Cortechs.ai | Q&A: Alignment to atlas explained

Q&A: Alignment to atlas explained

The Cortechs.ai Support team is often asked to clarify error messages when a series of images cannot be processed by NeuroQuant software. The number 1 question we receive has to do with alignment of brain to atlas being reported as unsuccessful.

Why is Alignment to Atlas Important?
To achieve high-quality segmentation results, NeuroQuant aligns each patient’s brain image to an atlas of the brain. Segmentation accuracy can be affected when the patient’s brain deviates from the reference brain atlas. Since correct brain atlas alignment is critical to the accuracy of the segmentation results, it is also critical to the accuracy of the calculated volumes.

What Does “Processing Failed: Alignment of Brain to Atlas Unsuccessful” Indicate?
This message will be displayed in cases where a patient’s brain anatomy is significantly different than the brain atlas, such as in patients with brain tumors, surgical resections, very large lesions, or severe asymmetry. Further processing of the scan may result in inaccurate segmentation. To ensure segmentation accuracy, NeuroQuant is designed with a quality check ensuring goodness of fit to neuroanatomical atlas

What is the Measurement Index?
The measurement index (MI) is a numerical measure of the similarity (or differences) between a patient’s brain scan and the anatomical brain atlas. The MI serves as a quality check to confirm goodness of fit to the brain atlas. The measurement index uses a cutoff value to reject any scan that can likely result in segmentation errors due to the brain atlas mismatch. For clinical use, the MI must be ≤5. Exceeding this alignment error threshold will cause processing to halt and an error report to be generated. A MI >5 prevents NeuroQuant analysis of a patient’s brain, indicating brain anatomy that is significantly different than the brain atlas based on the quality check.

Can Images Still Be Processed by NeuroQuant if the MI is >5?
In some cases, yes. When the MI is between 5 and 6, turning on Research Mode allows NeuroQuant to process images for research/non-clinical needs with relaxed atlas alignment checks, like in cases, for example, that failed due to the brain atlas alignment error. Research mode generates reports marked NOT FOR CLINICAL USE. The Research Mode setting increases tolerance for certain alignment errors but requires careful review of segmentation output by the radiologist to verify segmentation quality.

In the example below, gross structural abnormalities in a patient’s brain make good alignment to atlas impossible.

Cortechs.ai | Q&A: Alignment to atlas explained

Some cases, such as the second example, can also generate this error message, but are still candidates for NeuroQuant, when processed in Research Mode.

Cortechs.ai | Q&A: Alignment to atlas explained

More information about using NeuroQuant can be found your user manual.

More Resources

05/18/2025

Cortechs.ai and ALZ-NET Announce Strategic Collaboration to Improve Alzheimer’s Disease Care Through AI-Driven Imaging

This new strategic collaboration aims to enhance the quality of care for people living with Alzheimer’s disease.

05/16/2025

Case Study: NeuroQuant® for ARIA: Monitoring ARIA Progression in Early Alzheimer’s Disease

Dr. Suzie Bash highlights how advanced imaging with NeuroQuant for ARIA supported detection and monitoring of ARIA-E and ARIA-H in an 81-year-old patient.

05/13/2025

Dr. Ana M. Franceschi Joins Cortechs.ai Medical Advisory Board

Neuroimaging thought leader to enhance PET/MRI and dementia research impact through AI-powered tools

05/10/2025

All the Ways to Use the NeuroQuant Custom Report

With the ability to select structures from NeuroQuant’s 70+ structure parcellation atlas, the user has the power to truly personalize patient care!

05/04/2025

Introducing NeuroQuant MS Lesion Dynamics Computation: A Clearer Path to Understanding Disease Progression

Discover how the latest NeuroQuant MS update offers a clearer, more intuitive way to track lesion changes and understand disease progression over time.

05/02/2025

4 Reasons Why Over 1500 Medical Centers Worldwide Trust Cortechs.ai

Trusted by 1500+ medical centers, Cortechs.ai delivers AI-powered imaging tools that enhance diagnostic accuracy and streamline workflows.
Scroll to Top