Considerations and recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 3-Ex vivo...

Area of Science:

• Neuroimaging
• Biomedical Engineering
• Microscopy

Background:

• Preclinical diffusion MRI (dMRI) is valuable for methods development, biological characterization, and comparative anatomy.
• Ex vivo dMRI offers advantages like high spatial resolution, high signal-to-noise ratio (SNR), advanced diffusion contrasts, and direct histological validation.
• However, ex vivo dMRI presents unique challenges in tissue preparation, imaging, processing, and interpretation compared to in vivo studies.

Purpose of the Study:

• To provide a comprehensive set of recommendations and considerations for performing ex vivo dMRI on preclinical tissue.
• To outline best practices for image pre-processing, data processing, and comparisons with microscopy in ex vivo dMRI.
• To identify areas lacking established guidelines and suggest future research directions.

Main Methods:

• Review and synthesis of current practices in ex vivo dMRI for preclinical research.
• Focus on image pre-processing steps specific to ex vivo samples.
• Detailed discussion on data processing pipelines and comparison strategies with microscopy.

Main Results:

• Established guidelines for ex vivo dMRI image pre-processing and data analysis.
• Highlighted critical differences and considerations compared to in vivo dMRI protocols.
• Identified knowledge gaps and areas requiring further investigation in ex vivo dMRI methodology.

Conclusions:

• This work offers crucial guidance for optimizing ex vivo dMRI experiments in preclinical settings.
• Emphasizes the importance of standardized protocols for accurate tissue microstructure and connectivity analysis.
• Promotes data and code sharing through open-source platforms for advancing the field.