Manual Segmentation of the Human Choroid Plexus Using Brain MRI

We aim to establish an accessible and standardized protocol for manually segmenting the choroid plexus within the lateral third and fourth ventricles of the brain. We hope to address any common questions or problems that can arise when manually segmenting the choroid plexus, especially considering the complex nature of its location within the brain. Developing this protocol will lead to the creation of a large enough dataset consisting of ground truth segmentation maps that we can then use to train and develop algorithms that can accurately and automatically segment the choroid plexus.

In the future, this will lead to studies that investigate the role of the choroid plexus within various neurologic and neuropsychiatric disorders. To begin, import digital imaging and communications in medicine or DICOM data by clicking on the DCM button located at the upper-left corner of the toolbar and clicking the Import DICOM Files button. To adjust the brightness of an image, click adjust window and level of volume or left-click on the image and drag the mouse up or down.

Then left-click on the image slice and move the mouse to the left or right to adjust the contrast. Refer to the deep gray matter nuclei or the contrast scale bar's signal intensity, and ensure that it remains consistent throughout the segmentation to choose the suitable contrast for the choroid plexus. To start the segmentation of the lateral, third, and fourth ventricle choroid plexus, select the Segment Editor from the module's dropdown menu.

Now click on the dropdown menu for Segmentation to select different segmentations and rename the selected one. Use the master volume dropdown and pick the NIFTI or DICOM sets that need editing. Click the Add button two times to include two segments for the lateral ventricle choroid plexus.

Double-click on their titles and rename them as right lateral ventricle choroid plexus and left lateral ventricle choroid plexus. Click on the Add button once more to introduce segments for the choroid plexus of the third and fourth ventricles. Afterward, rename them as the third ventricle choroid plexus and the fourth ventricle choroid plexus respectively.

Begin with the lateral ventricle choroid plexus in the axial plane, and ensure to position images based on the bicommissural line. Use the trigonum collaterale as a reference point to locate the lateral ventricle choroid plexus. To start manual segmentation, select either the paint or draw tool located in the Effects section of the segment editor.

While using the paint tool, select the desired brush diameter for painting. Use the red nucleus level to determine when to stop segmenting the choroid plexus in the lateral ventricles. To locate the third ventricle choroid plexus, commence in the sagittal plane, and use the foramen of Monro, fornix, corpus callosum, thalamus, and internal cerebral vein as landmarks.

Similarly, for the fourth ventricle choroid plexus, begin in the sagittal plane and use the superior cerebellar peduncle, pons, and medulla as reference points to pinpoint the choroid plexus in the fourth ventricle. From the Modules dropdown menu, navigate to Quantification and select Segment Statistics. Then under the Inputs section, select the newly created segmentation map for quantification under the segmentation tool and select the MRI volume from the scaler volume.

For the output table, select the table option under output and hit Apply. A table displaying the choroid plexus volume in different units will appear. Click on the Save button located in the top-left part of the toolbar to store the generated files.

Preserve the segmentation files in the formats NRRD, NII. GZ, or TSV.