/-}90.54 for automatic T2-weighted, 1094.69{+/-}100.51 for automatic T1-weighted, 1066.56{+/-}96.52 for automatic MP2RAGE INV1, and 1156.18{+/-}121.87 for MP2RAGE INV2. All volumetry methods were significantly different (F=17.874; p<0.001) from the WDM volumes, except the automatic T1-weighted volumes. ConclusionWe demonstrate that SynthSeg accurately determines the brain volume in ex vivo-in situ T1-weighted MRI scans. Our results also suggest that given the contrast similarity between our ex vivo and in vivo sequences, the brain volumes of clinical studies are most probably sufficiently accurate, with some degree of underestimation depending on the sequence used.

neuroscience↗