Pictured: Miracle Ozzoude and Joel Ramirez, PhD

The human brain is made up of many complex and inter-connected parts; these parts have to work both separately and in concert with each other, for us to carry out our complex series of daily activities.

The cerebral cortex, made up of the brain’s “grey matter”, lies on the surface of the brain just underneath the skull. This outer area is where much of the brain’s processing function takes place. When the cortex atrophies (or shrinks), this can be an indicator of disease and dysfunction. Cortical atrophy can be measured through volume, or more simply through thickness measures.

ONDRI researchers Miracle Ozzoude, Dr. Joel Ramirez and colleagues have devised methods that substantially improve accuracy of cortical thickness measures.

This work allows clinicians to examine cortical thinning in all patients, with greater accuracy. In addition, the work provides measures of cortical thickness in patients with focal stroke and extreme white matter disease, which could not have been done prior to their work.1 

How to measure cortical thickness

Magnetic Resonance Imaging (MRI) is a key tool for measuring brain atrophy. When calculating volume or thickness, the brain is segmented – allowing the researchers to focus on the area of interest – as atrophy in different parts of the brain can be an indicator of different diseases.

Open-source software tools, such as FreeSurfer®, provide estimation of cortical thickness, based on the MRIs. Unfortunately, many automated tools like FreeSurfer® do not work very well for people with stroke and Cerebrovascular Disease (CVD).

In fact, Ozzoude and colleagues’ research, examining ONDRI’s Stroke and CVD study participants, found that between 11% and 62% of the time, using FreeSurfer® with no correction can result in failure – meaning that participants’ data would be removed from research studies for analysis, due to inaccurate thickness measures.

The correction described

What ONDRI researchers did was modify the FreeSurfer® software to correct for measurement errors, thereby increasing their ability to examine and accurately assess many more patients with Stroke and CVD. This work led to dramatic improvements.

For example:

  • For tissue segmentation, the corrected procedure’s “Acceptable” ratings increased from 38% to 92%.
  • For the cortical ribbon quality control, the “Fail” ratings were reduced from 11% (unmodified) to 0% (corrected).

Visually, the results of these correction procedures can be seen in the figures below. Note the detail missed in the uncorrected image.

red = grey matter, green/white = white matter, pink = lesion

Honouring ONDRI study participants

This important work resulted in an increase in measurement accuracy, which will allow clinicians to better track the progression of brain disease, especially in the Stroke and CVD patient populations.

Most importantly, these correction efforts, invested to reduce data loss and inaccuracies, recognize the significant time and effort study participants have donated to participate in the ONDRI research study – in that their data was included in analysis and conclusions.

The feasibility of this research was partially due to the high-quality MRI scans acquired from ONDRI’s Foundational study participants.

More to come in this series of ONDRI neuroimaging articles.

Link to logic flow chart and FreeSurfer® version used.

Read other ONDRI publications.


[1] This work is published as “Cortical Thickness Estimation in Individuals with Cerebral Small Vessel Disease, Focal Atrophy, and Chronic Stroke Lesions”, Frontiers in Neuroscience, December 2020