Method and system for analyzing images to quantify brain atrophy
A technique for reliably measuring brain atrophy based on image data, such as data collected as part of an MRI scan of a subject's brain. Rather than measure anatomical features of the brain in one of the scan planes as output by an MRI system, the image data is reformatted to generate a slice that may be transverse to those scan planes. The transverse slice is generated by determining a location of anatomical landmarks and reformatting the image data to represent a slice through these anatomical landmarks. The Anterior and Posterior Commissures are useful landmarks and ventricle area is a useful characteristic to measure from the slice. The rate of change of this measured characteristic can be tracked to determine disease progression and may be useful for diagnosis or evaluation of treatments, and the technique may be applied during clinical trials.
1. A method of analyzing image data comprising a 3-dimensional representation of a brain collected with an imaging device, the method comprising:
with at least one processor:
obtaining an indication of a position of a first anatomical landmark in a 3-dimensional representation of a brain collected during a first imaging session and an indication of a position of a second anatomical landmark in the 3-dimensional representation of the brain collected during the first imaging session; and
computing, from the 3-dimensional representation of the brain collected during the first imaging session, a first slice with an orientation in the 3-dimensions, wherein the orientation of the first slice is selected based on the obtained position of the first anatomical landmark and the obtained position of the second anatomical landmark such that the orientation of the first slice is not constrained by an orientation of the imaging device and the first slice encompasses:
a position selected based on at least the position of the first anatomical landmark and
a position selected based on at least the position of the second anatomical landmark;
obtaining an indication of a position of the first anatomical landmark in a 3-dimensional representation of a brain collected during a second imaging session and an indication of a position of a second anatomical landmark in the 3-dimensional representation of the brain collected during the second imaging session;
computing, from the 3-dimensional representation of the brain collected during the second imaging session, a second slice with an orientation in the 3-dimensions,
wherein the orientation of the second slice is selected based on the obtained position of the first anatomical landmark and the obtained position of the second anatomical landmark such that the orientation of the second slice is not constrained by an orientation of the imaging device, wherein the orientation of the second slice with respect to the orientation of the imaging device is different than the orientation of the first slice with respect to the orientation of the imaging device, and wherein the second slice encompasses:
a position selected based on at least the position of the first anatomical landmark and
a position selected based on at least the position of the second anatomical landmark; and
measuring a change in a characteristic of an anatomical feature based on a comparison of information from the first slice to information from the second slice to track the change in the characteristic of the anatomical feature over time.
2. The method of claim 1 , wherein obtaining an indication of a position of a first anatomical landmark and an indication of a position of a second anatomical landmark comprises receiving user input.
3. The method of claim 1 , wherein obtaining an indication of the position of the first anatomical landmark and an indication of the position of the second anatomical landmark comprises performing an automated analysis of the 3-dimensional representation.
4. The method of claim 1 , wherein the first anatomical landmark is an Anterior Commissure and the second anatomical landmark is a Posterior Commissure.
5. The method of claim 1 , wherein the anatomical feature is a third ventricle.
6. The method of claim 1 , wherein the measured characteristic of the anatomical feature is an area of the anatomical feature.
7. The method of claim 1 , wherein the measured characteristic of the anatomical feature comprises one or more of length, width, volume or circumference of the anatomical feature.
8. The method of claim 1 , wherein measuring a characteristic of the anatomical feature comprises:
with the at least one processor:
receiving user input identifying an approximate boundary of the anatomical feature in the first slice;
determining boundaries of the anatomical feature; and
computing an area within the determined boundaries.
9. The method of claim 1 , wherein
measuring a change in the characteristic of the anatomical feature comprises
measuring, based on the information from the first slice, the characteristic of the anatomical feature;
storing the measured characteristic of the anatomical feature from the first slice as a first measured characteristic;
measuring, based on the information from the second slice, the characteristic of the anatomical feature; and
measuring a change in the characteristic of the anatomical feature as a difference between the measured characteristic from the second slice and the first measured characteristic.
10. The method of claim 1 , wherein:
the method further comprises acquiring the image data during each of the first and second imaging sessions by performing a magnetic resonance imaging (MRI) scan on the brain of a subject, the image data comprising a plurality of parallel slices providing the 3-dimensional representation of the brain; and
wherein the orientation of each of the first slice and the second slice is transverse to the plurality of parallel slices.
