Tissue segmentation – separating gray matter and white matter – is the step where I have run into the most errors. One thing that is clear is that the age of the subject matters for tissue segmentation. When I have incorrectly entered the age of subjects, I have ended up with errors during this step. One of the main problems I am having is that our subjects were born very pre-term, and do not necessarily match the template for their current age or their term-adjusted age, but that will be the topic of another post.

Assuming you have a sample of infants born full-term and have accurately labeled their ages (in months) in the file name (e.g., S001-6-T1) for a 6-month-old infant (see my post on preparing your data for iBEAT) the tissue segmentation step is very straightforward. Simply open the tissue segmentation window, load your brain-extracted images, and click “Longitudinal tissue segmentation.” You will see a prompt asking whether you want to align the subject’s data across time. If you have longitudinal data, you should click “align.” If you do not have longitudinal data, you can click “align” or “skip.” I would click “align” with multiple scans for one timepoint (e.g., a T1 and T2 scan) because it will ensure that those scans are aligned before segmenting.

The tissue segmentation step seems to take the longest amount of time. If you check the “processing status” box at the bottom of the tissue segmentation box, it may estimate around 3 hours. I have found that although 3 hours is the estimated time, it usually takes less than an hour to complete.

Once it is completed, you will see an image with the ending “reoriented-strip-seg” for each timepoint. Note, that there will only be one image for each timepoint, even if you entered multiple brain extracted images for that timepoint. I recommend clicking on the “reoriented-strip-seg” image to see how it looks. When the age is incorrect, the gray and white matter outlines may look odd, or the image will not load and you will see an error message in the terminal window. I hope that you never see this error message, but unfortunately I have encountered it many times. I will write a separate post on all of the strategies I have tried to successfully segment the tissue after getting the error message. If your gray and white matter segmented in a way that looks odd/inaccurate, I would recommend double checking the age labels you used for that subject. If you have longitudinal data, click on each “reoriented-strip-seg” image separately. I have found that sometimes one of the timepoints will segment correctly, but the other timepoint produces an error.

If you have successfully segmented the tissue into gray and white matter, you can move onto the final iBEAT step: Brain Labeling. Click the button at from the tissue segmentation window to carry your segmented tissue images onto the next step, or open brain labeling from the main iBEAT window and load in your segmented tissue images.