The next step in iBEAT is brain extraction. If you are moving on from the image preprocessing step, you can open the brain extraction step directly from the image preprocessing window, and it will open with your subject images loaded. If you closed the image preprocessing window already, click the brain extraction button in the iBEAT startup box to open the brain extraction window. You will then load in your subject images using the button in the top left corner.

Brain extraction in iBEAT is fairly straightforward. The iBEAT manual recommends using the default options for brain extraction. Therefore, you can select all of your images and click “Brain Extraction.” Once the brain extraction is complete, the output images will be skull stripped (e.g., “S001-0-T1-reoriented-strip”). Be sure to check that these look correct. Compared to other skull stripping softwares (e.g., FSL’s BET), iBEAT’s skull stripping works very well for infant brains. However, it can still make mistakes, so it is important to check the brain extracted images.

If you see mistakes, you can manually correct them by right clicking on the reoriented-strip image in the list of subject images, and choosing “manual edits.” This will open a new window where you will see the 3 views of your image and a red overlay. This red overlay is the area that was extracted as brain. You can use the painter or eraser to add or remove sections that are labeled as brain. You can use a 3-d mask to change multiple slices at a time, or you can use a 2-d mask to change a single slice. You can use the scroll wheels on any view to move through the slices. The goal is to get the entire brain into the red section and to not have non-brain areas within the red section. When you think you have achieved this, you can click “Preview Edited Images,” which will open a window showing the extracted brain based on the changes you made. If you are satisfied with this, click “Extract Brain.” If you are not satisfied, continue editing.

You can return to this manual editing screen at any time, which is helpful if you thought that the brain extraction was acceptable, but are having trouble with the tissue segmentation step. To do so, return to the iBEAT startup window, click Tools, and choose Manual Brain Editor. You will want to open the reoriented (not reoriented-strip) image for your subject, which will also open the red overlay so that you can edit it.

Once you are satisfied with the brain extraction results, you can move on to tissue segmentation by clicking “Tissue Segmentation.” This will open a new window with your current subject images already loaded.