Developing a Cerebral Blood Flow Atlas for Blood Flow Mapping

Begin with a cerebral blood flow, or CBF map generated by magnetic resonance imaging-arterial spin labeling, a noninvasive method for measuring blood flow in the brain tissue.

Obtain a structural brain image and, using computational tools, segment the cerebral regions into functional regions.

Generate triplanar views, showing cross-sectional images of the brain in three planes, with each segmented region displayed in distinct colors to represent functional areas.

Integrate the CBF data with the segmented regions to map blood flow values to specific brain areas.

Bright colors indicate high blood flow, while warm shades represent low levels.

Use algorithms to process the CBF data and create an atlas for comparing blood flow levels across brain regions.

The fluctuating red line highlights the average CBF across regions, quantifying blood flow.

The atlas colors correspond to the color bar and represent the probability of blood flow levels in specific brain regions-red indicates a high probability, while blue indicates a low probability.

To begin, obtain patient data in neuroimaging informatics technology initiative, or NIFTI format. In a customized working directory, go to the directory housing the data within MATLAB's current working directory, and using the NIFTI read function, load the fluid-attenuated inversion recovery, or FLAIR, into the workspace. With this size function, check the dimensions of the FLAIR sequence. Then, call the FLAIR slice command to view the FLAIR sequence of the brain.

Using the bottom scroll bar, browse the different sequences. Then, similarly load and assess cerebral blood flow or CBF sequences. In the workspace, call the FLAIR segment function and run the pre-trained 3D U-Net-based image segmentation program to automatically generate triplanar views of cerebral functional regions segmentation.

Each color represents a distinct functional region. For real-time inspection of different cerebral functional regions, click and drag the center of the crosshair for an arbitrary 3D examination of the reconstructed brain anatomy. Press and drag the left mouse button over any region of the images for real-time modification of brightness and contrast levels. Release the mouse button to confirm and finalize the adjustments.

Call the CBF triplanar function to generate the triplanar graphic user interface view, displaying CBF spatial distribution across functional regions. Move the crosshair to allow examination of CBF distributions in regions of interest. Then, click the Data Tips button on the top right corner of the interface to display the CBF values at any position.

Press and drag the left mouse button over any region of the images for real-time modification of brightness and contrast levels. Release the mouse button to confirm and finalize the adjustments. Run the CBF Atlas function to convert the CBF spatial distribution into a CBF Atlas. Click the Zoom in/out button in the top right of the interface.