11. A method of performing a clinical trial involving a plurality of subjects, each subject being assigned to a group of a plurality of groups, the method comprising:
for each of the plurality of subjects, processing a first 3-dimensional representation of a brain of the subject collected with an imaging device during a first imaging session and second 3-dimensional representation of the brain collected with the imaging device during a second image session, wherein processing the first 3-dimensional representation comprises:
with at least one processor:
obtaining an indication of a position of a first anatomical landmark in the first 3-dimensional representation of a brain and an indication of a position of a second anatomical landmark in the first 3-dimensional representation of the brain;
generating a first slice through the first anatomical landmark and the second anatomical landmark from the first 3-dimensional representation, wherein the first slice has an orientation in the 3-dimensions, and wherein the orientation of the first slice is selected based on the obtained position of the first anatomical landmark and the obtained position of the second anatomical landmark such that the orientation of the first slice is not constrained by an orientation of the imaging device and the first slice encompasses:
a position selected based on at least the position of the first anatomical landmark and
a position selected based on at least the position of the second anatomical landmark;
measuring a characteristic of an anatomical feature in the first slice; and
storing the measured characteristic as a first measured characteristic in at least one computer-storage medium;
wherein processing the second 3-dimensional representation comprises:
with the at least one processor:
obtaining an indication of a position of the first anatomical landmark in the second 3-dimensional representation of a brain and an indication of a position of a second anatomical landmark in the second 3-dimensional representation of the brain;
generating a second slice through the first anatomical landmark and the second anatomical landmark from the second 3-dimensional representation, wherein the second slice has an orientation in the 3-dimensions, and wherein the orientation of the second slice is selected based on the obtained position of the first anatomical landmark and the obtained position of the second anatomical landmark such that the orientation of the second slice is not constrained by an orientation of the imaging device, wherein the orientation of the second slice with respect to the orientation of the imaging device is different than the orientation of the first slice with respect to the orientation of the imaging device, and wherein the second slice encompasses:
a position selected based on at least the position of the first anatomical landmark and
a position selected based on at least the position of the second anatomical landmark;
measuring the characteristic of the anatomical feature in the second slice; and
storing the measured characteristic as a second measured characteristic in the at least one computer-storage medium; and
computing from the stored first and second measured characteristics an indicator of an average change of the characteristic for each of the plurality of groups.
12. The method of claim 11 , wherein the indicator comprises an average rate of change.
13. The method of claim 12 , further comprising, with the at least one processor, determining whether differences in the average rate of change between groups are statistically significant.
14. The method of claim 11 , wherein:
each of the first and second 3-dimensional representation of the brain comprises a magnetic resonance imaging (MRI) image of the brain;
the first anatomical landmark is an Anterior Commissure and the second anatomical landmark is a Posterior Commissure;
the anatomical feature is a third ventricle; and
the measured characteristic of the anatomical feature is one or more of area, length, width, volume or circumference of the anatomical feature.
15. At least one non-transitory computer-readable medium,
comprising computer-executable instructions that, when executed by a processor, analyze image data collected with an imaging device by:
obtaining an indication of a position of a first anatomical landmark in a 3-dimensional representation of a brain collected during a first imaging session and an indication of a position of a second anatomical landmark in the 3-dimensional representation of the brain collected during the first imaging session; and
computing, from the 3-dimensional representation of the brain collected during the first imaging session, a first slice with an orientation in the 3-dimensions, wherein the orientation of the first slice is selected based on the obtained position of the first anatomical landmark and the obtained position of the second anatomical landmark such that the orientation of the first slice is not constrained by an orientation of the imaging device and the first slice encompasses:
a position selected based on at least the position of the first anatomical landmark and
a position selected based on at least the position of the second anatomical landmark;
obtaining an indication of a position of the first anatomical landmark in a 3-dimensional representation of a brain collected during a second imaging session and an indication of a position of the second anatomical landmark in the 3-dimensional representation of the brain collected during the second imaging session; and
computing, from the 3-dimensional representation of the brain collected during the second imaging session, a second slice with an orientation in the 3-dimensions, wherein the orientation of the second slice is selected based on the obtained position of the first anatomical landmark and the obtained position of the second anatomical landmark in the second 3-dimensional representation such that the orientation of the second slice is not constrained by an orientation of the imaging device, wherein the orientation of the second slice with respect to the orientation of the imaging device is different than the orientation of the first slice with respect to the orientation of the imaging device, and wherein the second slice encompasses:
a position selected based on at least the position of the first anatomical landmark and
a position selected based on at least the position of the second anatomical landmark; and
measuring a change in a characteristic of mi anatomical feature based on a comparison of information from the first slice to information from the second slice to track the change in the characteristic of the anatomical feature over time.
16. The at least one non-transitory computer-readable medium of claim 15 , wherein:
the computer-executable instructions for obtaining the indication of the position of the first anatomical landmark and the indication of the position of the second anatomical landmark comprises computer-executable instructions for analyzing the 3 dimensional representation of the brain to determine the position of the first anatomical landmark and the indication of the position of the second anatomical landmark.
17. The at least one non-transitory computer-readable medium of claim 15 , wherein:
the first anatomical landmark is an Anterior Commissure and the second anatomical landmark is a Posterior Commissure.
18. The at least one non-transitory computer-readable medium of claim 17 , wherein the anatomical feature is a ventricle.
19. The at least one non-transitory computer-readable medium of claim 18 , wherein:
the computer-executable instructions for measuring the change of the characteristic of the anatomical feature comprise computer-executable instructions for:
receiving user input identifying an approximate boundary of the anatomical feature in each of the first and second slices;
determining boundaries of the anatomical feature in each of the first and second slices; and
computing an area within the determined boundaries in each of the first and second slices.
20. The at least one non-transitory computer-readable medium of claim 19 , further comprising computer-executable instructions for storing the computed area in association with information relating to a clinical trial.